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2024-03-09 21:48:04

学一个英语表达：The world is my oyster ｜莎翁妙语_世界

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学一个英语表达：The world is my oyster ｜莎翁妙语

2020-06-12 03:04

来源:

学英语那点事

原标题：学一个英语表达：The world is my oyster ｜莎翁妙语

大家好，我是学姐。

今天来讲一个看起来有些奇怪，但又很有意思的表达：

The world is my oyster.

世界是我的"oyster"，这到底是什么鬼？

Oyster，翻译到中文是"牡蛎"的意思。

牛津高阶

Oyster 是重要的海洋生物资源，它的外层是两个凹凸不平的硬壳，用刀子敲开之后可以吃到鲜美的蚌肉。

牛津高阶

不知大家有买过生的牡蛎回家自己烹制吗？Oyster 的外壳通常闭的非常紧，想要自己敲开的话是非常困难的，经常会被拉破双手，鲜血直流。

也正因如此，Oyster 一词在英语中还被用来指代"沉默寡言的人；闭口不言的人"。

展开全文

例句：

The boy was dragged off to the police station，but he remained oyster.

那个小伙子被拉到警察署，但他一直咬紧牙关不说话。

The world is my oyster（世界是我的牡蛎），是莎士比亚的名言之一，它出自莎翁戏剧《The Merry Wives of Windsor》中的一个名叫Pistol的角色口中。

《The Merry Wives of Windsor》又名"温沙的风流娘儿们"或"快乐的温莎巧妇"（有没有一种听到名字就很想看的感觉），是一部由英国女王伊丽莎白钦点、莎士比亚在14天创作出的欢乐爱情喜剧，讲述了来自上流社会的约翰·福斯塔夫爵士与平民女人们间滑稽的风流韵事。

因为约翰·福斯塔夫爵士不肯借钱给恶棍 Pistol，被Pistol威胁道：

"Why then the world's mine oyster, / Which I with sword will open."

这个世界是我的牡蛎，我用刀就可以把它撬开。

后人引用时通常把 mine 替换做 my，用来指代一个人的梦想得以实现，他抓住了所有可能出现的机会，前途无量，心想事成。

The world is my oyster. I can do whatever I like. 这个世界是我的了，我可以随心所欲，做什么都可以。

比如，你身边有一个人，他不仅出生在大富之家，而且名校毕业，外表英俊，性格开朗，能力超群。这样的人，你就可以形容他说：

"The world is his oyster!"

例句：

The world is my oyster. I'm in love.

世界是我的了。我恋爱啦。

You have passed the hurdle and the world is your oyster.

你已克服了障碍，你可随心所欲了。

-END-

学姐说：

感谢你的认真阅读。Don't give up. The world is your oyster! 别放弃，这世界是你们的！

我建立了一个大学生英语学习社群（英语角），如果你想和大家一起练口语、交流学习难题，关注公众号“学英语那点事”关注后即可加入，群里都是对英语充满热情的小伙伴～返回搜狐，查看更多

责任编辑：

平台声明：该文观点仅代表作者本人，搜狐号系信息发布平台，搜狐仅提供信息存储空间服务。

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OYSTER中文(简体)翻译：剑桥词典

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oyster 在英语-中文（简体）词典中的翻译

oysternoun [ C ] uk

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/ˈɔɪ.stər/ us

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/ˈɔɪ.stɚ/

oyster noun [C]

(sea creature)

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a large flat sea creature that lives in a shell, some types of which can be eaten either cooked or uncooked, and other types of which produce pearls (= small round white precious stones)

牡蛎，蚝

oyster noun [C]

(PIECE OF CHICKEN)

(also chicken oyster) one of two small pieces of chicken at the bottom of the backbone, which taste particularly good

（位于鸡背下部的）蚝状鸡背肉

Chicken oysters are those juicy little chicken pieces hidden away between the leg and the backbone.

蚝状鸡背肉体积不大、味道鲜美，藏在鸡腿和背脊骨之间。

更多范例减少例句I didn't realise that chickens had an oyster. Apparently they have two.Other impressive dishes include macaroni with chicken oysters and smoked eel with horseradish cream. It arguably beats the thrill even of a roasted chicken's oyster.

(oyster在剑桥英语-中文（简体）词典的翻译 © Cambridge University Press)

oyster的例句

oyster

My interest in oysters would preclude me from giving an answer off the cuff.

来自 Hansard archive

该例句来自Hansard存档。包含以下议会许可信息开放议会许可v3.0

In this study, the monitored oysters were too young to experience significant parasite pressure.

来自 Cambridge English Corpus

Licences have been granted this year to import over 11 million seed oysters.

来自 Hansard archive

该例句来自Hansard存档。包含以下议会许可信息开放议会许可v3.0

The control experiment was designed as described above, but included uninfected flat oysters also placed on a mesh.

来自 Cambridge English Corpus

The operations were severely hampered by the almost complete absence of oysters.

来自 Cambridge English Corpus

Important differences in the number of parasites were observed between the 5 oysters of each sampling day.

来自 Cambridge English Corpus

Shellfish, and in particular oysters, cultured in faecal/ sewage contaminated seawater have been responsible for many outbreaks of viral gastroenteritis.

来自 Cambridge English Corpus

Everyone who is informed about the cultivation of oysters knows of the work done there on the means of controlling pests and growing oysters.

来自 Hansard archive

该例句来自Hansard存档。包含以下议会许可信息开放议会许可v3.0

示例中的观点不代表剑桥词典编辑、剑桥大学出版社和其许可证颁发者的观点。

oyster的翻译

中文（繁体）

牡蠣，蠔, （位於雞背下部的）蚝狀雞背肉…

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西班牙语

ostra, ostra de pollo, ostra [feminine…

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葡萄牙语

ostra, ostra [feminine]…

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in Dutch

阿拉伯语

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in Ukrainian

意大利语

俄语

（貝の）カキ, 牡蠣（かき）…

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istiridye, istridye…

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huître [feminine], huître…

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مَحار…

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østers [masculine], østers…

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flexitarian

A flexitarian way of eating consists mainly of vegetarian food but with some meat.

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oyster是什么意思_oyster的翻译_音标_读音_用法_例句_爱词霸在线词典

