您好，欢迎访问中国水产科学研究院 机构知识库！
中国水产科学研究院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

Genome-Wide Identification of Novel microRNAs from Genome Sequences Using Computational Approach in the Mudskipper (Boleophthalmus pectinirostris)

文献类型： 外文期刊

作者： Gong, Wangbao 1 ; Huang, Yong 2 ; Xie, Jun 1 ; Wang, Guangjun 1 ; Yu, Deguang 1 ; Sun, Xihong 2 ;

作者机构： 1.Chinese Acad Fishery Sci, Pearl River Fisheries Res Inst, Minist Agr, Key Lab Trop & Subtrop Fishery Resource Applicat, Guangzhou 510380, Guangdong, Peoples R China

2.Henan Univ Sci & Technol, Coll Anim Sci & Technol, Luoyang 471003, Peoples R China

关键词： microRNAs;Boleophthalmus pectinirostris;computational prediction;phylogenetic analysis

期刊名称：RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY （ 2020影响因子：0.796； 五年影响因子：0.862 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： MicroRNAs (miRNAs), approximately 22 nucleotides (nt) long, are small, non-coding RNA molecules with important regulatory functions in gene expression. They are mostly conserved among the organisms and this conservation makes them a good source for the identification of novel miRNAs by computational genomic homology. The miRNA repertoire of a major aquaculture species, Boleophthalmus pectinirostris, has been unknown until recently. Currently, the B. pectinirostris whole-genome sequences have been completed, making it more convenient for us to focus on computational prediction for novel miRNA homologs. Following a range of strict filtering criteria, a total of 62 potential miRNAs were identified for the first time; they belong to 39 different miRNA families. All these miRNAs were observed in the stem portion of the stable stem-loop structures. The minimum free energy (MFE) of the predicted miRNAs ranged from -21.6 to -62.7 kcal/mol with an average of -39.2 kcal/mol. The A + U ranged from 32.5 to 69.1% with an average value of 52.2%. The phylogenetic analysis of predicted miRNAs revealed that miR-23a-3p, miR-184-3p, miR-214-5p, and miR-338-3p from B. pectinirostris are evolutionary highly conserved showing more similarity with other fish species. To verify the predicted miRNAs, selected miRNAs representing 16 of the 39 families were confirmed by stem-loop RT-PCR, indicating that the computational approach that we used to identify the miRNAs is a highly efficient and affordable alternative method. Taken together, these findings provide a reference point for further research on miRNAs identification in fish species, meanwhile, our study also will be useful for further insight into biological functions of miRNAs and improved understanding of genome in B. pectinirostris.

  • 相关文献

[1]Complete mitochondrial genome of the mudskipper Boleophthalmus pectinirostris (Perciformes, Gobiidae): Repetitive sequences in the control region. Liu, Zhi Zhi,Wang, Cong Tao,He, An Yuan,Yang, Jin Quan,Tang, Wen Qiao,Liu, Zhi Zhi,Ma, Ling Bo.

[2]MicroRNAs对斑马鱼发育的调控. 丁雷,闫学春,孙效文,滕春波. 2011

[3]Identification and characterization of lymph organ microRNAs in red swamp crayfish, Procambarus clarkii infected with white spot syndrome virus. Du, Zhi-Qiang,Leng, Xiao-Yun,Jin, Yan-Hui,Shen, Xiu-Li,Li, Xin-Cang. 2017

[4]Identification of Differentially Expressed Micrornas Associate with Glucose Metabolism in Different Organs of Blunt Snout Bream (Megalobrama amblycephala). Miao, Ling-Hong,Pan, Wen-Jing,Huang, Xin,Ge, Xian-Ping,Liu, Bo,Miao, Ling-Hong,Lin, Yan,Ge, Xian-Ping,Ren, Ming-Chun,Zhou, Qun-Lan,Liu, Bo. 2017

[5]Regulation of pregnane-X-receptor and microRNAs on detoxification-related genes expressions in Mugilogobius abei under the exposure to diclofenac. Ku, Peijia,Wang, Chao,Nie, Xiangping,Ou, Ruikang,Li, Kaibing,Nie, Xiangping. 2018

[6]Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara female xEpinephelus lanceolatus male, and phylogenetic analysis in subfamily epinephelinae. Gao, Fengtao,Zhu, Ying,Yang, Guanpin,Gao, Fengtao,Wei, Min,Zhu, Ying,Guo, Hua,Chen, Songlin,Wei, Min. 2017

