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Article

Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton

by
Yongzhuo Guan
1,
Mingao Zhou
1,
Congyu Zhang
1,
Zixuan Han
1,
Yinbao Zhang
2,
Zhiguo Wu
1,* and
Yuxian Zhu
1,3,4,5
1
College of Life Sciences, Wuhan University, Wuhan 430072, China
2
Xinjiang Jinfengyuan Seed Co., Ltd., Aksu City 843100, China
3
Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
4
Hubei Hongshan Laboratory, Wuhan 430072, China
5
TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
*
Author to whom correspondence should be addressed.
Plants 2024, 13(15), 2079; https://doi.org/10.3390/plants13152079
Submission received: 27 June 2024 / Revised: 24 July 2024 / Accepted: 25 July 2024 / Published: 26 July 2024
(This article belongs to the Special Issue Molecular Insights into Cotton Fiber Gene Regulation)
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Abstract

The genomes and annotated genes of allotetraploid cotton Gossypium hirsutum have been extensively studied in recent years. However, the expression, regulation, and evolution of intergenic genes (ITGs) have not been completely deciphered. In this study, we identified a novel set of actively expressed ITGs in G. hirsutum cotton, through transcriptome profiling based on deep sequencing data, as well as chromatin immunoprecipitation, followed by sequencing (ChIP-seq) of histone modifications and how the ITGs evolved. Totals of 17,567 and 8249 ITGs were identified in G. hirsutum and Gossypium arboreum, respectively. The expression of ITGs in G. hirsutum was significantly higher than that in G. arboreum. Moreover, longer exons were observed in G. hirsutum ITGs. Notably, 42.3% of the ITGs from G. hirsutum were generated by the long terminal repeat (LTR) insertions, while their proportion in genic genes was 19.9%. The H3K27ac and H3K4me3 modification proportions and intensities of ITGs were equivalent to genic genes. The H3K4me1 modifications were lower in ITGs. Additionally, evolution analyses revealed that the ITGs from G. hirsutum were mainly produced around 6.6 and 1.6 million years ago (Mya), later than the pegged time for genic genes, which is 7.0 Mya. The characterization of ITGs helps to elucidate the evolution of cotton genomes and shed more light on their biological functions in the transcriptional regulation of eukaryotic genes, along with the roles of histone modifications in speciation and diversification.
Keywords: G. hirsutum; ITGs; LTR insertion; histone modification; evolution G. hirsutum; ITGs; LTR insertion; histone modification; evolution

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MDPI and ACS Style

Guan, Y.; Zhou, M.; Zhang, C.; Han, Z.; Zhang, Y.; Wu, Z.; Zhu, Y. Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton. Plants 2024, 13, 2079. https://doi.org/10.3390/plants13152079

AMA Style

Guan Y, Zhou M, Zhang C, Han Z, Zhang Y, Wu Z, Zhu Y. Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton. Plants. 2024; 13(15):2079. https://doi.org/10.3390/plants13152079

Chicago/Turabian Style

Guan, Yongzhuo, Mingao Zhou, Congyu Zhang, Zixuan Han, Yinbao Zhang, Zhiguo Wu, and Yuxian Zhu. 2024. "Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton" Plants 13, no. 15: 2079. https://doi.org/10.3390/plants13152079

APA Style

Guan, Y., Zhou, M., Zhang, C., Han, Z., Zhang, Y., Wu, Z., & Zhu, Y. (2024). Actively Expressed Intergenic Genes Generated by Transposable Element Insertions in Gossypium hirsutum Cotton. Plants, 13(15), 2079. https://doi.org/10.3390/plants13152079

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