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性状和疾病提供了资源。动物可以作为在人类身上难以分析或在农业上可能很重要的过程的模型。鸡的胚胎是最好的研究对象之一，因为它们很大，很容易获得（通过打开一个鸡蛋），此外，世界上大约20%的肉类和大多数鸡蛋消费来自养鸡业。研究鸟类的基因组很有吸引力，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更愿意研究鸟类，就像大多数人更愿意在整洁的房子里找东西，而不是在凌乱的房子里找一样。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。利用现有的鸡类信息，有可能生成这类鸟类的基因组图谱。很明显，下一个要看的鸟类是火鸡，火鸡在农业上也很重要，我们正在为这种动物绘制地图。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，即鸭子是未受影响的禽流感携带者，而鸡和火鸡等禽类可能死于禽流感。另一个有趣的物种是斑胸草雀。这些微小的鸟类是研究大脑过程的绝佳模型，因为它们“像人类一样彼此交谈”，很少有物种能做到这一点。其他包括鹅（出于农业原因），鸵鸟（在进化上，它与鸡相差甚远）和秃鹫（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，最好将两种方法结合起来。第一种方法是使用一种实验室技术（称为“FISH”）来点亮鸡的特定基因，然后在另一只鸟身上重复这个实验，以找出差异和相似之处。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。要找到感兴趣的基因，关键是要有一个参照点，这个参照点由染色体（带）上的横向条纹表示，每个条带都有一个唯一的标识号。在专门研究人类的网站上，如果你打开首页（www.ensembl.org/Homo_sapiens/），你会看到，在左手边，一个染色体的图表，完整的带。点击其中一条染色体，就有可能找到你感兴趣的基因。如果你对鸡做同样的检查（www.ensembl.org/Gallus_gallus/）你会看到染色体，但是条带信息是缺失的。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长度的四分之三，那么只给出了部分信息。说爱丁堡在英国的四分之三的地方，在东海岸，在福斯湾更准确。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，我们就可以提出关于乐队本身性质的问题。例如，“暗”波段是否比“亮”波段更缺乏基因？DNA的组成部分（称为“碱基”）在暗光带和亮光带等方面有区别吗？我们知道哺乳动物之间存在差异，但到目前为止，我们对鸟类是否也存在类似的情况知之甚少。将哺乳动物和鸟类进行比较将有助于进一步了解它们的进化过程。

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.