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首页> 外文期刊>BMC Bioinformatics >Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
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Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome

机译：鲤科鱼类中的比较基因组学：鲤鱼EST有助于斑马鱼基因组的注释

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Background Automatic annotation of sequenced eukaryotic genomes integrates a combination of methodologies such as ab-initio methods and alignment of homologous genes and/or proteins. For example, annotation of the zebrafish genome within Ensembl relies heavily on available cDNA and protein sequences from two distantly related fish species and other vertebrates that have diverged several hundred million years ago. The scarcity of genomic information from other cyprinids provides the impetus to leverage EST collections to understand gene structures in this diverse teleost group. Results We have generated 6,050 ESTs from the differentiating testis of common carp (Cyprinus carpio) and clustered them with 9,303 non-gonadal ESTs from CarpBase as well as 1,317 ESTs and 652 common carp mRNAs from GenBank. Over 28% of the resulting 8,663 unique transcripts are exclusively testis-derived ESTs. Moreover, 974 of these transcripts did not match any sequence in the zebrafish or fathead minnow EST collection. A total of 1,843 unique common carp sequences could be stringently mapped to the zebrafish genome (version 5), of which 1,752 matched coding sequences of zebrafish genes with or without potential splice variants. We show that 91 common carp transcripts map to intergenic and intronic regions on the zebrafish genome assembly and regions annotated with non-teleost sequences. Interestingly, an additional 42 common carp transcripts indicate the potential presence of new splicing variants not found in zebrafish databases so far. The fact that common carp transcripts help the identification or confirmation of these coding regions in zebrafish exemplifies the usefulness of sequences from closely related species for the annotation of model genomes. We also demonstrate that 5' UTR sequences of common carp and zebrafish orthologs share a significant level of similarity based on preservation of motif arrangements for as many as 10 ab-initio motifs. Conclusion Our data show that there is sufficient homology between the transcribed sequences of common carp and zebrafish to warrant an even deeper cyprinid transcriptome comparison. On the other hand, the comparative analysis illustrates the value in utilizing partially sequenced transcriptomes to understand gene structure in this diverse teleost group. We highlight the need for integrated resources to leverage the wealth of fragmented genomic data.
机译：背景技术测序的真核生物基因组的自动注释整合了诸如从头开始方法和同源基因和/或蛋白质的比对的方法的组合。例如，Ensembl中斑马鱼基因组的注释在很大程度上依赖于两个远缘鱼类和其他距今已有数亿年前的脊椎动物的cDNA和蛋白质序列。来自其他鲤科鱼类的基因组信息的匮乏，促使人们利用EST集合来了解这一多样化的硬骨鱼类的基因结构。结果我们从鲤鱼的分化睾丸中产生了6,050个EST，并将它们与CarpBase的9,303个非性腺EST以及GenBank的1,317个EST和652个鲤鱼mRNA进行了聚类。在所产生的8,663个独特的转录本中，超过28％是仅来自睾丸的EST。而且，这些转录物中的974个与斑马鱼或黑头min鱼EST集合中的任何序列都不匹配。总共1,843个独特的鲤鱼序列可以严格地定位到斑马鱼基因组（第5版），其中1,752个匹配的斑马鱼基因编码序列具有或不具有潜在的剪接变体。我们显示91条常见的鲤鱼转录本映射到斑马鱼基因组大会上的基因间和内含子区域，以及以非远亲序列注释的区域。有趣的是，另外有42条鲤鱼转录本表明，到目前为止，斑马鱼数据库中尚未发现新的剪接变体。普通鲤鱼转录本有助于识别或确认斑马鱼中这些编码区的事实，说明了来自密切相关物种的序列对于模型基因组注释的有用性。我们还证明了，基于鲤鱼和斑马鱼直系同源物的5'UTR序列基于多达10个ab-initio基序的基序排列的保留，具有很高的相似度。结论我们的数据表明，鲤鱼和斑马鱼的转录序列之间具有足够的同源性，可以进行更深的塞浦路斯转录组比较。另一方面，比较分析说明了利用部分测序的转录组来了解这个不同的硬骨鱼类群体的基因结构的价值。我们强调需要集成资源来利用大量分散的基因组数据。

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