潮间带冠轮动物笠贝（软体动物，笠贝目）和拉氏螺旋虫（环节动物，龙介虫科）的基因组草图组装及预测的微小RNA互补序列

Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida).

作者信息

Kenny Nathan J, Namigai Erica K O, Marlétaz Ferdinand, Hui Jerome H L, Shimeld Sebastian M

机构信息

Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.

Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.

出版信息

Mar Genomics. 2015 Dec;24 Pt 2:139-46. doi: 10.1016/j.margen.2015.07.004. Epub 2015 Aug 28.

DOI:10.1016/j.margen.2015.07.004

PMID:26319627

Abstract

MicroRNAs (miRNA) are small non-coding RNAs that act post-transcriptionally to regulate gene expression levels. Some studies have indicated that microRNAs may have low homoplasy, and as a consequence the phylogenetic distribution of microRNA families has been used to study animal evolutionary relationships. Limited levels of lineage sampling, however, may distort such analyses. Lophotrochozoa is an under-sampled taxon that includes molluscs, annelids and nemerteans, among other phyla. Here, we present two novel draft genomes, those of the limpet Patella vulgata and polychaete Spirobranchus (Pomatoceros) lamarcki. Surveying these genomes for known microRNAs identifies numerous potential orthologues, including a number that have been considered to be confined to other lineages. RT-PCR demonstrates that some of these (miR-1285, miR-1287, miR-1957, miR-1983 and miR-3533), previously thought to be found only in vertebrates, are expressed. This study provides genomic resources for two lophotrochozoans and reveals patterns of microRNA evolution that could be hidden by more restricted sampling.

摘要

微小RNA（miRNA）是一类小的非编码RNA，它们在转录后发挥作用以调节基因表达水平。一些研究表明，微小RNA可能具有较低的同源性，因此微小RNA家族的系统发育分布已被用于研究动物的进化关系。然而，有限的谱系抽样水平可能会扭曲此类分析。冠轮动物是一个抽样不足的分类群，包括软体动物、环节动物和纽形动物等其他门类。在这里，我们展示了两个新的基因组草图，即帽贝笠贝和多毛纲动物拉氏盘管虫的基因组草图。在这些基因组中搜索已知的微小RNA，发现了许多潜在的直系同源物，包括一些被认为仅限于其他谱系的微小RNA。逆转录聚合酶链反应（RT-PCR）表明，其中一些（miR-1285、miR-1287、miR-1957、miR-1983和miR-3533），以前被认为只在脊椎动物中发现，是有表达的。这项研究为两种冠轮动物提供了基因组资源，并揭示了微小RNA进化模式，而这些模式可能会被更有限的抽样所掩盖。