Genome-Wide Identification and Expression Analysis of m6A Writers, Erasers, and Readers in Litchi (Litchi chinensis Sonn.)

Liwen Tang; Jiali Xue; Xingyu Ren; Yue Zhang; Liqing Du; Feng Ding; Kaibing Zhou; Wuqiang Ma

doi:10.3390/genes13122284

Genome-Wide Identification and Expression Analysis of m6A Writers, Erasers, and Readers in Litchi (Litchi chinensis Sonn.)

Genes (Basel). 2022 Dec 4;13(12):2284. doi: 10.3390/genes13122284.

Authors

Liwen Tang^{1

2}, Jiali Xue^{1

2}, Xingyu Ren^{1

2}, Yue Zhang^{1

2}, Liqing Du³, Feng Ding⁴, Kaibing Zhou^{1

2}, Wuqiang Ma^{1

2}

Affiliations

¹ Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China.
² Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Horticulture College, School of Horticulture, Haikou 570228, China.
³ Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture & Rural Affairs, South Subtropical Crops Research Institute of Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
⁴ Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.

Abstract

N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in litchi was performed and 31 litchi m6A regulatory genes were identified in total, including 7 m6A writers, 12 m6A erases, and 12 readers. Phylogeny analysis showed that all three of the kinds of litchi m6A regulatory proteins could be divided into three groups; domains and motifs exhibited similar patterns in the same group. MiRNA target site prediction showed that 77 miRNA target sites were located in 25 (80.6%) litchi m6A regulatory genes. Cis-elements analysis exhibited that litchi m6A regulatory genes were mainly responsive to light and plant hormones, followed by environmental stress and plant development. Expression analysis revealed litchi m6A regulatory genes might play an important role during the peel coloration and fruit abscission of litchi. This study provided valuable and expectable information of litchi m6A regulatory genes and their potential epigenetic regulation mechanism in litchi.

Keywords: erasers; expression analysis; fruit abscission; fruit coloration; litchi; m6A modification; readers; writers.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epigenesis, Genetic
Fruit / genetics
Litchi*
MicroRNAs* / metabolism
Plants / genetics

Substances

MicroRNAs

Grants and funding

This work was supported by the Natural Science Foundation of Hainan Province (2019RC082 and 320QN191), initial funding from Hainan University that introduced high-level personnel (KYQD(2R)1970), the National Natural Science Foundation of China (32260750), and Ministry of Agriculture Opening Project Fund of Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture & Rural Affairs.