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

基因组计划为研究许多特征和疾病提供了资源。动物可以被用作人类难以分析的过程的模型，或者在农业上可能是重要的。鸡有最好的胚胎可以研究，因为它们很大，很容易接触到(通过打开鸡蛋)，此外，世界上大约20%的肉类和鸡蛋消费来自养鸡。这个基因组之所以吸引人去研究，是因为它很小，因为鸟类中的垃圾DNA比哺乳动物中的少。因此，对脊椎动物基因组感兴趣的科学家宁愿观察鸟类，就像大多数人宁愿在整洁的房子里寻找东西一样，而不是在凌乱的房子里寻找东西。2004年宣布了对鸡基因组的描述，为开始研究其他鸟类铺平了道路。利用现有的鸡信息，有可能为这种鸟类生成基因组图。下一个明显值得关注的鸟类是火鸡，火鸡在农业上也很重要，我们正在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期刊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会死于禽流感。另一个有趣的物种是斑马雀。这些微小的鸟类是研究大脑过程的极佳模型，因为它们以一种很少有物种能做到的方式相互交谈，就像人类一样。其他鸟类包括鹅(出于农业原因)、鸵鸟(在进化上与鸡相距甚远)和秃鹰(因为该物种濒临灭绝，而且它的染色体与其他鸟类非常不同)。有很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，最好将两种方法结合起来。第一种是使用实验室技术(称为“鱼”)来激活鸡的特定基因，然后在另一只鸟身上重复这一实验，以找出不同之处和相似之处。第二种方法是使用计算机比较已经确定的相似基因序列。基因位于染色体上，就像城市和城镇位于岛屿和大陆上一样。寻找感兴趣的基因的关键是有一个参考点，这个参考点由染色体(带)上的横向条纹表示，每条染色体都有一个唯一的识别号。在这个专门介绍人类的网站上，如果你打开首页(www.ensembl.org/Homo_Sapiens/)，你会在左边看到一张染色体图，上面有带。通过点击这些染色体中的一个，就有可能找到你感兴趣的基因。然而，如果你对鸡做同样的操作(www.ensembl.org/Gallus_Gallus/)，那么你确实会看到染色体，但没有显带信息。当然，你仍然可以找到你的基因，但这要困难得多。打个比方，如果你说爱丁堡大约是英国全长的四分之三，那么你只给出了部分信息。说爱丁堡在英国北部约四分之三的地方，在东海岸，在福斯湾，要准确得多。因此，我们建议进行实验，使我们能够在鸡的网站上添加条带信息。有了这些信息，我们就可以问关于乐队本身的性质的问题。例如，“暗”波段是否比浅色波段更缺乏基因？DNA组成单元(称为“碱基”)的组成在暗带和亮带等方面是否有所不同？我们知道哺乳动物之间存在差异，但到目前为止，我们还不知道鸟类是否也存在类似的情况。哺乳动物和鸟类的比较将提供对它们进化的进一步洞察。

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.