The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

Gongbo Lv; Xing Zheng; Yitian Duan; Yunyong Wen; Bin Zeng; Mingqiang Ai; Bin He

doi:10.7717/peerj.11526

The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

PeerJ. 2021 May 26:9:e11526. doi: 10.7717/peerj.11526. eCollection 2021.

Authors

Gongbo Lv^#¹, Xing Zheng^#¹, Yitian Duan², Yunyong Wen¹, Bin Zeng^{1

3}, Mingqiang Ai¹, Bin He¹

Affiliations

¹ College of Life Sciences, Jiangxi Science & Technology Normal University, Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, Nanchang, Jiangxi, China.
² Renmin University of China, School of Information, Beijing, China.
³ Shenzhen Technology University, College of Pharmacy, Shenzhen, Guangdong, China.

^# Contributed equally.

Abstract

The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.

Keywords: Expression pattern; GRAS transcription factor; Genome-wide analysis; Root-knot nematode; Watermelon (Citrullus lanatus).

Grants and funding

This study was funded by the International S&T Cooperation Project of Jiangxi Provincial (Grant NO. 20142BDH80003), the Science Funds of Natural Science Foundation of Jiangxi Province (20114BAB205039), Jiangxi Province Science Foundation (Grant NO. 20202BABL203043 and 20202BAB215003), and the Innovation Fund Designated for Graduate Students of Jiangxi Science and Technology Normal University (YC2020-X20). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.