er是什么意思_oyster的翻译_音标_读音_用法_例句_爱词霸在线词典首页翻译背单词写作校对词霸下载用户反馈专栏平台登录oyster是什么意思_oyster用英语怎么说_oyster的翻译_oyster翻译成_oyster的中文意思_oyster怎么读,oyster的读音,oyster的用法,oyster的例句翻译人工翻译试试人工翻译翻译全文简明柯林斯牛津oysterTOEFL英 [ˈɔɪstə(r)]美 [ˈɔɪstər]释义n.牡蛎; <俚>守秘密的人; 鸡背肉; 沉默寡言的人大小写变形:Oyster点击人工翻译，了解更多人工释义词态变化复数: oysters;实用场景例句全部牡蛎Oyster beds, on the mudflats, are a form of fish farming.滩涂牡蛎养殖场是一种水产养殖方式。牛津词典He had two dozen oysters and enjoyed every one of them.他吃了两打牡蛎，每一只都吃得津津有味。柯林斯高阶英语词典You're young, you've got a lot of opportunity. The world is your oyster.你还年轻，机会有的是。世界是属于你的。柯林斯高阶英语词典After the damp weather all the drawers became as fast as a Kentish oyster.湿季过后所有的抽屉都如肯特郡的牡蛎一般关得死死的.期刊摘选This should be the first in China to build oyster shell of the house written.这应是我国最早建蚝壳屋的文字记载.期刊摘选Tianjin how to sell crafts of the pearl oyster?天津市哪有卖工艺品珍珠贝的?期刊摘选It is not difficult to open an oyster with a sword.用剑来开牡蛎并非难事.期刊摘选Oyster pearl cultivation and the environment is a very very deep relationship.牡蛎珍珠养殖和环境之间有着非常非常密切的关系.期刊摘选I am that grain of salt, and I am also the nacre tears that the oyster cried.我是那粒沙, 也是牡蛎哭泣时流出的珍珠泪.期刊摘选I think I'll have some oyster cocktail first.我想我先来点生蚝杯.期刊摘选The oyster covers the piece of shell with a pearly substance known as nacre.牡蛎分泌一种叫做“珠母贝”的珍珠状物质覆盖那一小片贝壳.期刊摘选B: We'll take the Season Vegetables in Oyster Sauce , the String beans and the Mushroom Soup.我们的蔬菜有蚝油菜心、杯芥菜和干煽四季豆, 汤有鱼翅汤和蘑菇汤.期刊摘选I think I'll take oyster.我想我要点牡蛎.期刊摘选Oyster is the only seafood I like; I dislike the rest.牡蛎是我唯一喜欢吃的海味; 其余的我都不喜欢.期刊摘选The oyster tastes fresh and tender.海蛎子的肉鲜嫩可口.期刊摘选Would you like a little Worcestershire sauce with your fried oyster?您喜欢要点辣酱油蘸炸牡蛎吗 ?期刊摘选I enjoy eating oyster; it's really delicious.我喜欢吃牡蛎, 它味道真美.《简明英汉词典》Will you like a little worcestershire sauce with your fried oyster?您喜欢要占辣酱蘸炸牡蛎吗 ?期刊摘选Abalone slice with oyster sauce is the best of our kitchen.蚝油鲍鱼生是我们厨房的最拿手的好菜.期刊摘选What noise annoys an oyster most?什么噪声最使一只牡蛎困恼?期刊摘选That oyster closed up its valves.那个牡蛎把壳合拢起来.期刊摘选You have passed the hurdle and the world is your oyster.你已克服了障碍,你可随心所欲了.期刊摘选Dinner, scallop and oyster unlimited supply, lunch and limited supply.晚市时,扇贝、生蚝为无限量供应, 午市则限量供应哦.期刊摘选The world is sb .'s oyster.人生最得意[最有前途]的时刻.《现代英汉综合大词典》We experimented by forcing plankton into the oyster.实验时我们把浮游生物注入珠蚌中.期刊摘选One day, a man came swimming to the depths of the sea, and he saw the lonely oyster.一天, 一个男人游到了深海处, 然后他发现了那只孤独的牡蛎.期刊摘选Jean and his workers place a small piece of shell in the oyster.吉恩和他的工人们在牡蛎中放一小片贝壳.超越目标英语第4册The problem has become so serious that some oyster beds have vanished entirely.这个问题已经变得如此严重以致于一些牡蛎苗床已完全消失.期刊摘选Oyster beds, on the mudflats, are a form of fish farming.滩涂牡蛎养殖场是一种水产养殖方式。《牛津高阶英汉双解词典》Fishermen fear valuable oyster and mussel beds could be decimated.渔民们害怕宝贵的牡蛎和贻贝层会被破坏。柯林斯例句收起实用场景例句英英释义Noun1. marine mollusks having a rough irregular shell; found on the sea bed mostly in coastal waters2. edible body of any of numerous oysters3. a small muscle on each side of the back of a fowlVerb1. gather oysters, dig oysters收起英英释义词组搭配the world is your oysteryou are in a position to take the opportunities that life has to offer你可随心所欲了收起词组搭配同义词shellwhite常用俚语(The) world is one’s oyster. 世界属于某人。 (意指某人可以控制一切。尤指某人日子过得不错、很兴旺、幸福。)I feel like the world is my oyster today.今天我觉得好像世界是属于我的。The world is my oyster! I' m in tove! 我很幸福!我恋爱了!释义词态变化实用场景例句英英释义词组搭配同义词常

Oysters | National Geographic

Skip to contentNewslettersSubscribeMenuPlease be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.1 / 21 / 2An eastern oyster (Crassostrea virginica) photographed at Sedge Island Natural Resource Education Center in New JerseyAn eastern oyster (Crassostrea virginica) photographed at Sedge Island Natural Resource Education Center in New JerseyPhotograph by Joel Sartore, National Geographic Photo ArkAnimalsPhoto ArkOystersShareTweetEmailCommon Name: OystersScientific Name: OstreidaeType: InvertebratesDiet: OmnivoreGroup Name: Colony, bed, reefAverage Life Span In Captivity: Up to 20 yearsSize: 3 inches to 14 inchesSize relative to a teacup: There are many food items in the world that evoke the question, “How hungry did the first person to eat that have to be?” But few such dishes can rival the raw oyster for unpalatable appearance and general “ick” factor.As FoodIf undaunted by the oyster’s rough, rock-hard, nearly-impossible-to-open shell, the undoubtedly famished first taster would then have confronted the gray, slimy, almost phlegmatic appearance of its plump body. Once beyond any primal gag reflex though, this seminal slurper would have been surprisingly rewarded with the oyster’s delicate, toothy texture, rich flavor, and salty liquor. Oysters are also high in calcium, iron, and protein. Admittedly, they’re not for everyone, but adventurous humans the world over have enjoyed oysters, raw and cooked, for thousands of years.Habitat and RangeAlthough it is possible for food oysters to produce pearls, they should not be confused with actual pearl oysters, which are from a different family of bivalves. True oysters, which belong to the Ostreidae family, are found throughout the world’s oceans, usually in shallow waters and in colonies called beds or reefs. Among the most popular and heavily harvested species are the eastern American oyster (Crassostrea virginica), found in Atlantic waters from Canada to Argentina, and the Pacific oyster (Crassostrea gigas), found from Japan to Washington state and as far south as Australia.ShellsOyster shells are usually oval or pear-shaped, but will vary widely in form depending on what they attach to. They are generally whitish-gray in outer shell color, and their inside shell is usually a porcelain white. They have extremely strong adductor muscles to close their shells when threatened.BehaviorOysters feed by extracting algae and other food particles from the water they are almost constantly drawing over their gills. They reproduce when the water warms by broadcast spawning, and will change gender once or more during their lifetime.Threats to SurvivalCommercial harvesting of oysters is regulated throughout most of their range, and they are not currently listed as threatened or endangered. However, they are extremely sensitive to water quality and susceptible to coastal pollution, and populations in many areas where they were once abundant have dwindled or disappeared. They can also retain toxins in their flesh, making them unhealthy for human consumption.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.1 / 91 / 9This photo was submitted to Your Shot, our photo community on Instagram. Follow us on Instagram at @natgeoyourshot or visit us at natgeo.com/yourshot for the latest submissions and news about the community.This photo was submitted to Your Shot, our photo community on Instagram. Follow us on Instagram at @natgeoyourshot or visit us at natgeo.com/yourshot for the latest submissions and news about the community.Photograph by Moritz Werthschulte, National Geographic Your ShotShareTweetEmailGo FurtherAnimalsHow do fireflies get their glow? We finally have some answers.AnimalsHow do fireflies get their glow? We finally have some answers.Bird flu is spreading from pole to pole. Here’s why it matters.AnimalsBird flu is spreading from pole to pole. 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Oyster · World 带你了解生蚝的营养价值 - 知乎

