Defining the functional landscapes of metazoan genomes

定义后生动物基因组的功能景观

• 批准号: BB/F007590/1
• 负责人: Chris Ponting
• 金额: $ 24.93万
• 依托单位: MRC Harwell Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FF007590%2F1
• 关键词: Defining; functional; landscapes; metazoan; genomes

'Why are some genomes really big and others quite compact?', 'What is all that 'junk' doing in our genomes?', and 'How do limbs, fins, and faces develop and evolve?' These are 3 of the 125 Big Questions in Science, identified by Science magazine on 1 July 2005. To answer these, and other questions, requires a letter-by-letter comparison of genomes -- the books-of-life -- from very different animals. Seeing whether each letter is conserved, or else replaced, does not however tell the full story, since we also need to consider whether letters are added or deleted. Taken together, the conservation, or the insertion or deletion, of letters can highlight those parts of the books-of-life that underlie the basic biology of all animals, and others that specify the differences between species. A fourth Big Question, named by Science, is 'How much will new technologies lower the cost of [genome] sequencing?' This is beginning to be answered: sequencing will soon become so cheap that many, if not all, of the animals of interest to biologists will have their genomes sequenced by 2010. Our group has already served an apprenticeship analysing the genomes of humans, mice, rats, dogs, and chickens, with an over-arching aim of pinpointing the letters of the human genome that contribute to human health. We now wish to consider all available genomes from across the animal kingdom in order to address the Big Questions in Science. In this project, we shall find genes that encode protein, and others that do not, in each of these genomes. We then will calculate the relative contributions of protein-coding genes and non-protein-coding genes in specifying (a) the ancient biology of animals, and (b) the biology that distinguishes branches of the animal evolutionary tree. As we cannot answer all other interesting questions, we will provide comprehensive information on the internet to allow other biologists from around the world to benefit from them.

“为什么有些基因组真的很大，而另一些却相当紧凑？”，“这些‘垃圾’在我们的基因组里做了什么？”，以及“肢体、鳍和脸是如何发育和进化的？”这些是2005年7月1日《科学》杂志确定的125个《科学》大问题中的3个。要回答这些和其他问题，需要逐个字母地比较来自非常不同动物的基因组--生命之书。然而，只看每个字母是否被保存或替换并不能说明全部情况，因为我们还需要考虑字母是被添加还是被删除。总而言之，字母的保存或插入或删除可以突出生命之书中构成所有动物基本生物学的部分，以及其他指明物种之间差异的部分。《科学》杂志提出的第四个大问题是，新技术将在多大程度上降低[基因组]测序的成本？这一点开始得到解答：测序很快就会变得如此便宜，以至于到2010年，生物学家感兴趣的许多动物都将完成基因组测序。我们的团队已经完成了分析人类、小鼠、大鼠、狗和鸡的基因组的学徒工作，总体目标是找出有助于人类健康的人类基因组的字母。我们现在希望考虑动物王国中所有可用的基因组，以便解决科学中的大问题。在这个项目中，我们将在每个基因组中找到编码蛋白质的基因，以及其他不编码蛋白质的基因。然后，我们将计算蛋白质编码基因和非蛋白质编码基因在确定(A)动物的古代生物学和(B)区分动物进化树分支的生物学方面的相对贡献。由于我们无法回答所有其他有趣的问题，我们将在互联网上提供全面的信息，让世界各地的其他生物学家从这些信息中受益。

项目成果

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

• DOI: 10.1186/1471-2164-14-95
• 发表时间: 2013-02-12
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Rands CM;Darling A;Fujita M;Kong L;Webster MT;Clabaut C;Emes RD;Heger A;Meader S;Hawkins MB;Eisen MB;Teiling C;Affourtit J;Boese B;Grant PR;Grant BR;Eisen JA;Abzhanov A;Ponting CP
• 通讯作者: Ponting CP

Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles.

• DOI: 10.1093/gbe/evt060
• 发表时间: 2013
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Li YI;Kong L;Ponting CP;Haerty W
• 通讯作者: Haerty W

The genome of the green anole lizard and a comparative analysis with birds and mammals.

• DOI: 10.1038/nature10390
• 发表时间: 2011-08-31
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Alfoeldi, Jessica;Di Palma, Federica;Grabherr, Manfred;Williams, Christina;Kong, Lesheng;Mauceli, Evan;Russell, Pamela;Lowe, Craig B.;Glor, Richard E.;Jaffe, Jacob D.;Ray, David A.;Boissinot, Stephane;Shedlock, Andrew M.;Botka, Christopher;Castoe, Todd A.;Colbourne, John K.;Fujita, Matthew K.;Moreno, Ricardo Godinez;ten Hallers, Boudewijn F.;Haussler, David;Heger, Andreas;Heiman, David;Janes, Daniel E.;Johnson, Jeremy;de Jong, Pieter J.;Koriabine, Maxim Y.;Lara, Marcia;Novick, Peter A.;Organ, Chris L.;Peach, Sally E.;Poe, Steven;Pollock, David D.;de Queiroz, Kevin;Sanger, Thomas;Searle, Steve;Smith, Jeremy D.;Smith, Zachary;Swofford, Ross;Turner-Maier, Jason;Wade, Juli;Young, Sarah;Zadissa, Amonida;Edwards, Scott V.;Glenn, Travis C.;Schneider, Christopher J.;Losos, Jonathan B.;Lander, Eric S.;Breen, Matthew;Ponting, Chris P.;Lindblad-Toh, Kerstin
• 通讯作者: Lindblad-Toh, Kerstin

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes.

• DOI: 10.1186/gb-2010-11-7-r72
• 发表时间: 2010
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Chodroff RA;Goodstadt L;Sirey TM;Oliver PL;Davies KE;Green ED;Molnár Z;Ponting CP
• 通讯作者: Ponting CP

Transcribed dark matter: meaning or myth?

• DOI: 10.1093/hmg/ddq362
• 发表时间: 2010-10-15
• 期刊: HUMAN MOLECULAR GENETICS
• 影响因子: 3.5
• 作者: Ponting, Chris P.;Belgard, T. Grant
• 通讯作者: Belgard, T. Grant