[7]The complete mitochondrial genome of Shizothorax grahami (Cypriniformes: Cyprinidae). Zheng, Zonglin,Yu, Ermeng,Li, Zhifei,Ou, Hongxia,Wang, Guangjun. 2016

[8]Cloning, Sequence Characterization and Phylogenetic Analysis on Full-Length cDNA of Growth Hormone from Southern Flounder (Paralichthys lethostigma). Zang, Xiao-Nan,Liu, Shun-Mei,Zhang, Xue-Cheng,Liu, Bin,Lei, Ji-Lin. 2011

[9]Phylogenetic analysis of four Vibrio strains of pathogenic bacteria based on hemolysin genes and 16S rRNA genes. Wang, Xiuli,Yuan, Ye,Wang, Hongyue,Chang, Yaqing,Qiu, Xuemei,Zhou, Qunlan,Zhu, Jian,Cui, Yudong. 2009

[10]Complete mitochondrial genome of summer flounder Paralichthys dentatus (Pleuronectiformes, Paralichthyidae). Xu, Yongjiang,Liu, Xuezhou,Shi, Bao,Wang, Bin,Xu, Yongjiang,Liu, Xuezhou,Shi, Bao,Wang, Bin. 2016

[11]The complete mitochondrial genome of Alburnus chalcoides aralensis. Geng, Longwu,Jiang, Haifeng,Yang, Jian,Xu, Min,Xu, Wei,Yang, Jian,Xu, Min. 2015

[12]Molecular analysis of grass carp reovirus HZ08 genome segments 1-3 and 5-6. Zhang, Chao,Wang, Qing,Shi, Cunbin,Zeng, Weiwei,Liu, Yongkui,Wu, Shuqin,Zhang, Chao,Liu, Yongkui. 2010

[13]The complete mitochondrial genome of Ancherythroculter kurematsui (Cypriniformes: Cyprinidae). Wang, G. J.,Yu, E. M.,Xie, J.,Wei, N.,Wu, J. R.,Li, J. S.,Zheng, Z. L.. 2016

[14]Cloning, expression and methylation analysis of piwil2 in half-smooth tongue sole (Cynoglossus semilaevis). Zhang, Liyan,Zhao, Wen,Zhang, Liyan,Liu, Wanjun,Shao, Changwei,Zhang, Ning,Li, Hailong,Liu, Kun,Dong, Zhongdian,Qi, Qian,Chen, Songlin,Liu, Wanjun,Dong, Zhongdian,Qi, Qian.

[15]The complete mitochondrial genome of the crucian carp, Carassius carassius (Cypriniformes, Cyprinidae). Cheng, Lei,Liang, Li-Qun,Sun, Xiao-Wen,Cheng, Lei.

[16]Identification of an isolate of Saprolegnia ferax as the causal agent of saprolegniosis of Yellow catfish (Pelteobagrus fulvidraco) eggs. Cao, Haipeng,Xu, Jialu,Ou, Renjian,He, Shan,Yang, Xianle,Zheng, Weidong.

[17]Cloning and sequence analysis of the partial sequence of the rbcL from Bryopsis hypnoides. Tian, C,Wang, GC,Ye, NH,Zhang, BY,Fan, XL,Zeng, CK.

[18]Diagnosis and ORF Gene Sequencing Analysis of The Nervous Necrosis Virus (NNV) Isolated from Cultured Pearl Gentian Grouper, Epinephelus lanceolatus x Epinephelus fuscoguttatus, in China. Ma, Rong-Rong,Wang, Yin-Geng,Liao, Mei-Jie,Zhang, Zheng,Rong, Xiao-Jun,Li, Bin,Ma, Rong-Rong,Yang, Xian-Le. 2014

[19]The complete mitochondrial genome of Cleithenes herzenstein and its phylogenetic analysis. Zhang Bo,Song Wenping,Liu Kefeng,Zheng Debin,Ma Chao,Xiao Guangxia.

[20]The complete mitochondrial genome of Barbus capito (Cypriniformes, Cyprinidae). Dong, Xiao-Li,Xu, Wei,Wei, Ying-Ying,Xu, Qi-You.

作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：中国水产科学研究院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台