杨柳科 MIR1444 基因的起源与进化。

Origin and evolution of MIR1444 genes in Salicaceae.

机构信息

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

出版信息

Sci Rep. 2017 Jan 10;7:39740. doi: 10.1038/srep39740.

DOI:10.1038/srep39740

PMID:28071760

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5223194/

Abstract

miR1444s are functionally significant miRNAs targeting polyphenol oxidase (PPO) genes for cleavage. MIR1444 genes were reported only in Populus trichocarpa. Through the computational analysis of 215 RNA-seq data, four whole genome sequences of Salicaceae species and deep sequencing of six P. trichocarpa small RNA libraries, we investigated the origin and evolution history of MIR1444s. A total of 23 MIR1444s were identified. Populus and Idesia species contain two MIR1444 genes, while Salix includes only one. Populus and Idesia MIR1444b genes and Salix MIR1444s were phylogenetically separated from Populus and Idesia MIR1444a genes. Ptr-miR1444a and ptr-miR1444b showed sequence divergence. Compared with ptr-miR1444b, ptr-miR1444a started 2 nt upstream of precursor, resulting in differential regulation of PPO targets. Sequence alignments showed that MIR1444 genes exhibited extensive similarity to their PPO targets, the characteristics of MIRs originated from targets through an inverted gene duplication event. Genome sequence comparison showed that MIR1444 genes in Populus and Idesia were expanded through the Salicoid genome duplication event. A copy of MIR1444 gene was lost in Salix through DNA segment deletion during chromosome rearrangements. The results provide significant information for the origin of plant miRNAs and the mechanism of Salicaceae gene evolution and divergence.

摘要

miR1444s 是一种功能显著的 miRNA，可以靶向多酚氧化酶（PPO）基因进行切割。MIR1444 基因仅在杨属中报道过。通过对 215 个 RNA-seq 数据、4 个杨柳科物种的全基因组序列和 6 个杨属小 RNA 文库的深度测序的计算分析，我们研究了 MIR1444s 的起源和进化历史。共鉴定出 23 个 MIR1444s。杨属和柳属含有两个 MIR1444 基因，而柳属只含有一个。杨属和柳属的 MIR1444b 基因与杨属和柳属的 MIR1444a 基因在系统发育上是分开的。Ptr-miR1444a 和 ptr-miR1444b 表现出序列差异。与 ptr-miR1444b 相比，ptr-miR1444a 在前体的上游起始 2nt，导致对 PPO 靶标的差异调节。序列比对表明，MIR1444 基因与其 PPO 靶标表现出广泛的相似性，MIR 起源于靶标通过反转基因重复事件的特征。基因组序列比较表明，杨属和柳属的 MIR1444 基因通过 Salicoid 基因组重复事件扩增。在染色体重排过程中，通过 DNA 片段缺失，柳属中的 MIR1444 基因丢失了一个拷贝。研究结果为植物 miRNA 的起源和杨柳科基因进化和分化的机制提供了重要信息。