Oyster · World 带你了解生蚝的营养价值 - 知乎首发于OysterWorld切换模式写文章登录/注册Oyster · World 带你了解生蚝的营养价值OysterWorld进口世界各国高品质无污染海域鲜活生蚝。生蚝文化传播者及搬运工『 Oyster · World Oyster business value 』『说到生蚝可能很多人都会产生第一画面就是街边烤生蚝 10元3个，北方人称之为海蛎子，牡蛎。今天在这里告诉大家真相并非如此，牡蛎和生蚝是两种完全不同的东西,虽然很多时候和很多地方也把“生蚝”称为牡蛎，或者严格地说，生蚝属于牡蛎的一种。由于适合生长条件的限制，它的数量上比其它品种的少，因此它的经济价位一般比较高。』（When it comes to raw oysters may cause the first picture is a lot of people will roast oyster 10 yuan 3 from the street, the north called oysters, oysters. Tell you the truth here today is not the case, oysters and raw oysters are two completely different things, although a lot of time and a lot of places also called the \"oyster\" oysters, or strictly speaking, oyster belongs to a kind of oyster. As a result of the limitation of suitable growth conditions, its number is less than the other varieties, so its economy is generally high prices.）〖就锌含量而言，牡蛎和生蚝的差别却十分惊人：每100g生蚝含锌71.2mg，而同样重量的牡蛎含锌只有9.39mg，生蚝是普通牡蛎的7.6倍。就锌含量而言，生蚝绝对是佼佼者，遥遥领先于其他天然食物，再无一种食物可以望其项背。还有蚝肉蛋白质含量超过40％，营养丰富，味道鲜美，素有“海中牛奶”之称，同时还可入药。因此，营养学一向推崇的含锌量“最高”的牡蛎是指“生蚝”，而不是普通的牡蛎。锌，对男人来说，是构成ＪＹ的很重要的元素，你懂得。〗（In terms of content of zinc, oysters and the difference of raw oysters are staggering: 71.2 mg per 100 g oyster containing zinc, and the same weight of oyster zinc only 9.39 mg, oyster is 7.6 times that of ordinary oysters. In terms of content of zinc, oyster is absolutely outstanding, well ahead of other natural food, all kinds of food can be nearly as well. And oyster meat protein content more than 40%, nutritious, delicious, known as "milk" in the sea, at the same time can also be used as a medicine. Nutrition, therefore, have always admired the zinc content of oyster "highest" refers to "oyster", rather than ordinary oysters. Zinc, for men, is a very important element of JY, you know.）「生蚝是唯一可以生食的贝类，在很多国家很普遍，对人体也有多种保健功能。」（Oysters are the only raw shellfish, are common in many countries, also have a variety of health care function to human body.）生蚝所含有的营养成分以及功效:糖原：糖原是生蚝的主要成分，具有迅速补充，恢复体力，提高肌体免疫力的作用。蛋白质：生蚝中蛋白质含量高脂肪含量少，故又称之为"海底牛奶"，在生蚝干，也就是豉中体现更加明显。生蚝具有调节整个大脑皮层的功能,对于美容养颜、滋阴补血、补肾壮阳都有不错的效果。古文有: 生用镇静、软坚、解热的效力良好；煅用则涩而带燥，收敛固涩之力较强。注：大部分海鲜的性寒，生蚝也不例外，体质特别寒凉的人建议少吃。碳酸钙：其成分具有收敛、制酸、止痛等作用，有助于胃及十二指肠溃疡的愈合。实验证明：生蚝制剂白牡片能治疗豚鼠实验性溃疡和防止大鼠实验性胃溃疡的发生，并能抑制大鼠游离酸和总酸的分泌。牛磺酸：生蚝中所含的牛黄酸有明显的保肝利胆作用，可以防治孕期肝内胆汁瘀积症。微量元素：生蚝中所含的微量元素和糖元，可以促进胎儿的生长发育、矫治孕妇贫血和加快孕妇体力的恢复。磷：生蚝中所含的磷很丰富，因为钙被人体吸收需要磷的帮助，所以又是补钙的最好食品。维生素b12：生蚝中所含的维生素B12，是一般食物所或缺的，维生素B12中的钻元素可以有效预防恶性贫血，因此具有活跃造血功能的作用。氨基酸：生蚝中所含的蛋白质中含有多种优良的氨基酸：（1）这些氨基酸可以除去体内的有毒物质，可解毒；（2）氨基乙磺酸可以降低血胆固醇浓度，因此又可预防动脉硬化。钙：生蚝中所含的钙元素，使皮肤滑润、钙使肤色好看，看起来特别有血色。钾和维生素 : 生蚝中所含的钾元素，可治疗皮肤干燥及粉刺；维生素可使皮肤光润，同时可以调节油脂的分泌。核酸 : 生蚝中所含的核酸，是蛋白质合成的重要成分，能延缓皮肤老化，减少皱纹的形成。随着年龄的增长，人体合成核酸的能力逐渐降低，只能从食物中摄取，人们日常所饮的牛奶在这方面明显不及"海底牛奶"。锌 : 生蚝中所含的锌元素，研究发现，锌对生殖器官的发育和性功能的完善至关重要，前列腺及精液中含有丰富的锌才有利于精子的生存和活动。否则，一方面会使睾丸组织结构萎缩，精子生长异常且活动力减弱；另一方面会使男性的雄性激素水平明显下降。硒 : 生蚝中所含的硒元素，则能阻止体内有害物质对精子细胞膜的氧化损伤，方可保护精子。活性肽 : 对人体有多种保健功能，由于人体胃酸的破坏作用，生吃只是获取了生蚝中一少部分的营养，未被人体完全吸收利用。Raw oysters have nutrition composition and efficacy :Glycogen, glycogen is the main element of the oyster, has rapidly supplement, restores the physical strength, improve the body immunity function.Protein: high protein content in the raw oysters, less fat, so it is also called the "sea of milk", in oyster dry, namely is more obvious in fish. Oysters have adjust the function of the cerebral cortex, the blood tonic, beauty to raise colour, ziyin kidney strong sun has a good effect. Ancient prose are: raw with calm, soft firm, antipyretic effect is good; But with dry calcined with is acerbity, solid acerbity force of strong convergence. Note: most of the seafood sex cold, oyster is not exceptional also, special cold constitution suggest eating less.Calcium carbonate: its composition have convergence, acid and pain effect, helps to gastric and duodenal ulcer healing. Experimental results show: the formulation of oyster white stag can cure on guinea pig experimental ulcer and prevent the occurrence of experimental gastric ulcer in rats, and inhibit the secretion of free acid and total acid in rats.Taurine: oysters in the bezoar acid has obvious cholagogic effect, protect liver can prevention and treatment of intrahepatic bile YuJi disease during pregnancy.Trace elements: oysters contain trace elements and repletion, pregnant women can contribute to the growth and development of the fetus, correction of anemia and speed up the pregnant women of strength.P: oysters contain phosphorus is very rich, because calcium is absorbed by the human body needs the help of phosphorus, so it is the best food calcium.Vitamin b12: oysters contain vitamin b12, is general food or lack of vitamin b12 in the drill elements can effectively prevent pernicious anemia, so have the function of the active hematopoietic function.Amino acids, protein content in the raw oysters contain a variety of excellent amino acids:(1) these amino acids can remove toxic substances in the body, to detoxify;(2) the taurine can lower blood cholesterol concentration, therefore, can prevent hardening of the arteries.Calcium: calcium contained in raw oysters, make the skin smooth, make skin beautiful, calcium seems particularly bloody.Potassium and vitamin: oysters contain potassium, to treat dry skin and acne; Vitamin can make the skin smooth, and can regulate the secretion of oils and fats.Nucleic acids: nucleic acids contained in raw oysters, are the important components of protein synthesis, can delay the ageing of the skin, and reduce the formation of wrinkles. As the growth of the age, the body's ability to synthesis of nucleic acids gradually reduce, can only be from food intake, daily milk drink by significantly less than "the seabed milk" in this regard.Zinc, zinc contained in raw oysters, the study found that zinc for the perfection of the development of reproductive organs and sexual function is crucial, prostate and semen contains abundant activity and is conducive to the survival of sperm and zinc. Otherwise, on the one hand, can make the structure of testicular tissue atrophy, developed abnormal sperm and activity weakened; On the other hand will make men significantly lower testosterone levels.Selenium: oysters contains selenium element, it can prevent the body from harmful substances oxidative damage of sperm membrane, can protect the sperm.Active peptide: a variety of health care function to human body, because the damage, stomach acid raw are but a few nutrients, obtained the oyster one not be fully absorbed by human body use.『 Oyster · World 宗旨：求质不求量！』发布于 2017-04-27 13:50生蚝牡蛎美食家赞同 111 条评论分享喜欢收藏申请转载文章被以下专栏收录OysterWorld进口世界各国高品质无污染海域鲜活生蚝外

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15 Facts About Oysters and the Need to Protect Them

Healthy populations buffer coastlines, boost economies, and benefit marine life

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By: Holly Binns & Joseph Gordon

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15 Facts About Oysters and the Need to Protect Them

Oysters are small mollusks, typically growing 3 to 5 inches long, but they play an outsized role in marine ecosystems and coastal economies.

