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Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections Qi, Yong-Li; Xue, Liang-Jiao; El-Kassaby, Yousry A.; Guo, Ying

Abstract

The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families are shared by the studied four species, and 31 families are species-specific, which might be related to local adaptation. Additionally, multiple miRNA-related single nucleotide polymorphisms (SNPs) were found, indicating that polymorphisms in pre-miRNA hairpins were likely to affect miRNA biogenesis. This study expanded the breadth and depth of miRNA annotations and provided valuable resources for further exploring the diversity and function of poplar miRNAs.

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Title
Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections
Creator
Qi, Yong-Li; Xue, Liang-Jiao; El-Kassaby, Yousry A.; Guo, Ying
Publisher
Multidisciplinary Digital Publishing Institute
Date Issued
2022-06-02
Description
The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families are shared by the studied four species, and 31 families are species-specific, which might be related to local adaptation. Additionally, multiple miRNA-related single nucleotide polymorphisms (SNPs) were found, indicating that polymorphisms in pre-miRNA hairpins were likely to affect miRNA biogenesis. This study expanded the breadth and depth of miRNA annotations and provided valuable resources for further exploring the diversity and function of poplar miRNAs.
Subject
Populus; poplar sections; microRNA (miRNA); single-nucleotide polymorphism (SNP)
Genre
Article
Type
Text
Language
eng
Date Available
2022-09-23
Provider
Vancouver : University of British Columbia Library
Rights
CC BY 4.0
DOI
10.14288/1.0420435
URI
http://hdl.handle.net/2429/82753
Affiliation
Forestry, Faculty of; Non UBC; Forest and Conservation Sciences, Department of
Citation
Forests 13 (6): 873 (2022)
Publisher DOI
10.3390/f13060873
Peer Review Status
Reviewed
Scholarly Level
Faculty; Researcher
Rights URI
https://creativecommons.org/licenses/by/4.0/
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CC BY 4.0