Genome assembly. chromosomal organization and comparative genomics of multiple bird species: beyond "catalogues of genes"

基因组组装。

• 批准号: BB/K008161/1
• 负责人: Darren Griffin
• 金额: $ 68.24万
• 依托单位: University of Kent
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK008161%2F1
• 关键词: Genome; assembly.; chromosomal; organization; comparative

Imagine trying to navigate through a town with only the index from your A-Z to guide you and not the street map. In essence, this is what happens when the genome of a new species is sequenced. Old fashioned technology used to "sketch the outline of the streets" first before filling in the gaps with the gene sequence. The new technology (so called "Next Generation Sequencing") is much cheaper and quicker but is quite poor at sorting out where the genes are in relation to one another. Essentially, Next Generation Sequencing assemblies are little more than catalogues of genes with little structure of the overall genome apparent. Fortunately this problem can be rectified using a technique called "FISH" that can take the data from next generation sequencing projects and visualise directly the genes as they appear in their rightful place in the genome. In this project we intend to do this with 25-30 recently completed genome sequences from birds. Birds are among the most diverse animals with around 10,000 living species. Many are models for human disease and development and are critical to agriculture (both meat and eggs). Others are threatened or endangered and, with impending global warming, molecular tools for the study of ecology and conservation of birds are essential. It is also possible to compare the overall structure of one genome with another, somewhat like comparing the maps of towns with similar layouts. We have developed online tools that can directly visualize the similarities and differences between the genomes of several birds at a time. Of course the differences between these bird genomes came about through changes that happened during evolution. One of the main aims of this project is to find out how and why this occurred. We have a number of ideas such as we think there may be different "gene signatures" at the places in the genome where evolutionary rearrangements are more or less likely to occur. We think that the whole process may be related to the mechanisms by which our genes recombine in our germ cells. We also think there may be a role for small pieces of DNA that "float around" these bird genomes. Finally, we have received overwhelming support from numerous laboratories all over the world, all of whom are interested in bird genomics and who would wish to use our online resource to ask biological questions of their own. For this reason we feel that this project not only will help us understand evolution in birds but also establish the UK as a central international hub for work of this kind.

想象一下，试图在一个城镇中导航，只有A-Z的索引来引导你，而不是街道地图。从本质上讲，这就是一个新物种的基因组测序时所发生的事情。老式的技术通常是先“勾勒出街道的轮廓”，然后再用基因序列填补空白。新技术（所谓的“下一代测序”）更便宜，更快，但在整理基因之间的关系方面却很差。从本质上讲，下一代测序组装只不过是基因的目录，整个基因组的结构几乎没有明显的。幸运的是，这个问题可以通过一种名为“FISH”的技术来解决，该技术可以从下一代测序项目中获取数据，并直接可视化基因，因为它们出现在基因组中的正确位置。在这个项目中，我们打算用25-30个最近完成的鸟类基因组序列来做这件事。鸟类是最多样化的动物之一，大约有10，000种。许多是人类疾病和发展的模型，对农业（肉类和蛋类）至关重要。另一些则受到威胁或濒临灭绝，随着全球变暖的临近，研究生态学和保护鸟类的分子工具至关重要。也可以将一个基因组的整体结构与另一个基因组进行比较，有点像比较具有相似布局的城镇地图。我们开发了在线工具，可以直接可视化几种鸟类基因组之间的相似性和差异。当然，这些鸟类基因组之间的差异来自进化过程中发生的变化。这个项目的主要目的之一是找出这是如何以及为什么发生的。我们有很多想法，比如我们认为在基因组中或多或少可能发生进化重排的地方可能有不同的“基因签名”。我们认为，整个过程可能与我们的基因在生殖细胞中重组的机制有关。我们还认为，“漂浮在”这些鸟类基因组周围的小片段DNA可能发挥了作用。最后，我们得到了来自世界各地众多实验室的大力支持，他们都对鸟类基因组学感兴趣，并希望利用我们的在线资源提出自己的生物学问题。出于这个原因，我们认为这个项目不仅将帮助我们了解鸟类的进化，而且还将使英国成为这类工作的国际中心。

项目成果

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens.

• DOI: 10.3390/biology10090876
• 发表时间: 2021-09-06
• 期刊: Biology
• 影响因子: 4.2
• 作者: Abdelmanova AS;Dotsev AV;Romanov MN;Stanishevskaya OI;Gladyr EA;Rodionov AN;Vetokh AN;Volkova NA;Fedorova ES;Gusev IV;Griffin DK;Brem G;Zinovieva NA
• 通讯作者: Zinovieva NA

Additional file 1: of Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

附加文件1：鸟类祖先核型重建揭示了宏观和微观染色体进化史的差异

• DOI: 10.6084/m9.figshare.7175525
• 发表时间: 2018
• 作者: Damas J

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.

• DOI: 10.1093/gbe/evw166
• 发表时间: 2016-08-25
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Farré M;Narayan J;Slavov GT;Damas J;Auvil L;Li C;Jarvis ED;Burt DW;Griffin DK;Larkin DM
• 通讯作者: Larkin DM

Additional file 2: of Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

附加文件2：鸟类祖先核型的重建揭示了宏观和微观染色体进化史的差异

• DOI: 10.6084/m9.figshare.7175537
• 发表时间: 2018
• 作者: Damas J

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

• DOI: 10.1101/gr.213660.116
• 发表时间: 2017-05
• 期刊: Genome research
• 影响因子: 7
• 作者: Damas J;O'Connor R;Farré M;Lenis VPE;Martell HJ;Mandawala A;Fowler K;Joseph S;Swain MT;Griffin DK;Larkin DM
• 通讯作者: Larkin DM