Integrative and comparative genomic studies of seven model avian species. Evolutionary perspectives on gross genomic changes and on G-bands

七种模式鸟类的综合和比较基因组研究。

• 批准号: BB/E010652/1
• 负责人: Darren Griffin
• 金额: $ 46.51万
• 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: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE010652%2F1
• 关键词: Integrative; comparative; genomic; studies; seven

Genome projects provide resources to study many traits and diseases. Animals may be used as models for processes that are difficult to analyse in humans or may be important agriculturally. Chickens have among the best embryos to study because they are large and easily accessible (by opening an egg), in addition, about 20% of world meat and most egg consumption arises via chicken farming. The genome is attractive to examine because it is small, because there is less 'junk' DNA in birds than mammals. Scientists interested in the genomes of vertebrates would therefore rather look at birds just as most people would rather look for something in a tidy house than a messy one. A description of the chicken genome was announced in 2004 and paved the way to start work on other birds. It is possible to generate genome maps for such birds using available chicken information. An obvious next bird to look at is the turkey, turkey is also of agricultural importance and we are in the advanced stages of making a map for this animal. Other interesting species include ducks; the recent reports both in the popular press and scientific journals have highlighted the fact that ducks are unaffected carriers of bird flu where birds like chickens and turkeys can die from it. Another interesting species is zebra finch. These tiny aviary birds are excellent models for examining brain processes because they 'talk to one another like humans' in a way that few species can. Others include goose (for agricultural reasons), ostrich (evolutionarily, it is very far removed from chicken) and vulture (as the species is endangered and because its chromosomes are very different to other birds). There are many ways in which this so-called 'comparative genomics' can be achieved. In our experience it is best to combine two approaches. The first is to use a laboratory technique (called 'FISH') to light up specific genes in chicken then repeat the experiment in another bird to spot where differences and similarities lie. The second is to use a computer and compare similar gene sequences already established. Genes are located on chromosomes, much in the same way as cities and towns are located on islands and continents. Essential to finding a gene of interest is to have a point of reference that is represented by lateral stripes across the chromosomes (bands), each of which has a unique identification number. In the website dedicated to humans, if you open up the front page (www.ensembl.org/Homo_sapiens/) then you will see, on the left hand side, a diagram of chromosomes, complete with bands. By clicking on one of these chromosomes it is possible to find your gene of interest. If you do the same for chicken (www.ensembl.org/Gallus_gallus/) however then you do see chromosomes but the banding information is absent. Of course you can still find your gene but it is much more difficult. An analogy might be, if you say Edinburgh is about three quarters of the way up the length of the UK, only partial information is given. Saying that Edinburgh is about three quarters of the way up the UK, on the east coast, on the Firth of Forth is much more accurate. We therefore propose to perform experiments that will enable us to add banding information to the chicken web site. With this information we can then ask questions about the nature of the bands themselves. For instance, are the 'dark' bands more gene-poor than the light ones? Does the composition of the building blocks of DNA (called 'bases') differ in dark and light bands and so on. We know that there are differences in mammals but, as yet, have little idea about whether similar situations pertain in birds. Comparisons of mammals and birds will provide further insight into their evolution.

基因组计划为研究许多性状和疾病提供了资源。动物可以用作在人类中难以分析的过程的模型，或者在农业上可能是重要的。鸡是最好的胚胎研究之一，因为它们很大，很容易获得（通过打开鸡蛋），此外，世界上大约20%的肉类和大部分鸡蛋消费来自养鸡业。基因组之所以很有吸引力，是因为它很小，因为鸟类的“垃圾”DNA比哺乳动物少。因此，对脊椎动物基因组感兴趣的科学家们宁愿研究鸟类，就像大多数人宁愿在整洁的房子里找东西，也不愿在凌乱的房子里找东西一样。2004年公布了鸡基因组的描述，为开始研究其他鸟类铺平了道路。利用现有的鸡的信息，有可能为这些鸟类绘制基因组图谱。下一个要看的明显的鸟类是火鸡，火鸡在农业上也很重要，我们正处于为这种动物绘制地图的高级阶段。其他有趣的物种包括鸭子;最近在大众媒体和科学杂志上的报道都强调了这样一个事实，即鸭子是禽流感的未受影响的携带者，鸡和火鸡等鸟类可能死于禽流感。这些微小的鸟类是研究大脑过程的绝佳模型，因为它们“像人类一样相互交谈”，很少有物种能做到。其他包括鹅（出于农业原因），鸵鸟（从进化上讲，它与鸡相距甚远）和秃鹫（因为该物种濒临灭绝，并且因为它的染色体与其他鸟类非常不同）。有许多方法可以实现这种所谓的“比较基因组学”。根据我们的经验，最好将联合收割机两种方法结合起来。第一种是使用一种实验室技术（称为“FISH”）来照亮鸡的特定基因，然后在另一只鸡身上重复实验，以发现差异和相似之处。第二种方法是使用计算机比较已经建立的相似基因序列。基因位于染色体上，就像城镇位于岛屿和大陆上一样。找到感兴趣的基因的关键是要有一个参考点，该参考点由染色体上的横向条纹（条带）表示，每个条纹都有一个唯一的识别号。在人类的网站上，如果你打开首页（www.ensembl.org/Homo_sapiens/），你会看到，在左手边，是一张染色体图，上面有完整的条带。通过点击其中一条染色体，可以找到您感兴趣的基因。然而，如果你对鸡做同样的事情（www.ensembl.org/Gallus_gallus/），那么你确实看到了染色体，但没有条带信息。当然，你仍然可以找到你的基因，但这要困难得多。一个类比可能是，如果你说爱丁堡大约是英国长度的四分之三，只给出了部分信息。说爱丁堡位于英国东海岸的四分之三，位于福斯湾，要准确得多。因此，我们建议进行实验，这将使我们能够添加带信息的鸡网站。有了这些信息，我们就可以问一些关于乐队本身性质的问题。例如，“暗”带是否比亮带更缺乏基因？我们知道哺乳动物中存在差异，但到目前为止，对鸟类是否存在类似的情况还知之甚少。哺乳动物和鸟类的比较将为它们的进化提供进一步的见解。

项目成果

Gene duplication and fragmentation in the zebra finch major histocompatibility complex.

• DOI: 10.1186/1741-7007-8-29
• 发表时间: 2010-04-01
• 期刊: BMC biology
• 影响因子: 5.4
• 作者: Balakrishnan CN;Ekblom R;Völker M;Westerdahl H;Godinez R;Kotkiewicz H;Burt DW;Graves T;Griffin DK;Warren WC;Edwards SV
• 通讯作者: Edwards SV

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

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes.

• DOI: 10.1186/s13059-018-1544-8
• 发表时间: 2018-10-05
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Damas J;Kim J;Farré M;Griffin DK;Larkin DM
• 通讯作者: Larkin DM

Differences in pregnancy outcomes in donor egg frozen embryo transfer (FET) cycles following preimplantation genetic screening (PGS): a single center retrospective study.

• DOI: 10.1007/s10815-016-0832-z
• 发表时间: 2017-01
• 期刊: Journal of assisted reproduction and genetics
• 影响因子: 3.1
• 作者: Coates A;Bankowski BJ;Kung A;Griffin DK;Munne S
• 通讯作者: Munne S

Time lapse: A glimpse into prehistoric genomics.

延时摄影：史前基因组学一瞥。

• DOI: 10.1016/j.ejmg.2019.03.004
• 发表时间: 2020
• 期刊: European journal of medical genetics
• 影响因子: 1.9
• 作者: Griffin DK