Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
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DOI：
10.1186/1471-2105-7-s5-s2
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发表时间：
2006-01-01
影响因子：
3
通讯作者：
Orban, Laszlo
中科院分区：
文献类型：
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作者：
Christoffels, Alan;Bartfai, Richard;Orban, Laszlo
背景资料：测序的真核生物基因组的自动注释集成了诸如从头算方法和同源基因和/或蛋白质的比对的方法的组合。例如，在Ensembl中对斑马鱼基因组的注释在很大程度上依赖于来自两种远亲鱼类和其他脊椎动物的可用cDNA和蛋白质序列，这些鱼类和脊椎动物在数亿年前已经分化。从其他鲤科动物的基因组信息的稀缺提供了动力，利用EST收集，以了解基因结构，在这个不同的硬骨鱼group.Results：我们已经产生了6,050 ESTs从普通鲤鱼（鲤鱼）的睾丸分化和聚类9,303非性腺ESTs从CarpBase，以及1,317 ESTs和652普通鲤鱼mRNA从GenBank。在所得到的8，663个独特的转录本中，超过28%是完全来自睾丸的EST。此外，974个转录本与斑马鱼或黑头呆鱼EST库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定位到斑马鱼基因组（第5版）中，其中1，752个匹配斑马鱼基因的编码序列，有或没有潜在的剪接变体。我们发现，91个常见的鲤鱼转录映射到斑马鱼基因组组装和非硬骨鱼序列注释区域的基因间和内含子区域。有趣的是，另外42个常见的鲤鱼转录本表明可能存在迄今为止在斑马鱼数据库中未发现的新剪接变体。事实上，普通鲤鱼成绩单有助于识别或确认这些编码区在斑马鱼证明了有用的序列密切相关的物种的注释模型基因组。基于多达10个从头开始基序的基序排列的保留，我们还证明鲤鱼和斑马鱼直系同源物的5 'UTR序列具有显着的相似性。结论：我们的数据表明鲤鱼和斑马鱼的转录序列之间存在足够的同源性，值得进行更深入的鲤鱼转录组比较。另一方面，比较分析说明了利用部分测序的转录组，以了解在这个不同的硬骨鱼组的基因结构的价值。我们强调需要整合资源，以利用丰富的碎片化基因组数据。
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.