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Did you know a raw oyster is still alive as you eat it? Or that people have consumed them since prehistoric times? Or that oysters filter and clean water while they eat?

Oysters play a big role in marine and coastal environments but face many threats, from pollution to changing ocean conditions to dredging. That’s why it’s critical to restore reefs and safeguard oyster habitat. Here are 15 things you might be surprised to learn about Eastern oysters:

A healthy adult oyster can filter the amount of water it takes to fill a small bathtub every day. Oysters feed by pumping water through their gills and in the process capture algae and other particles, sort of like a strainer. So by cleaning the water, oysters help maintain the balance of their ecosystems.

Oysters change gender. Most start out male, but some change to female after they spawn once or twice.

Oyster reefs are one of the most imperiled marine habitats on Earth, with 85% to 90% of wild reefs lost over the past century.

Very few oysters produce jewelry-quality pearls on their own; that usually requires a human prying open a cultivated oyster’s shell to insert a grain of sand or other seeding material. Oysters make pearls when such foreign substances lodge in their shells. The oyster deposits layers of nacre, the material that makes up pearls, around the foreign body to wall it off and reduce irritation.

To reproduce, oysters spawn tiny larvae that move through the water and settle on a surface, such as other oyster shells, where they will grow for the rest of their lives. Once attached, these larvae are called spat. As generations of spat grow into adults, they form oyster beds or reefs.

Oyster reefs help diffuse energy from storms and tides, which helps safeguard coastlines by preventing erosion and protecting estuary waters that serve as breeding grounds for marine life. Extremely strong storms can bury or move these reefs.

Oysters live in brackish and saltwater bays, estuaries, tidal creeks, shallow ocean areas, and intertidal zones—regions submerged at high tide and exposed at low tide.

A great egret moves through an oyster bed. Reefs offer food for many shorebirds.

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Many marine animals hide from predators in oyster reefs and eat tiny organisms that are drawn there. Reefs host animals ranging from crabs, mussels, and snails to herring, anchovies, and menhaden. These environments provide food for turtles, shorebirds, and recreationally and commercially valuable fish such as red drum, flounder, striped bass, and spotted sea trout.

Oysters have three-chambered hearts that pump colorless blood throughout their bodies. They breathe with gills, just like fish.

Wild oysters can live 25 to 30 years, but typically most don’t survive past six years.

Eastern oysters are prey for stone crabs, fish such as black drum, some kinds of sea snails, and sponges that bore holes in oyster shells to find homes.

Today, oyster populations are at historic lows. Erosion from development, along with wetland loss, pollution, overharvesting, changing ocean conditions, freshwater discharges, disease, and damaging fishing gear, have wiped out some populations and caused others to plummet.

Oyster shells are recyclable. Restaurants and other groups in coastal communities collect them to build new reefs.

Governments, conservation groups, researchers, and others along America’s coastlines are building new reefs from recycled shells, concrete, and crushed limestone. They are also growing oysters in tanks and farms to meet consumer demand.

Some oyster reefs are set aside as sanctuaries—places where oysters are left alone so their populations can recover and potentially spread even beyond the sanctuary boundaries.

For small mollusks, oysters play an outsized role in coastal communities, so protecting and restoring them makes sense for economies, the marine environment, and our plates.

Holly Binns directs The Pew Charitable Trusts’ U.S. Conserving Marine Life program in the Gulf of Mexico and U.S. Caribbean; Joseph Gordon directs the program along the Atlantic coast.

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The oyster genome reveals stress adaptation and complexity of shell formation | Nature

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The oyster genome reveals stress adaptation and complexity of shell formation

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The oyster genome reveals stress adaptation and complexity of shell formation

Guofan Zhang1 na1, Xiaodong Fang2 na1, Ximing Guo3 na1, Li Li1 na1, Ruibang Luo2,4 na1, Fei Xu1 na1, Pengcheng Yang2 na1, Linlin Zhang1 na1, Xiaotong Wang1 na1, Haigang Qi1, Zhiqiang Xiong2, Huayong Que1, Yinlong Xie2,4, Peter W. H. Holland5, Jordi Paps5, Yabing Zhu2, Fucun Wu1, Yuanxin Chen2, Jiafeng Wang1, Chunfang Peng2, Jie Meng1, Lan Yang2, Jun Liu1, Bo Wen2, Na Zhang1, Zhiyong Huang2, Qihui Zhu1, Yue Feng2, Andrew Mount6, Dennis Hedgecock7, Zhe Xu8, Yunjie Liu2, Tomislav Domazet-Lošo9, Yishuai Du1, Xiaoqing Sun2, Shoudu Zhang1, Binghang Liu2,4, Peizhou Cheng1, Xuanting Jiang2, Juan Li1, Dingding Fan2, Wei Wang1, Wenjing Fu2, Tong Wang1, Bo Wang2, Jibiao Zhang1, Zhiyu Peng2, Yingxiang Li1, Na Li2, Jinpeng Wang1, Maoshan Chen2, Yan He3, Fengji Tan2, Xiaorui Song1, Qiumei Zheng2, Ronglian Huang1, Hailong Yang2, Xuedi Du1, Li Chen2, Mei Yang1, Patrick M. Gaffney10, Shan Wang3, Longhai Luo2, Zhicai She1, Yao Ming2, Wen Huang1, Shu Zhang2, Baoyu Huang1, Yong Zhang2, Tao Qu1, Peixiang Ni2, Guoying Miao1, Junyi Wang2, Qiang Wang1, Christian E. W. Steinberg11, Haiyan Wang1, Ning Li2, Lumin Qian3, Guojie Zhang2, Yingrui Li2, Huanming Yang2, Xiao Liu1, Jian Wang2, Ye Yin2 & …Jun Wang2,12,13 Show authors

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volume 490, pages 49–54 (2012)Cite this article

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AbstractThe Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

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Minjie Hu, Xiaobin Zheng, … Yixian Zheng

