Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.).

Yuqing Li,Chunyan Wei,Na Dong,Tao Dong,Tengfei Qin,Qinglian Wang,Ruiyang Zhou,Runrun Sun,Quanjia Chen,Yaxin Zhang

doi:10.3390/genes10120947

Yuqing Li, Chunyan Wei + Show 8 more

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https://doi.org/10.3390/genes10120947

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Abstract

Cotton plays an important role in the economy of many countries. Many studies have revealed that numerous genes and various metabolic pathways are involved in anther development. In this research, we studied the differently expressed mRNA and lncRNA during the anther development of cotton between the cytoplasmic male sterility (CMS) line, C2P5A, and the maintainer line, C2P5B, using RNA-seq analysis. We identified 17,897 known differentially expressed (DE) mRNAs, and 865 DE long noncoding RNAs (lncRNAs) that corresponded to 1172 cis-target genes at three stages of anther development using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DE mRNAs; and cis-target genes of DE lncRNAs probably involved in the degradation of tapetum cells, microspore development, pollen development, and in the differentiation, proliferation, and apoptosis of the anther cell wall in cotton. Of these DE genes, LTCONS_00105434, LTCONS_00004262, LTCONS_00126105, LTCONS_00085561, and LTCONS_00085561, correspond to cis-target genes Ghir_A09G011050.1, Ghir_A01G005150.1, Ghir_D05G003710.2, Ghir_A03G016640.1, and Ghir_A12G005100.1, respectively. They participate in oxidative phosphorylation, flavonoid biosynthesis, pentose and glucuronate interconversions, fatty acid biosynthesis, and MAPK signaling pathway in plants, respectively. In summary, the transcriptomic data indicated that DE lncRNAs and DE mRNAs were related to the anther development of cotton at the pollen mother cell stage, tetrad stage, and microspore stage, and abnormal expression could lead to anther abortion, resulting in male sterility of cotton.

Highlights

In recent years, with the development of sequencing technology, numerous genes and gene families have been identified
A total of 178,166 transcripts were detected in 18 anther tissues of cotton, and 28,047 novel long noncoding RNAs (lncRNAs) were identified using the following four programs: Coding Potential Calculator (CPC), txCdsPredict, CNCI, and Pfam (Figure 1A); and 46,245 novel mRNAs and 103,874 known transcripts were identified
Many lncRNAs transcripts were mainly composed of 1–7 exons, whereas mRNAs had a wide range of exons, 1–10 (Figure 1B)

Summary

Introduction

With the development of sequencing technology, numerous genes and gene families have been identified. Long noncoding RNA (lncRNA) is considered a part of the “dark” or “junk” transcriptomes. LncRNAs are defined as being larger than 200 nucleotides in length, and play vital regulatory roles in biological processes in plants and animals [5,6,7], such as plant growth and development, epigenetics, and stress response [5,7]. They have important regulatory functions in organisms, and are strictly regulated at the transcriptional and post-transcriptional levels [8]. Studies have shown that lncRNAs have high stage- and tissue-specific expression patterns [9,10]

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