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Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs
BACKGROUND: MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression. RESULTS: This study used high-throughput sequencing technology for the...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558743/ https://www.ncbi.nlm.nih.gov/pubmed/31185902 http://dx.doi.org/10.1186/s12870-019-1853-4 |
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author | Zhang, Sufang Yan, Shanshan Zhao, Jiali Xiong, Huanhuan An, Peiqi Wang, Junhui Zhang, Hanguo Zhang, Lei |
author_facet | Zhang, Sufang Yan, Shanshan Zhao, Jiali Xiong, Huanhuan An, Peiqi Wang, Junhui Zhang, Hanguo Zhang, Lei |
author_sort | Zhang, Sufang |
collection | PubMed |
description | BACKGROUND: MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression. RESULTS: This study used high-throughput sequencing technology for the first time in Larix olgensis, predicted 78 miRNAs, including 12,229,003 reads sRNA, screened differentially expressed miRNAs. Predicting target genes was helpful for understanding the miRNA regulation function and obtained 333 corresponding target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation were analysed, mostly including nucleic acid binding, plant hormone signal transduction, pantothenate and CoA biosynthesis, and cellulose synthase. This study will lay the foundation for clarifying the complex miRNA-mediated regulatory network for growth and development. In view of this, spatio-temporal expression of miR396, miR950, miR164, miR166 and miR160 were analysed in Larix olgensis during the growth stages of not lignified, beginning of lignification, and completely lignified in different tissues (root, stem, and leaf) by quantitative real-time PCR (qRT-PCR). There were differences in the expression of miRNAs in roots, stems and leaves in the same growth period. At 60 days, miR160, miR166 and miR396–2 exhibited the highest expression in leaves. At 120 days, most miRNAs in roots and stems decreased significantly. At 180 days, miRNAs were abundantly expressed in roots and stems. Meanwhile, analysis of the expression of miRNAs in leaves revealed that miR396–2 was reduced as time went on, whereas other miRNAs increased initially and then decreased. On the other hand, in the stems, miR166–1 was increase, whereas other miRNAs, especially miR160, miR164, miR396 and miR950–1, first decreased and then increased. Similarly, in the roots, miR950–2 first decreased and then increased, whereas other miRNAs exhibited a trend of continuous increase. CONCLUSIONS: The present investigation included rapid isolation and identification of miRNAs in Larix olgensis through construction of a sRNA library using Solexa and predicted 78 novel miRNAs, which showed differential expression levels in different tissues and stages. These results provided a theoretical basis for further revealing the genetic regulation mechanism of miRNA in the growth and development of conifers and the verification of function in target genes. |
format | Online Article Text |
id | pubmed-6558743 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65587432019-06-13 Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs Zhang, Sufang Yan, Shanshan Zhao, Jiali Xiong, Huanhuan An, Peiqi Wang, Junhui Zhang, Hanguo Zhang, Lei BMC Plant Biol Research Article BACKGROUND: MiRNAs (microRNA) are 18–24 nt endogenous noncoding RNAs that regulate gene expression at the post-transcriptional level, including tissue-specific, developmental timing and evolutionary conservation gene expression. RESULTS: This study used high-throughput sequencing technology for the first time in Larix olgensis, predicted 78 miRNAs, including 12,229,003 reads sRNA, screened differentially expressed miRNAs. Predicting target genes was helpful for understanding the miRNA regulation function and obtained 333 corresponding target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation were analysed, mostly including nucleic acid binding, plant hormone signal transduction, pantothenate and CoA biosynthesis, and cellulose synthase. This study will lay the foundation for clarifying the complex miRNA-mediated regulatory network for growth and development. In view of this, spatio-temporal expression of miR396, miR950, miR164, miR166 and miR160 were analysed in Larix olgensis during the growth stages of not lignified, beginning of lignification, and completely lignified in different tissues (root, stem, and leaf) by quantitative real-time PCR (qRT-PCR). There were differences in the expression of miRNAs in roots, stems and leaves in the same growth period. At 60 days, miR160, miR166 and miR396–2 exhibited the highest expression in leaves. At 120 days, most miRNAs in roots and stems decreased significantly. At 180 days, miRNAs were abundantly expressed in roots and stems. Meanwhile, analysis of the expression of miRNAs in leaves revealed that miR396–2 was reduced as time went on, whereas other miRNAs increased initially and then decreased. On the other hand, in the stems, miR166–1 was increase, whereas other miRNAs, especially miR160, miR164, miR396 and miR950–1, first decreased and then increased. Similarly, in the roots, miR950–2 first decreased and then increased, whereas other miRNAs exhibited a trend of continuous increase. CONCLUSIONS: The present investigation included rapid isolation and identification of miRNAs in Larix olgensis through construction of a sRNA library using Solexa and predicted 78 novel miRNAs, which showed differential expression levels in different tissues and stages. These results provided a theoretical basis for further revealing the genetic regulation mechanism of miRNA in the growth and development of conifers and the verification of function in target genes. BioMed Central 2019-06-11 /pmc/articles/PMC6558743/ /pubmed/31185902 http://dx.doi.org/10.1186/s12870-019-1853-4 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Zhang, Sufang Yan, Shanshan Zhao, Jiali Xiong, Huanhuan An, Peiqi Wang, Junhui Zhang, Hanguo Zhang, Lei Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title | Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title_full | Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title_fullStr | Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title_full_unstemmed | Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title_short | Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs |
title_sort | identification of mirnas and their target genes in larix olgensis and verified of differential expression mirnas |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558743/ https://www.ncbi.nlm.nih.gov/pubmed/31185902 http://dx.doi.org/10.1186/s12870-019-1853-4 |
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