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Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses
- Source :
- The Plant journal : for cell and molecular biology. 99(4)
- Publication Year :
- 2019
-
Abstract
- Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57 862 high-quality full-length mRNA sequences derived from 18 362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in-cis and in-trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R-gene-mediated disease resistance, may be regulated by nat-siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis-NAT pairs and subgroups of trans-NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis-NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis-NATs, while transposon insertion contributed to the formation of most new cis-NATs. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Plant Science
Biology
01 natural sciences
03 medical and health sciences
Gene Expression Regulation, Plant
Pepper
Gene expression
Genetics
RNA, Antisense
RNA, Messenger
Gene
Comparative genomics
Regulation of gene expression
Gene Expression Profiling
fungi
food and beverages
Cell Biology
Gene expression profiling
030104 developmental biology
MRNA Sequencing
Capsicum
Functional genomics
010606 plant biology & botany
Subjects
Details
- ISSN :
- 1365313X
- Volume :
- 99
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- The Plant journal : for cell and molecular biology
- Accession number :
- edsair.doi.dedup.....dba7380e87d7541c9d4ee1ade50d0ee9