Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice

文献类型： 外文期刊

第一作者： Liu, Qingpo

作者： Liu, Qingpo;Wang, Hong;Hu, Haichao;Liu, Qingpo;Wang, Hong;Hu, Haichao;Zhang, Hengmu

作者机构：

关键词： Rice;miRNA;Positive selection;Evolution;Domestication

期刊名称：MOLECULAR GENETICS AND GENOMICS （ 影响因子：3.291； 五年影响因子：3.257 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： The next-generation sequencing of tens to hundreds of plant genotypes made the uncovering of miRNA genes evolution available at the genome-wide level. Using the combinations of population genetics and evolutionary biology approaches, we have identified 21 miRNA loci having significant negative Tajima's D and Fu and Li's D* and F* values, of which 14 miRNAs (ps-miRNAs) showing clear signatures of positive selection in domesticated rice. The average sequence diversity (pi) of the 21 miRNAs in cultivated rice is only 13.8 % of that in their wild progenitors. Interestingly, protein-coding genes immediately flanking these ps-miRNAs are apparently under weaker selective constraints. Totally, the 21 miRNAs are predicted to target 68 mRNA genes, of which 12 targets are estimated to have endured positive selection during rice evolution. In addition, the expression pattern and potential biological functions of ps-miRNAs targets are further investigated by searching published micro-array data and different mutant databases, respectively. We conclude that miRNAs, like protein-coding genes, should be crucial for driving rice evolution. These analyses may deepen our understanding on the miRNA genes evolution and functions during rice domestication.

分类号： Q7

  • 相关文献

[1]Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers. Zhang, Chi-Hong,Li, Dao-Yuan,Pan, Da-Jian,Jia, Ji-Zeng,Dong, Yu-Shen.

[2]Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication. Tang, Tian,Wu, Chung-I,Shi, Suhua,Yu, Yanchun,Wang, Yonghong,Li, Jiayang,Yu, Yanchun,Wang, Yonghong,Li, Jiayang,Qian, Qian,Yan, Meixian,Zeng, Dali,Han, Bin,Han, Bin,Wu, Chung-I,Wu, Chung-I.

[3]DNA methylation polymorphism in annual wild soybean (Glycine soja Sieb. et Zucc.) and cultivated soybean (G. max L. Merr.). Zhong, Xiaofang,Gong, Lei,Ma, Yan,Qi, Bao,Liu, Bao,Wang, Yumin,Liu, Xiaodong,Dong, Yingshan. 2009

[4]Molecular and geographic evolutionary support for the essential role of GIGANTEAa in soybean domestication of flowering time. Wang, Yan,Gu, Yongzhe,Gao, Huihui,He, Chaoying,Gu, Yongzhe,Gao, Huihui,Qiu, Lijuan,Chang, Ruzhen,Chen, Shouyi. 2016

[5]A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based on Adh1a sequences. Xu, Xin-wei,Ge, Song,Xu, Xin-wei,Ke, Wei-dong,Yu, Xiao-ping,Wen, Jun,Ge, Song.

[6]Genetic diversity of the azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) gene pool as assessed by SSR markers. Tomooka, N.,Kaga, A.,Isemura, T.,Vaughan, D. A.,Xu, H. X.,Jing, T..

[7]Nonfunctional alleles of long-day suppressor genes independently regulate flowering time. Zheng, Xiao-Ming,Wang, Junrui,Qiao, Weihua,Zhang, Lifang,Cheng, Yunlian,Yang, Qingwen,Feng, Li. 2016

[8]Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Dzikiewicz, Katherine M.,Li, Lei,Peng, Zhi-Yu,Liu, Tingting,Deng, Xing-Wang,Peng, Zhi-Yu,Li, Songgang,Zhu, Qi-Hui,Zhang, Huiyong,Liu, Tingting,Ma, Ligeng,Deng, Xing-Wang,Zhang, Huiyong,Wang, Xiangfeng,Deng, Xing-Wang,Hu, Guocheng,Wei, Xinghua,Sun, Zongxiu,Zhu, Zhengge,Zhu, Qi-Hui,Ge, Song. 2009

[9]Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice. Liu, Qing,Yang, Tifeng,Zhang, Shaohong,Mao, Xingxue,Zhao, Junliang,Wang, Xiaofei,Dong, Jingfang,Liu, Bin,Liu, Qing,Yang, Tifeng,Zhang, Shaohong,Mao, Xingxue,Zhao, Junliang,Wang, Xiaofei,Dong, Jingfang,Liu, Bin,Yu, Ting. 2017

[10]SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. Tang, Weijie,Wu, Tingting,Sun, Juan,Jiang, Yue,Yu, Jun,Tang, Jianpeng,Chen, Gaoming,Wang, Chunming,Wan, Jianmin,Ye, Jian,Tang, Weijie,Wang, Chunming,Wan, Jianmin. 2016

[11]Repression of microRNA biogenesis by silencing of OsDCL1 activates the basal resistance to Magnaporthe oryzae in rice. Zhang, Dandan,Tang, Mingzhi,Wu, Dianxing,Zhang, Dandan,Tang, Mingzhi,Wu, Dianxing,Zhang, Dandan,Tang, Mingzhi,Dong, Bo,Zhou, Bo,Liu, Muxing,Zhang, Zhengguang,Liu, Muxing,Zhang, Zhengguang,Zhou, Bo.

[12]Molecular Identification and Analysis of Arsenite Stress-Responsive miRNAs in Rice. Liu, Qingpo,Zhang, Hengmu.

[13]Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat. Kong, XY,Gu, YQ,You, FM,Dubcovsky, J,Anderson, OD.

[14]Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.). Jiang, Jiahuan,Tan, Lubin,Zhu, Zuofeng,Fu, Yongcai,Liu, Fengxia,Cai, Hongwei,Sun, Chuanqing,Jiang, Jiahuan. 2012

[15]Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica. Liu, Jing,Du, Jianchang,Zhang, Jiefu,Du, Jianchang,Liu, Shengyi,Du, Jianchang. 2017

[16]Mannose selection system used for cucumber transformation. He, Zhengquan,Duan, ZhenZhen,Liang, Wei,Chen, Faju,Yao, Wei,Liang, Hongwei,Yue, Chaoyin,Sun, Zongxiu,Chen, Fan,Dai, Jianwu. 2006

[17]Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots. Li, Chun,Li, Meng,Zhang, Yuan-Ming,Li, Chun,Dunwell, Jim M.. 2012

[18]De novo assembly and characterization of the Hucho taimen transcriptome. Tong, Guang-Xiang,Xu, Wei,Zhang, Yong-Quan,Zhang, Qing-Yu,Yin, Jia-Sheng,Kuang, You-Yi. 2018

[19]The impact of positive selection and mutation in prevalence of representative O/Mya-98 foot and mouth disease strains during 2009-2010. Kuang, Wendong,Bai, Xingwen,Qi, Guocai,Hao, Xiaofang,Li, Pinghua,Lu, Zengjun,Bao, Huifang,Sun, Pu,Wu, Lei,Liu, Zaixin. 2012

[20]Evidence for positive selection in Ser/Thr protein kinases (STKs) genes of Trichodesmium erythraeum. Liang, Chengwei,Zhang, Xiaowen. 2009

作者其他论文 更多>>

微信小程序