title: Comparative analysis of known miRNAs across platyhelminths.
abstract: MicroRNAs (miRNAs) are a subtype of small regulatory RNAs that are involved in numerous biological processes through small RNA-induced silencing networks. In an attempt to explore the phylogeny of miRNAs across five platyhelminths, we integrated annotated miRNAs and their full genomes. We identified conserved miRNA clusters and, in particular, miR-71/2 was conserved from planarian to parasitic flatworms and was expanded in free-living Schmidtea mediterranea. Analysis of 22 miRNA loci provided compelling evidence that most known miRNAs are conserved across platyhelminths. Meanwhile, we also observed alterations of known protein-coding genes flanking miRNA(s), such as transcriptional direction conversion and locus relocation, in around ~ 41% of 22 known miRNA loci. Compared with Echinococcus multilocularis, the majority of these events occurred in evolution-distant Hymenolepis microstoma, Schistosoma japonicum or/and S. mediterranea. These results imply rearrangement events occurred near the known miRNA loci.
authors.affiliation: Department of Ophthalmology of Shanghai Tenth People's Hospital and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Jin
authors.forename: Lixia
authors.initials: L
authors.lastname: Lu
authors.forename: Hailong
authors.initials: H
authors.lastname: Su
authors.forename: Zhongzi
authors.initials: Z
authors.lastname: Lou
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.forename: Yadong
authors.initials: Y
authors.lastname: Zheng
authors.forename: Guo-Tong
authors.initials: GT
authors.lastname: Xu
mesh_terms: D024509:3' Flanking Region; D024506:5' Flanking Region; D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D018509:DNA, Helminth / Q000737:chemistry / Q000378:metabolism; D030561:Databases, Nucleic Acid; D048209:Echinococcus granulosus / Q000235:genetics / Q000378:metabolism; D048210:Echinococcus multilocularis / Q000235:genetics / Q000378:metabolism; D015321:Gene Rearrangement; D056426:Genetic Loci; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D005810:Multigene Family; D010802:Phylogeny; D010932:Planarians / Q000235:genetics / Q000378:metabolism; D010986:Platyhelminths / Q000235:genetics / Q000378:metabolism*; D018510:RNA, Helminth / Q000737:chemistry / Q000378:metabolism*; D012549:Schistosoma japonicum / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D018509:DNA, Helminth; D035683:MicroRNAs; D018510:RNA, Helminth
keywords: miRNA; miRNA cluster; miRNA locus; platyhelminth; rearrangement