Genomics of post-bottleneck recovery in the northern elephant seal

Article

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21 February 2024

A. Rus Hoelzel, Georgios A. Gkafas, … Songhai Li

MainOceans cover approximately 71% of the Earth’s surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species1. Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change2,3. As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world’s oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation4. Understanding biomineralization and molluscan shell formation is, thus, a major area of interest5. Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more thorough understanding of oyster biology and the evolution of Lophotrochozoa. One of the main challenges, however, is the high levels of polymorphism present in oysters and many marine invertebrates6,7,8. To overcome this, an oyster derived from four generations of full-sibling mating (coefficient of inbreeding, F = 0.59) was used for genome sequencing and assembly (Supplementary Text B1) through fosmid pooling, next-generation sequencing (NGS) and hierarchical assembling. Combining these genomic data with transcriptomes from different organs, different developmental stages and adults challenged with stressors, in addition to mass spectrometric analysis of shell proteins, allowed us to explore characteristics of the oyster genome and key aspects of molluscan biology related to stress response and shell formation.Sequencing and hierarchical assemblyNGS technology has been successfully applied for de novo genome sequencing and assembly using whole-genome shotgun strategies9,10,11,12,13. We initially generated 155-fold Illumina whole-genome shotgun reads (Supplementary Table 1), but could not adequately assemble them owing to high levels of polymorphism and abundant repetitive sequences (Supplementary Text B2 and Supplementary Fig. 1). As possible alternative sequencing strategies—such as the addition of longer Roche 454 reads12,13 or traditional bacterial artificial chromosome (BAC)-to-BAC sequencing—are expensive, we opted instead for a more cost-effective fosmid-pooling strategy. In brief, a fosmid library was constructed, and 145,170 clones (∼tenfold genome coverage) were evenly and randomly assigned into 1,613 pools, each of which was sequenced to ∼60-fold depth and assembled separately (Fig. 1 and Supplementary Table 1). Contigs from each pool were merged into supercontigs, totalling 1,002 megabases (Mb) (Supplementary Text B4.1–3), which was larger than genome-size estimates of 637 Mb from flow cytometry or 545 Mb from k-mer (k-base fragment) analysis (Supplementary Text B1, 2.3), owing to failure of some allelic variants to merge (Supplementary Figs 3 and 4). Self-to-self whole-genome alignment with LASTZ14 and sequencing depth information were used to remove redundancy in the assembly (Supplementary Text B4.4). The resulting 446 Mb of the assembly were retained for further scaffolding using paired-end data (Fig. 1). The final assembly comprised 559 Mb, with a contig N50 size (at which 50% of assembly was covered) of 19.4 kilobases (kb) and a scaffold N50 size of 401 kb (Supplementary Text B4.5 and Supplementary Table 3). Over 90% of the assembly was covered by the longest 1,670 (14%) scaffolds.Figure 1:

Fosmid-pooling strategy for oyster genome assembly.

Genomic DNA was randomly sheared into fragments. a, b, A 40-kb-insert fosmid library was constructed (a), and 145,170 fosmid clones were randomly selected and assigned into 1,613 pools, each containing 90 clones covering 0.57% of the diploid genome (b). For each pool, three Illumina short-insert barcoded libraries (two 200 bp and one 500 bp) were constructed and ∼60-fold coverage of 90-bp reads (20-fold per library) were generated, and assembled using SOAPdenovo with optimizing parameters. Assemblies from each pool were further corrected and reassembled if unexpected connections were detected owing to high similarity sequences from different fosmids, and gaps were filled by local assembly. c, Fosmid scaffolds were split into contigs at unfilled regions, leaving no undetermined bases in the sequences. Each base was assigned a Phred-like quality score determined by its coverage and alignment mismatches, and these sequences were merged into supercontigs using the overlap layout consensus method. Redundancy was removed using self-to-self alignment and sequencing depth information. d, Whole-genome shotgun Illumina libraries (200-bp to 20-kb inserts) from sheared genomic DNA were constructed for mated-pair Illumina sequencing. e, The fosmid supercontigs were linked into scaffolds using (1) the whole-genome shotgun sequences; (2) inferred paired-end information extracted from assembled pool scaffolds with a span size ranging from 50 bp to 37.5 kb; and (3) 225,000 fosmid ends sequenced using Sanger technology.

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Full size imageTo assess the completeness of the assembly, 105-fold coverage of short-insert library reads (<2 kb) that participated in assembly (Supplementary Table 1) were aligned against the assembly. Over 99% of these reads were successfully mapped, using a combination of Burrows–Wheeler Aligners15 and the more sensitive LASTZ (Supplementary Fig. 5 and Supplementary Table 4). The integrity of the assembly is further demonstrated by the successful mapping of 99% of the BAC sequenced obtained using the Sanger sequencing technique, and 98% of ∼68,000 expressed sequence tags from 454 sequencing (Supplementary Text B5, Supplementary Fig. 6 and Supplementary Tables 5 and 6). Fosmid pooling has been used for re-sequencing16,17, and our results show that the combination of fosmid pooling, NGS and hierarchical assembly provides a new, cost-effective alternative for de novo sequencing and assembly of complex genomes.Polymorphism and repetitive sequencesTo understand polymorphism in the oyster genome, we analysed allelic variation in the assembled genome (inbred) and one re-sequenced wild oyster (wild) (Supplementary Text C1). The inbred genome contained 3.1 million single-nucleotide polymorphisms and 258,405 short insertion/deletion (indels, 1–40 base pairs (bp)) yielding a sequence polymorphism rate of 0.73%, whereas the wild genome had 3.8 million single-nucleotide polymorphisms and 238,182 indels, or a polymorphism rate of 1.3% (Supplementary Table 7), comparable to previous estimates18. This 44% reduction in polymorphism in the inbred genome is smaller than the 59.4% predicted from four generations of brother–sister mating, indicating that selection favouring heterozygotes had occurred19. The polymorphism combining inbred and wild (among four haplotypes) was 2.3%, higher than that in most studied animal genomes20,21 but comparable to that in known high-polymorphism species7. In inbred and wild, we found 3,094 short indels located in coding regions inferred to cause frameshift variants in 2,665 genes, providing an important source for recessive lethal mutations.k-mer-based analysis of the oyster genome showed that ∼35% of 17-mers had at least two identical copies in the genome, suggesting an abundance of repetitive sequences (Supplementary Fig. 1). Similarly, homology searching and ab initio prediction found 202 Mb (36% of the genome) in repetitive sequences (Supplementary Text C2 and Supplementary Table 8). Over 62% of the detected repeats could not be assigned to known categories, reflecting the paucity of genomic information from molluscs22. Large numbers of transposase (359) and reverse-transcriptase (779) gene fragments were detected; over 96% of these had detectable transcripts (Supplementary Fig. 8). Alignment of the wild sequence against the assembly identified 20,605 deletions (>100 bp), over 80% of which overlapped with detected transposable elements, suggesting that transposable elements may have an active role in shaping genome variation. Using MITE-hunter23, we detected 157,007 copies of miniature inverted-repeat transposable elements (MITEs), accounting for a remarkable 8.82% of the genome (Supplementary Text C2.3 and Supplementary Table 9). Pair-wise comparisons show extremely low sequence divergence in some MITE families (Supplementary Fig. 9), indicating that they may still be active.Gene annotation and developmental genomicsA total of 28,027 genes were predicted encoding 50 amino acids or more by combining de novo prediction and evidence-based searches using reference genomes, oyster expressed sequence tags and transcriptomes from multiple organs and developmental stages (Supplementary Text D1 and E1 and Supplementary Fig. 11), with 96.1% showing expression (reads per kb per million mapped reads (RPKM) > 1 in at least one transcriptome; Supplementary Text D2). Of the inferred proteins, 21,085 matched entries in the SWISS-PROT, InterPro or TrEMBL databases. These genes plus their transcriptome profile from 7 adult organs and at 38 developmental stages provide valuable resources for comparative genomics analysis (Supplementary Text E2 and 3), functional inference and studies on development and organogenesis (Supplementary Text F2 and Supplementary Fig. 15).One notable finding of developmental interest is that the oyster Hox gene cluster is broken into four sections (Fig. 2) with flanking non-Hox genes (Supplementary Fig. 16). We did not find a clear Antennapedia gene, which is present in other bivalves such as Pecten and Yoldia24 (Supplementary Fig. 17). Disruption of the Hox cluster, as also observed in tunicates, nematodes and drosophilids, has been attributed to the loss of temporal co-linearity and modified developmental control25. Supporting this model, we find that Hox genes in the oyster are not activated in an order matching their identity or genomic position, with, for example, HOX4 and HOX1 peaking before gastrulation, LOX5 and POST2 during the trochophore stage and HOX5 during the pediveliger stage (Supplementary Fig. 18 and Supplementary Table 15).Figure 2: Clustering of Hox genes in Pacific oyster Crassostrea gigas , polychaete annelid Capitella teleta , fruitfly Drosophila melanogaster , lancelet Branchiostoma floridae and Homo sapiens.Oblique lines indicate regions of Hox cluster that are non-contiguous or interrupted. Blue denotes anterior Hox genes, yellow denotes paralogy group 3 Hox genes, green and purple denote central Hox genes and red denotes posterior Hox genes.

