Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus
Abstract Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic im...
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5117-8 |
| _version_ | 1818286537618489344 |
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| author | Enhui Shen Xintian Zhu Shuijin Hua Hongyu Chen Chuyu Ye Longhua Zhou Qing Liu Qian-Hao Zhu Longjiang Fan Xi Chen |
| author_facet | Enhui Shen Xintian Zhu Shuijin Hua Hongyu Chen Chuyu Ye Longhua Zhou Qing Liu Qian-Hao Zhu Longjiang Fan Xi Chen |
| author_sort | Enhui Shen |
| collection | DOAJ |
| description | Abstract Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family. |
| first_indexed | 2024-12-13T01:26:10Z |
| format | Article |
| id | doaj.art-482bbe87b1564071abc226d51e2df977 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T01:26:10Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-482bbe87b1564071abc226d51e2df9772022-12-22T00:04:07ZengBMCBMC Genomics1471-21642018-10-0119111310.1186/s12864-018-5117-8Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napusEnhui ShenXintian ZhuShuijin Hua0Hongyu Chen1Chuyu Ye2Longhua Zhou3Qing Liu4Qian-Hao Zhu5Longjiang Fan6Xi Chen7Institute of Crop and Utilization of Nuclear Technology, Zhejiang Academy of Agricultural SciencesInstitute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityInstitute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityInstitute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityCSIRO Agriculture and FoodCSIRO Agriculture and FoodInstitute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityInstitute of Crop Sciences & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityAbstract Background Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis. Results A total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels. Conclusions We demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family.http://link.springer.com/article/10.1186/s12864-018-5117-8Brassica napuslncRNACoexpressionOil biosynthesisConservation |
| spellingShingle | Enhui Shen Xintian Zhu Shuijin Hua Hongyu Chen Chuyu Ye Longhua Zhou Qing Liu Qian-Hao Zhu Longjiang Fan Xi Chen Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus BMC Genomics Brassica napus lncRNA Coexpression Oil biosynthesis Conservation |
| title | Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus |
| title_full | Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus |
| title_fullStr | Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus |
| title_full_unstemmed | Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus |
| title_short | Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus |
| title_sort | genome wide identification of oil biosynthesis related long non coding rnas in allopolyploid brassica napus |
| topic | Brassica napus lncRNA Coexpression Oil biosynthesis Conservation |
| url | http://link.springer.com/article/10.1186/s12864-018-5117-8 |
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