Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis

Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid (S ), its diploid parents, and th...

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Published inGenes Vol. 11; no. 12; p. 1500
Main Authors Wang, Panqiao, Yu, Xiaqing, Zhu, Zaobing, Zhai, Yufei, Zhao, Qinzheng, Meng, Ya, Li, Ji, Lou, Qunfeng, Chen, Jinfeng
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 12.12.2020
MDPI
Subjects
allopolyploid
Chlorophyll
Chloroplasts
Chromosomes
Cucumis
Diploids
DNA methylation
Epigenetics
Gene expression
Genomes
Hybridization
Interspecific hybridization
lncRNAs
Non-coding RNA
Polyploidy
transcriptome
lncRNAs
Cucumis
allopolyploid
interspecific hybridization
transcriptome
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Summary:Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid (S ), its diploid parents, and the F hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in , 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S , which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.
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These authors contributed equally to this work.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes11121500