Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs
Abstract 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 f...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-06-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1853-4 |
| _version_ | 1824009333265924096 |
|---|---|
| author | Sufang Zhang Shanshan Yan Jiali Zhao Huanhuan Xiong Peiqi An Junhui Wang Hanguo Zhang Lei Zhang |
| author_facet | Sufang Zhang Shanshan Yan Jiali Zhao Huanhuan Xiong Peiqi An Junhui Wang Hanguo Zhang Lei Zhang |
| author_sort | Sufang Zhang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-18T21:08:52Z |
| format | Article |
| id | doaj.art-ee46e6e6b7224d81af4ba046eac61bcd |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-18T21:08:52Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-ee46e6e6b7224d81af4ba046eac61bcd2022-12-21T20:52:36ZengBMCBMC Plant Biology1471-22292019-06-0119112010.1186/s12870-019-1853-4Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAsSufang Zhang0Shanshan Yan1Jiali Zhao2Huanhuan Xiong3Peiqi An4Junhui Wang5Hanguo Zhang6Lei Zhang7State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Chinese Academy Of Forestry)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University)Abstract 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.http://link.springer.com/article/10.1186/s12870-019-1853-4miRNALarix olgensisTarget geneDifferential expression |
| spellingShingle | Sufang Zhang Shanshan Yan Jiali Zhao Huanhuan Xiong Peiqi An Junhui Wang Hanguo Zhang Lei Zhang Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs BMC Plant Biology miRNA Larix olgensis Target gene Differential expression |
| 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 | miRNA Larix olgensis Target gene Differential expression |
| url | http://link.springer.com/article/10.1186/s12870-019-1853-4 |
| work_keys_str_mv | AT sufangzhang identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT shanshanyan identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT jializhao identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT huanhuanxiong identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT peiqian identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT junhuiwang identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT hanguozhang identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas AT leizhang identificationofmirnasandtheirtargetgenesinlarixolgensisandverifiedofdifferentialexpressionmirnas |