Genome-wide identification and analysis of DEAD-box RNA helicases in Gossypium hirsutum

Ruotong Rao; Xiaoyu Huang; Xinting Wang; Xuelong Li; Huiping Liao; Nigara Abuduwaili; Xiuzhen Wei; Dengdi Li; Gengqing Huang

doi:10.1016/j.gene.2024.148495

Genome-wide identification and analysis of DEAD-box RNA helicases in Gossypium hirsutum

Gene. 2024 Apr 24:920:148495. doi: 10.1016/j.gene.2024.148495. Online ahead of print.

Authors

Ruotong Rao¹, Xiaoyu Huang², Xinting Wang², Xuelong Li², Huiping Liao², Nigara Abuduwaili³, Xiuzhen Wei³, Dengdi Li⁴, Gengqing Huang⁵

Affiliations

¹ Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China. Electronic address: raoruotong@apm.ac.cn.
² Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
³ Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China.
⁴ Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China. Electronic address: dengdili@ccnu.edu.cn.
⁵ Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China. Electronic address: gqhuang@ccnu.edu.cn.

PMID: 38663690
DOI: 10.1016/j.gene.2024.148495

Abstract

DEAD-box RNA helicases, a prominent subfamily within the RNA helicase superfamily 2 (SF2), play crucial roles in the growth, development, and abiotic stress responses of plants. This study identifies 146 DEAD-box RNA helicase genes (GhDEADs) and categorizes them into four Clades (Clade A-D) through phylogenetic analysis. Promoter analysis reveals cis-acting elements linked to plant responses to light, methyl jasmonate (MeJA), abscisic acid (ABA), low temperature, and drought. RNA-seq data demonstrate that Clade C GhDEADs exhibit elevated and ubiquitous expression across different tissues, validating their connection to leaf development through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Notably, over half of GhDEADs display up-regulation in the leaves of virus-induced gene silencing (VIGS) plants of GhVIR-A/D (members of m⁶A methyltransferase complex, which regulate leaf morphogenesis). In conclusion, this study offers a comprehensive insight into GhDEADs, emphasizing their potential involvement in leaf development.

Keywords: DEAD-box RNA Helicase Gene Family; GhVIR; Gossypium hirsutum; Leaf development.