Genome-wide identification of novel microRNAs from genome sequences using computational approach in the mudskipper (Boleophthalmus pectinirostris)
- Авторлар: Gong W.1, Huang Y.2, Xie J.1, Wang G.1, Yu D.1, Sun X.2
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Мекемелер:
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute
- College of Animal Science and Technology
- Шығарылым: Том 43, № 4 (2017)
- Беттер: 397-408
- Бөлім: Article
- URL: https://journals.rcsi.science/1068-1620/article/view/228584
- DOI: https://doi.org/10.1134/S1068162017040161
- ID: 228584
Дәйексөз келтіру
Аннотация
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.
Негізгі сөздер
Авторлар туралы
Wangbao Gong
Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute
Email: huangyong1979111@126.com
ҚХР, Guangzhou, 510380
Yong Huang
College of Animal Science and Technology
Хат алмасуға жауапты Автор.
Email: huangyong1979111@126.com
ҚХР, Luoyang, 471003
Jun Xie
Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute
Email: huangyong1979111@126.com
ҚХР, Guangzhou, 510380
Guangjun Wang
Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute
Email: huangyong1979111@126.com
ҚХР, Guangzhou, 510380
Deguang Yu
Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute
Email: huangyong1979111@126.com
ҚХР, Guangzhou, 510380
Xihong Sun
College of Animal Science and Technology
Email: huangyong1979111@126.com
ҚХР, Luoyang, 471003