Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.
Sequencing and characterisation of an extensive Atlantic salmon (Salmo salar L.) microRNA repertoire.
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DOI：
10.1371/journal.pone.0070136
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Houston RD
中科院分区：
文献类型：
--
作者：
Bekaert M;Lowe NR;Bishop SC;Bron JE;Taggart JB;Houston RD
大西洋鲑鱼(Salmo salar L.)是鲑科的一员，是具有生态和文化意义的图腾物种，在体育渔业和水产养殖方面也具有重要的经济意义。这些因素促进了该物种基因组资源的不断发展，进一步促进了基础和应用研究。MicroRNAs(MiRNA)是一种小的内源性非编码RNA分子，通过转录后调控调控靶基因的空间和时间表达。虽然已经对许多其他物种的miRNA进行了详细的描述，但大西洋鲑鱼的情况还不是这样。为了从大西洋鲑鱼中识别miRNAs，我们构建了18个个体(鱼苗，孵化后4个月)的全鱼miRNA文库，并用Illumina高通量测序(总共354,505,167对末端阅读)对它们进行了表征。我们报道了一个广泛的部分新颖的miRNA序列库，包括888个miRNA基因(547个独特的成熟miRNA序列)，量化它们在基础条件下的表达水平，检查它们与其他物种的miRNAs的同源性，并确定它们预测的目标基因。我们还确定了大西洋鲑鱼参考基因组序列草案中miRNA基因的位置和假定的拷贝数。本研究中实验确定的大西洋鲑鱼miRNAs为鲑鱼类功能基因组研究提供了一个强大的大规模资源。在鲑鱼物种最近发生的全基因组复制事件之后，有机会探索鲑鱼miRNAs的进化，并研究miRNAs在基因表达调控中的作用，特别是它们对重要经济和生态性状变异的贡献。
Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits.
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影响因子：
4.4
作者：
Koop, Ben F.;von Schalburg, Kristian R.;Leong, Jong;Walker, Neil;Lieph, Ryan;Cooper, Glenn A.;Robb, Adrienne;Beetz-Sargent, Marianne;Holt, Robert A.;Moore, Richard;Brahmbhatt, Sonal;Rosner, Jamie;Rexroad, Caird E., III;McGowan, Colin R.;Davidson, William S.
通讯作者：
Davidson, William S.
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
7
作者：
Morin, Ryan D.;O'Connor, Michael D.;Marra, Marco A.
通讯作者：
Marra, Marco A.
影响因子：
3.7
作者：
Meng F;Hackenberg M;Li Z;Yan J;Chen T
通讯作者：
Chen T
DOI：
10.1186/1748-7188-6-26
发表时间：
2011-11-24
期刊：
Algorithms for molecular biology : AMB
影响因子：
--
作者：
Lorenz R;Bernhart SH;Höner Zu Siederdissen C;Tafer H;Flamm C;Stadler PF;Hofacker IL
通讯作者：
Hofacker IL