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Full size imageAdaptation to environmental stressComparison with seven other sequenced genomes identified 8,654 oyster-specific genes (Supplementary Text E3.1) that are probably important in the evolution and adaptation of oysters and other molluscs. With oysters being the only representative, these genes could be shared by other molluscs. Among these genes, gene ontology terms related to ‘protein binding’, ‘apoptosis’, ‘cytokine activity’ and ‘inflammatory response’ are highly enriched (P < 0.0001; Supplementary Text E2 and Supplementary Table 17), indicating over-representation of some host-defence genes against biotic and abiotic stress. Manual examination shows that several gene families related to defence pathways, including protein folding, oxidation and anti-oxidation, apoptosis and immune responses, are expanded in C. gigas (Fig. 3a and Supplementary Table 18). The oyster genome contains 88 heat shock protein 70 (HSP70) genes, which have crucial roles in protecting cells against heat and other stresses, compared with ∼17 in humans and 39 in sea urchins. Phylogenetic analysis finds clustering of 71 oyster HSP70 genes to themselves, suggesting that the expansion is specific to the oyster (Supplementary Fig. 19). Also expanded are cytochrome P450 (Supplementary Fig. 20) and multi-copper oxidase gene families, which are important in the biotransformation of endobiotic and xenobiotic chemicals26, and extracellular superoxide dismutases, which are important in defence against oxidative stress. The oyster genome has 48 genes coding for inhibitor of apoptosis proteins (IAPs), compared with 8 in humans and 7 in sea urchins, indicating a powerful anti-apoptosis system in oysters. Genes encoding lectin-like proteins, including C-type lectin, fibrinogen-related proteins and C1q domain-containing proteins (C1QDCs), are highly over-represented in the oyster genome (P < 0.0001; Supplementary Table 18); these genes have important roles in the innate immune response in invertebrates27,28,29. Interestingly, many immune-related genes, including genes coding for Gram-negative bacteria-binding proteins, peptidoglycan-recognition proteins, defensin, C-type-lectin-domain-containing proteins and C1QDCs, are highly expressed in the digestive gland (Supplementary Fig. 21), indicating that the digestive system of this filter feeder is an important first-line defence organ against pathogens.Figure 3: Expansion, expression and pathway distribution of defence-related genes in Crassostrea gigas.a, Expansion and expression of key genes in major stress-response pathways in C. gigas. Genes include HSPs and HSF in the heat-shock response; GRP78, CRT, CNX, GRP94, PERK, IRE1 and EIF2a in the endoplasmic reticulum unfolded-protein response (UPRER); IAPs, BCL2 like, BAG, BI1, caspases, FADD and TNFR in apoptotic pathways; CYP450 and MO in oxidation; and SOD, GPX, PRX and CAT in anti-oxidation. Boxes with bold black borders indicate gene families (HSPs, IAPs and SODs) expanded in C. gigas, and the filled colours correspond to their degree of upregulation in RPKMtreatment/RPKMcontrol by stress, found in 61 transcriptomes from oysters challenged with 9 types of stressors (Supplementary Text G2 and Supplementary Table 23). b, Venn diagram of common and unique genes expressed in response to temperature, salinity, air exposure and heavy-metal stress (zinc, cadmium, copper, lead and mercury), showing overlap of responses. c, Number of genes with and without detectable paralogues differentially expressed under stress and normal conditions, showing that genes responding to stress are more likely to have paralogues (P < 1 × 10−10; χ2 test). Green sections of the pie chart represent 1,442, 809, 358, 550 and 7,938 paralogues for air exposure, metal, temperature, salinity and normal conditions, respectively.

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Full size imageTo investigate genome-wide responses to stress, we sequenced 61 transcriptomes from C. gigas subjected to nine stressors, including temperature, salinity, air exposure and heavy metals (Supplementary Text G1 and Supplementary Tables 19 and 20). We found that 5,844 genes were differentially expressed under at least one stressor, and genes responding to different stressors showed significant overlap (Fig. 3b and Supplementary Fig. 23a). Air exposure induced a response from the largest number of genes (4,420), indicating that air exposure is a major stressor and that oysters have evolved an extensive gene set in defence. Genes differentially expressed in response to stress are more likely to have paralogues (Fig. 3c), suggesting that expansion and selective retention of duplicated defence-related genes are probably important to oyster adaptation. Under most stressors, genes coding for HSPs, histones, IAPs and protein biogenesis were upregulated, and those for protein degradation downregulated, pointing to concerted responses to maintain cellular homeostasis30 (Supplementary Text G3 and Supplementary Table 21). Genes involved in the unfolded protein response to cellular stress in the endoplasmic reticulum (coding for calreticulin, calnexin, 78- and 94-kDa glucose-regulated proteins) were upregulated, indicating that protein quality control is critical in cellular homeostasis under stress.Air exposure induced up to 67-fold upregulation of five highly expressed IAPs (Supplementary Fig. 24a). Other inhibitors of apoptosis were also upregulated: BCL2 up to fourfold and BAG up to 12-fold (Supplementary Fig. 24b). These apoptosis inhibitors were also highly upregulated under heat and low salinity stress. These findings, along with the expansion of IAPs, suggest that a powerful anti-apoptosis system exists and may be critical for the amazing endurance of oysters to air exposure and other stresses. The existence of an intrinsic apoptosis pathway in invertebrates has been controversial, and parts of the pathways have only recently been demonstrated for two lophotrochozoans31,32. The finding of key genes belonging to both intrinsic (BAX, BAK, BAG, BCL2, BI1 and procaspase) and extrinsic (TNFR and caspase 8) apoptosis pathways indicates that oysters have advanced apoptosis systems. Powerful inhibition of apoptosis as shown by genomic and transcriptomic analyses may be central to the ability of oysters to tolerate prolonged air exposure and other stresses.Heat stress induced a ∼2,000-fold increase in expression of five highly inducible HSP70 genes or a 13.9-fold increase in average expression of all HSP70 genes, amounting to 4.2% of all transcripts (Supplementary Figs 24c and 25). The genomic expansion and massive upregulation of HSP genes help to explain why C. gigas can tolerate temperatures as high as 49 °C when exposed to summer sun at low tide33. HSP genes were also upregulated under other stressors and may be central to the oyster defence against all stresses (Supplementary Fig. 25). HSP genes may also inhibit apoptosis by binding to effector caspases34.Genes involved in signal transduction, including genes coding for G-protein-coupled receptors and Ras GTPase, were also activated by stressors (Supplementary Fig. 24f) and over-represented in the oyster genome (Supplementary Table 11). These regulators may have a role in orchestrating stress responses, which seem to be well coordinated (Fig. 3a and Supplementary Fig. 25). The expansion of key defence genes and the strong, complex transcriptomic response to stress highlight the sophisticated genomic adaptations of the oyster to sessile life in a highly stressful environment.Shell formationCalcified shells provide critical protection against predation and desiccation in sessile marine animals such as oysters. Molluscan shells consist of calcium carbonate (CaCO3) crystals of either aragonite or calcite embedded in an elaborate organic matrix. Two models have been advanced for molluscan shell formation. The matrix model posits that mineralization occurs in a mantle-secreted matrix of chitin, silk fibroin and acidic proteins35,36. Chitin and silk proteins are proposed to provide matrix structure, whereas acidic proteins control the nucleation and growth of CaCO3 crystals. The cellular model suggests that biomineralization is cell-mediated; that is, crystals are formed in haemocytes and then deposited at the mineralization front37.We searched the oyster genome for genes implicated in shell formation in previous studies and examined their expression in different tissues and at different stages (Supplementary Text H1, 2). We also sequenced peptides from shells, mapped them to the genome and identified 259 shell proteins (Supplementary Text H3 and Supplementary Table 24). Although our search found evidence for the involvement of chitin, we did not find any silk-like proteins encoded in the oyster genome (Supplementary Text H2) but found, instead, many diverse proteins that may have roles in matrix construction and modification. Notably, a gene coding for a fibronectin-like protein was highly expressed at the early developmental stage, when larval shells are formed, in unison with chitin synthase (Fig. 4a) and was mostly expressed in the adult mantle (40× other organ average; Fig. 4b); the fibronectin-like protein was among the most abundant proteins found in oyster shells. Genes coding for laminin and some collagen proteins were also highly expressed in the mantle (Supplementary Fig. 27a) and found in shells. These are typical extracellular matrix (ECM) proteins, and their presence in shells suggests that the shell matrix has similarities to the ECM of animal connective tissues and basal lamina. Unlike silk fibroins that can self assemble38, the formation of fibronectin fibrils in the ECM is cell mediated39. Oyster fibronectin-like proteins have five type-III domains for integrin binding and cell adhesion. Genes coding for integrins were highly expressed in haemocytes (4× other organ average, Supplementary Fig. 27b). Thus, haemocytes may organize fibronectin-like fibril formation in the shell matrix as they do in ECM.Figure 4:

