Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L

Shulin Shen; Fujun Sun; Meichen Zhu; Si Chen; Mingwei Guan; Rui Chen; Fang Tang; Nengwen Yin; Xinfu Xu; Zhanglin Tang; Jiana Li; Kun Lu; Cunmin Qu

doi:10.1371/journal.pone.0234411

Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L

PLoS One. 2020 Jun 8;15(6):e0234411. doi: 10.1371/journal.pone.0234411. eCollection 2020.

Authors

Shulin Shen^{1

2}, Fujun Sun^{1

2}, Meichen Zhu^{1

2}, Si Chen^{1

2}, Mingwei Guan^{1

2}, Rui Chen^{1

2}, Fang Tang^{1

2}, Nengwen Yin^{1

2}, Xinfu Xu^{1

2}, Zhanglin Tang^{1

2}, Jiana Li^{1

2}, Kun Lu^{1

2}, Cunmin Qu^{1

2}

Affiliations

¹ Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China.
² Academy of Agricultural Sciences, Southwest University, Chongqing, China.

Abstract

The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.

Publication types

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

MeSH terms

Amino Acid Sequence
Arabidopsis Proteins / genetics
Brassica / genetics*
Brassica / growth & development
Brassica napus / genetics*
Brassica napus / growth & development
Chromosome Mapping
Conserved Sequence
Gene Duplication
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant*
Genome, Plant
Homeodomain Proteins / genetics
Multigene Family
Phylogeny
Plant Proteins / genetics
Synteny

Substances

APETALA2 protein, Arabidopsis
Arabidopsis Proteins
Homeodomain Proteins
Plant Proteins

Grants and funding

This study was funded by the National Major Science and Technology Projects of China (2018ZX08020001), National Natural Science Foundation of China (31830067), Fundamental Research Funds for Central Universities of the Central South University (XDJK2019C099), Fundamental Research Funds for Central Universities of the Central South University (XDJK2020B030), Chongqing Postdoctoral Research Foundation (CN) (XmT2018057), 111 project (CN) (B12006), and Modern Agro-industry Technology Research System (CN) (CARS-12). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.