Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar).
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar).
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DOI：
10.1186/1471-2164-10-502
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发表时间：
2009-10-30
期刊：
影响因子：
4.4
通讯作者：
Høyheim B
中科院分区：
文献类型：
--
作者：
Andreassen R;Lunner S;Høyheim B
一个国际研究联盟目前正在计划对大西洋鲑鱼基因组进行测序。 cDNA 全长测序插入片段 (FLIC) 是对任何物种的基因组序列进行正确注释和聚类的重要工具。鲑鱼祖先中相对较新的基因组复制引起的大量高度相似的重复序列对基因组计划来说是一个特殊的挑战。因此，FLICS 将成为大西洋鲑鱼测序项目极其有用的资源。除了有助于区分重复的基因组区域和确定正确的基因结构之外，FLIC 也是功能基因组研究和研究控制基因表达的调控元件的重要资源。与大量可用的 EST 相比，包括来自鲑鱼基因组计划 (SGP) 贡献的 23 个发育和组织特异性 cDNA 文库的 EST，已确定 cDNA 插入全长的序列数量很少。生成了来自 560 个幼龄前白色肌肉组织特异性 cDNA 的高质量全长插入序列，登录号为 [GenBank：BT043497 - BT044056]。五百一十 (91%) 的转录本使用基因本体 (GO) 术语进行注释，其中 440 个 FLIc 可能包含完整的编码序列 (cCDS)。序列信息用于鉴定假定的旁系同源物、表征鲑鱼Kozak基序、聚腺苷酸化信号变异以及鉴定可能参与特定基因调节的基序。最后，鉴定了 3'UTR 中的保守 7 聚体，其中一些与 miRNA 靶序列相同。本文描述了来自组织和发育阶段特定 cDNA 文库的第一个大西洋鲑鱼 FLIc。我们已经证明许多 FLIc 包含完整的编码序列 (cCDS)。这表明 SGP 生成的剩余 cDNA 文库代表了有价值的 cCDS FLIc 来源。 3'UTR 中 7-mers 的保守性表明这些基序具有重要的功能。其中一些 7-mers 和 miRNA 靶序列之间的同一性表明它们也是 Salmo salar 转录本中的 miRNA 靶标。
Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in Salmo salar transcripts as well.
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