Genes related to shell formation identified from mass spectroscopy analysis of shell proteins and transcriptome data.

a, Relative expression (y axis) of genes coding for chitin synthase (gene CGI_10009438) and fibronectin-like (CGI_10016964) in early development corresponds to the formation of shell gland and first larval shells, as seen in scanning electron microscope photos. White arrow denotes the invagination that forms the shell gland. Developmental stages (x axis) and their timeline are defined in Supplementary Table 12. b, In adults, chitin synthase and fibronectin-like proteins (same colour as in a) are almost exclusively expressed in the mantle compared with other organs. Fibronectin-like is also one of the most abundant proteins found in the shell. c, Distribution of shell proteins in diverse Kyoto encyclopedia of genes and genomes (KEGG) pathways indicative of general cellular functions. d, Expression of 26 tyrosinase genes in the mantle edge, mantle pallial and other organs. Tyrosinases are abundant in shells and their higher expression in the non-pigmented mantle pallial indicate that their functions are not limited to melanogenesis but are related to shell formation.

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Full size imageThe involvement of cells in shell formation is further supported by the functional diversity of proteins detected in shells. Many housekeeping proteins, such as elongation factor 1α and ribosomal proteins, were found in the shell; indeed, most oyster shell proteins are not structural proteins but are distributed in diverse metabolic pathways (Fig. 4c and Supplementary Table 25). This functional diversity of shell proteins mirrors that of cells, which is unexpected under the matrix model. Furthermore, 84% of the 259 shell proteins identified are not classical secreted proteins (Supplementary Text H3.4 and Supplementary Table 24); they may be part of cells or deposited by exosomes40. Supporting the presence of exosomes, 61 of the 259 shell proteins matched proteins in the exosome database41. Cells and exosome-like vesicles containing calcite crystals have been observed at the mineralization front37,42, although their significance in shell formation is debated. This study provides molecular evidence for their presence inside shells and their probable participation in shell formation.Many shell proteins are enzymes that may be involved in matrix construction or modification. A homologue of penicillin-binding protein is exclusively expressed in mantle (72× other organ average) and highly abundant in shells (Supplementary Fig. 27d). Penicillin-binding protein is a transpeptidase that crosslinks glycopeptides in bacterial cell walls43 and may have similar functions in the shell matrix. Another notable enzyme found is tyrosinase. The oyster genome has an expanded set of 26 genes coding for tyrosinase, compared with one in Caenorhabditis elegans and two in humans; most genes coding for tyrosinase are mantle specific (Fig. 4d) and highly enriched among shell proteins (P = 8 × 10−6). Although tyrosinase is a key enzyme in melanogenesis44,45, it is most highly expressed in the non-pigmented pallial mantle (Fig. 4d), indicating that it has other functions in the oyster. The mantle secretes tyrosine-rich proteins46, and oxidation of tyrosine may be essential for shell matrix maturation. Several proteinases and proteinase inhibitors are highly mantle specific and abundant in shells, and may be involved in matrix formation, modification and protection (Supplementary Table 24). Together, these results indicate that oyster shell matrix is not formed simply by self-assembling silk-like proteins but by diverse proteins through complex assembly and modification processes that may involve haemocytes and exosomes.Concluding remarksWe sequenced and assembled the genome of the Pacific oyster using an inbred individual, short-read NGS and a new fosmid-pooling and hierarchical assembly strategy. The draft assembly provided insight into a molluscan genome characterized by high polymorphism, abundant repetitive sequences and active transposable elements. Genomic, transcriptomic and proteomic analyses show unique adaptations of oysters to sessile life in a highly stressful intertidal environment and the complexity of shell formation. The oyster genome sequence and comprehensive transcriptome data provide valuable resources for studying molluscan biology and lophotrochozoan evolution, and for genetic improvement of oysters and other important aquaculture species.Methods SummaryThe sequenced Pacific oyster is an inbred female produced by four generations of brother–sister mating. Genome sequences were produced with Illumina platform using fosmid pooling and assembled with a new hierarchical assembly strategy. Fosmid ends were sequenced by Sanger. Gene models were obtained by integrating results of de novo gene prediction and alignment-based methods based on homology and transcriptomic evidence. Transcriptomes were sequenced with Illumina platform. The proteome of the shell was obtained by mass spectrometry. All methods are described in detail in the Supplementary Information.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

AFTI00000000

Gene Expression Omnibus

GSE31012

Sequence Read Archive

SRA040229

SRA043580

Data deposits

The oyster genome project has been deposited at DDBJ/EMBL/GenBank under the accession number AFTI00000000. All short-read data have been deposited into the Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under the accession number SRA040229. Short-read data of re-sequencing have been deposited in the SRA under the accession number SRA043580. Raw sequencing data of transcriptomes have been deposited in the Gene Expression Omnibus under the accession number GSE31012. Genomic data are also available at the Comprehensive Library for Modern Biotechnology (CLiMB) repository: doi:10.5524/100030 (ref. 47).

