Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Oxford University Press
2015
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765792/ |
| id |
pubmed-4765792 |
|---|---|
| recordtype |
oai_dc |
| spelling |
pubmed-47657922016-03-04 Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus Shen, Enhui Zou, Jun Hubertus Behrens, Falk Chen, Li Ye, Chuyu Dai, Shutao Li, Ruiyan Ni, Meng Jiang, Xiaoxue Qiu, Jie Liu, Yang Wang, Weidi Zhu, Qian-Hao Chalhoub, Boulos Bancroft, Ian Meng, Jinling Cai, Daguang Fan, Longjiang Research Paper The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors’ genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. Oxford University Press 2015-12 2015-09-10 /pmc/articles/PMC4765792/ /pubmed/26357884 http://dx.doi.org/10.1093/jxb/erv420 Text en © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Shen, Enhui Zou, Jun Hubertus Behrens, Falk Chen, Li Ye, Chuyu Dai, Shutao Li, Ruiyan Ni, Meng Jiang, Xiaoxue Qiu, Jie Liu, Yang Wang, Weidi Zhu, Qian-Hao Chalhoub, Boulos Bancroft, Ian Meng, Jinling Cai, Daguang Fan, Longjiang |
| spellingShingle |
Shen, Enhui Zou, Jun Hubertus Behrens, Falk Chen, Li Ye, Chuyu Dai, Shutao Li, Ruiyan Ni, Meng Jiang, Xiaoxue Qiu, Jie Liu, Yang Wang, Weidi Zhu, Qian-Hao Chalhoub, Boulos Bancroft, Ian Meng, Jinling Cai, Daguang Fan, Longjiang Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus |
| author_facet |
Shen, Enhui Zou, Jun Hubertus Behrens, Falk Chen, Li Ye, Chuyu Dai, Shutao Li, Ruiyan Ni, Meng Jiang, Xiaoxue Qiu, Jie Liu, Yang Wang, Weidi Zhu, Qian-Hao Chalhoub, Boulos Bancroft, Ian Meng, Jinling Cai, Daguang Fan, Longjiang |
| author_sort |
Shen, Enhui |
| title |
Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
|
| title_short |
Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
|
| title_full |
Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
|
| title_fullStr |
Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
|
| title_full_unstemmed |
Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus
|
| title_sort |
identification, evolution, and expression partitioning of mirnas in allopolyploid brassica napus |
| description |
The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors’ genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. |
| publisher |
Oxford University Press |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765792/ |
| _version_ |
1613542784232325120 |