Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird.
Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird.
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DOI：
10.1186/1471-2164-10-s2-s8
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发表时间：
2009-07-14
期刊：
影响因子：
4.4
通讯作者：
Edwards SV
中科院分区：
文献类型：
--
作者：
Chapus C;Edwards SV
随着鸡基因组草图的发表和最近从非鸟类爬行动物和鸟类中产生的几个BAC克隆文库，现在有可能在爬行动物中进行更详细的比较基因组研究。特别令人感兴趣的是将哺乳动物和非鸟类爬行动物的大的、重复丰富的基因组转化为最低限度的鸡基因组的基因组事件。我们已经使用配对BAC末端序列（BES）从美国短吻鳄（短吻鳄mississippiensis），画龟（画龟）和鸸鹋（Dromaius novaehollaniensis）调查模式的序列分歧，基因和retroelement内容，和微共线性这些物种和鸡之间。从总共11，967个策展的BES中，我们使用严格的BLAST协议分别成功地将鳄鱼，海龟和鸸鹋中的725，773和2597个序列映射到鸡基因组草图中的位点。最常见的是，序列映射到鸡基因组中的单个位点。在分别获得的1675、1828和2936对鳄鱼、海龟和鸸鹋的BES中，总共有34对（短吻鳄，2%），24（海龟，1.3%）和479（鸸鹋，16.3%）对被发现以高置信度和正确的方向和BAC大小的标记间距离映射到单个鸡染色体，包括25个这样的配对命中在鸸鹋映射到鸡Z染色体。通过确定这三个物种的BAC克隆的一个子集的插入大小，我们还发现了一个显着的相关性，在鳄鱼和海龟和鸡的标记间距离，与预期的基础上的基因组大小的比例的斜率。我们的研究结果表明，大量的小规模染色体重排和缺失的谱系导致鸡已大大减少了检测到的同线性的数量之间观察到的鸡和鳄鱼，海龟，和鸸鹋基因组，并意味着小缺失广泛发生在整个基因组的爬行动物和鸟类的祖先导致约50%的减少基因组大小观察到的鸟类相比，爬行动物。我们还绘制并确定了来自这些物种的数百个新BAC克隆中可能的基因区域。
With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.