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Zhang, G. et al. Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030 (2012)Download referencesAcknowledgementsWe acknowledge H. Wu, F. Zhang, Q. Tang, Z. Zhu, X. Xu, H. Lin, J. Lei, Z. Xiang, N. Li, J. Xiang and J. Jia for their support of the oyster genome project. We thank F. Han, X. Liu, R. Wu, L. Wang, Y. Wu, L. Yan, H. Niu, H. Li, Y. Wang, J. Liang, Z. Jia, J. Davis and Taylor Shellfish Farms for assistance with DNA, RNA and protein extraction, data analysis and oyster culture, and Y. Lu, C. Lin, H. Peng, Y. Ren, X. Xu, R. Chen and D. Zhang for library construction and sequencing. We thank L. Song, B. Z. Liu, Q. Li, Z. Yu, C. Ke, J. Yu, B. Liu, X. Sun, R. W. Chapman, Y. Han, S. R. Wessler, D. Arendt, E. H. Davidson, J. S. Evans, B. Brown, P. Boudry and B. Lieb for discussions. We thank other faculty and staff at the Institute of Oceanology, Chinese Academy of Science, BGI-Shenzhen and Rutgers who contributed to the oyster genome project. We acknowledge grant support from the National High-Technology Research and Development Program of China (863 program; 2010AA10A110), National Basic Research Program of China (973 Program; 2010CB126401 and 2010CB126402), 863 program (2012AA10A405), Basic Research Program Supported by Shenzhen City (JC2010526019), Shenzhen Key Laboratory of Transomics Biotechnologies (CXB201108250096A), National Natural Science Foundation of China (40730845), Mollusc Research and Development Center, CARS, Shenzhen Key Laboratory of Gene Bank for National Life Science, Taishan Scholar and Scholar Climbing Programs of Shandong. X.G. acknowledges funding from the US Department of Agriculture (2009-35205-05052 and NJ32108) and the Chinese Academy of Science Marine Functional Genomics Oversea Team and Taishan Scholar Fund; P.W.H.H. acknowledges funding from the European Research Council (EU FP7 ERC grant [268513]11); and J.P. acknowledges funding from Beatriu de Pinós of the Generalitat de Catalunya (2009 BP-DGR). We are grateful to Dalian Zhangzidao Fishery Group Co. Ltd for providing support.Author informationAuthor notesGuofan Zhang, Xiaodong Fang, Ximing Guo, Li Li, Ruibang Luo, Fei Xu, Pengcheng Yang, Linlin Zhang and Xiaotong Wang: These authors contributed equally to this work.Authors and AffiliationsInstitute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, ChinaGuofan Zhang, Li Li, Fei Xu, Linlin Zhang, Xiaotong Wang, Haigang Qi, Huayong Que, Fucun Wu, Jiafeng Wang, Jie Meng, Jun Liu, Na Zhang, Qihui Zhu, Yishuai Du, Shoudu Zhang, Peizhou Cheng, Juan Li, Wei Wang, Tong Wang, Jibiao Zhang, Yingxiang Li, Jinpeng Wang, Xiaorui Song, Ronglian Huang, Xuedi Du, Mei Yang, Zhicai She, Wen Huang, Baoyu Huang, Tao Qu, Guoying Miao, Qiang Wang, Haiyan Wang & Xiao LiuBGI-Shenzhen, Shenzhen, 518083, ChinaXiaodong Fang, Ruibang Luo, Pengcheng Yang, Zhiqiang Xiong, Yinlong Xie, Yabing Zhu, Yuanxin Chen, Chunfang Peng, Lan Yang, Bo Wen, Zhiyong Huang, Yue Feng, Yunjie Liu, Xiaoqing Sun, Binghang Liu, Xuanting Jiang, Dingding Fan, Wenjing Fu, Bo Wang, Zhiyu Peng, Na Li, Maoshan Chen, Fengji Tan, Qiumei Zheng, Hailong Yang, Li Chen, Longhai Luo, Yao Ming, Shu Zhang, Yong Zhang, Peixiang Ni, Junyi Wang, Ning Li, Guojie Zhang, Yingrui Li, Huanming Yang, Jian Wang, Ye Yin & Jun WangHaskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, 08349, New Jersey, USAXiming Guo, Yan He, Shan Wang & Lumin QianHKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Hong KongRuibang Luo, Yinlong Xie & Binghang LiuDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UK, Peter W. H. Holland & Jordi PapsDepartment of Biological Sciences, Clemson University, 29634, South Carolina, USAAndrew MountDepartment of Biological Sciences, University of Southern California, Los Angeles, 90089, California, USADennis HedgecockAtlantic Cape Community College, Mays Landing, 08330, New Jersey, USAZhe XuLaboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, P.P. 180, HR-10002, Zagreb, Croatia, Tomislav Domazet-LošoSchool of Marine Science and Policy, University of Delaware, Lewes, 19958, Delaware, USAPatrick M. GaffneyInstitute of Biology, Humboldt Universität zu Berlin Arboretum, Späthstraße 80/81, 12437 Berlin, Germany, Christian E. W. SteinbergDepartment of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark, Jun WangThe Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200 Copenhagen, Denmark, Jun WangAuthorsGuofan ZhangView author publicationsYou can also search for this author in

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PubMed Google ScholarContributionsG.Z. and X.G. conceived the study and designed scientific objectives. G.Z., Jun W. and X.G. led the project and manuscript preparation. Jun W., X.F. and Y.Y. developed the sequencing strategy. L. Li and X.F. managed the project. R.L. (leader), Yr.L., Z.H., Y.L., Xq.S., B.L., X.J., W.F., Qm.Z., H.Y., L. Luo, B. Wang, Y.M. and P.N. conducted assembly and evaluation; X.F. (leader), P.Y., Zq.X., Y.X., Yb.Z., Y.C., C.P., Y.F., D.F., L.Y., Z.P., Na L., X.W., M.C., L.C., S.Z., Jy.W., Ning L., Gj.Z. and Yr.L. performed genome annotation and data analysis; L. Li, F.X., Hy.Q., F.W., Sd.Z., Jp.W., X.D., J.Z., Q.W. and L.Q. cultured oysters and provided materials; Hg.Q. (leader), L. Li, Jf.W., Z.S. and H.W. performed polymorphism analysis and validation; F.X. (leader), P.W.H.H., J.P., T.D.L., P.Y., J. Liu, X.W., L. Li, N.Z., J. Li, W.W., Yx.L., M.Y. and W.H. conducted developmental biology studies and data analysis; L.Z. (leader), X.G., J.M., Qh.Z., Y.D., C.E.W.S., P.C., B.H., T.Q. and G.M. conducted stress studies and data analysis; X.W. (leader), X.G., T.W., Z. Xu, Y.H., A.M., Xr.S., R.H., B. Wen, F.T. and Y.Z. conducted shell-formation studies and data analysis. Hm.Y. and Jian W. supervised sequencing, assembly and bioinformatics analysis. X.G., S.W. and F.X. performed flow-cytometry analysis. D.H. and P.M.G. provided inbred oysters, BAC sequences and advice. L.Q. and X.L. participated in discussions and provided suggestions. X.G., X.F., L. Li, R.L., F.X., P.Y., L.Z., X.W., Hg.Q. and P.W.H.H. did most of the writing with contributions from all authors.Corresponding authorsCorrespondence to

Guofan Zhang, Ximing Guo, Ye Yin or Jun Wang.Ethics declarations

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Supplementary informationSupplementary InformationThis file contains Supplementary Text and Data, which includes Supplementary Materials, Methods and Results (see Contents list for details), Supplementary Figures 1-29, Supplementary Tables 1-13, 15- 20, 23, 25, and 28-29 (see separate zipped file for Supplementary Tables 14, 21, 22, 24, 26 and 27). (PDF 7838 kb)Supplementary TablesThis file contains Supplementary Tables 14, 21, 22, 24, 26 and 27. (ZIP 14755 kb)PowerPoint slidesPowerPoint slide for Fig. 1PowerPoint slide for Fig. 2PowerPoint slide for Fig. 3PowerPoint slide for Fig. 4Rights and permissions

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Reprints and permissionsAbout this articleCite this articleZhang, G., Fang, X., Guo, X. et al. The oyster genome reveals stress adaptation and complexity of shell formation.

Nature 490, 49–54 (2012). https://doi.org/10.1038/nature11413Download citationReceived: 30 January 2012Accepted: 11 July 2012Published: 19 September 2012Issue Date: 04 October 2012DOI: https://doi.org/10.1038/nature11413Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard

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Editorial SummaryOyster genome reveals defence mechanismsOysters are keystone species in estuarine ecology and among the most important aquaculture species worldwide. The sequencing and assembly of the genome of the Pacific oyster, Crassostrea gigas, are now reported. Comparisons with other genomes reveal an expansion of defence genes as an adaptation to life as a sessile species in the intertidal zone, a surprisingly complex pathway for shell formation and dramatic evolution of genes related to larval development, highlighting their adaptive significance for marine invertebrates.show all

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