杨树基因组中染色体基因丰度分化及EST序列对基因覆盖度的检测(英文)

Differentiation of Gene Richness on Duplicated Chromosomes and Survey of Genes Captured by ESTs in Poplar Genome

高等植物基因组中,大部分序列为非表达序列,基因序列所占的比例很小,了解基因在基因组中的分布是研究基因组结构的一个重要方面。在美国能源部资助下,一个毛果杨无性系的基因组测序已经完成并对公众发布。杨树全基因组序列的完成,为我们了解林木基因组中基因的分布提供了一个特例。在本文中,我们利用泊松分析对杨树基因组中基因在各个染色体上的密度进行了检测,结果表明杨树基因组中各条染色体的基因含量存在显著差异。杨树全基因组测序项目揭示现代杨树基因组起源于一次古全基因组复制事件(称为杨柳科基因组复制),所以杨树基因组不同染色体间存在很大的同源复制片段。但是我们的研究显示,杨树基因组中大多数高度同源的染色体上基因的密度与染色体间的同源性没有明显关系,这说明杨柳科全基因组复制事件后,各个高度同源染色体上的基因发生了流失,且基因流失的速率是不一样的。同时本文还对近九万条毛果杨EST序列进行了比对分析,结果显示这些EST序列覆盖的基因仅占杨树基因组中基因总数的16.8%左右。EST测序虽然是发现基因的一个重要手段,但小规模EST测序对基因的覆盖度很低,所以小规模EST测序的应用价值是有限的。

In higher plant genomes,most sequences are unexpression sequence,the proportion of a genome that encodes for genes may be very small.Understanding gene distribution in the genome is a very important aspect for invastigating the genome structure.Funded by the U.S.Department of Energy,a clonal Populus trichocarpa genome sequencing has been completed and released to the public.The accomplishment of poplar genome offers us a unique opportunity to survey the gene distribution in the genome of a forest tree.In this paper,based on Poisson calculator,we investigated the gene density of various chromosomes in poplar genome.As a result,we found that gene density is significantly different among chromosomes in poplar genome.Modern poplar genome arose from an ancient whole genome duplication event,known a ＂salicoid duplication＂.Thus poplar genome shared large duplication segments among different chromosome members.However,our results demonstrated that gene abundance pattern was different from the chromosomal duplication pattern of poplar genome.This implied the duplicated genes lost at different rates on the duplicated chromosomes following the salicoid duplication.Meanwhile,based on alignment with about 90 thousands ESTs,we found that only 16.8% of the predicted gene models in poplar genome had EST proofs.Although,EST sequencing is an attractive alternative to whole genome sequencing for gene identification,the power of small scale EST sequencing study should be properly evaluated since with limited number of EST sequences,genes captured by ESTs are fairly limited.