Comparative Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C4 Plant

Abstract

The emergence and expression of the YABBY gene family (YGF) coincided with the evolution of leaves in seed plants, and was integral to the early evidence of lamina followed by reproductive development. YGF contains six subclasses, i.e., CRC, INO, FIL, YAB2, YAB3, and YAB5. This study aims to extract the genome sequences of the YGF in Bienertia sinuspersici, an important model plant for single-cell C₄ (SCC₄), non-Kranz photosynthesis. A comparative genomic analysis was undertaken with Vitis vinefera, Arabidopsis thaliana, Brassica rapa, and Chenopodium quinoa. Six copies of YGF were present in B. sinuspersici and A. thaliana with a single copy of each YGF subgroup. V. vinefera possessed seven copies of YGF with duplicates in FIL and YAB2 subgroups, but no YAB3. B. rapa and C. quinoa after whole genome duplication contained additional copies of YGF. The gene structure and conserved motifs were analyzed among the YGF. In addition, the relative quantification of YGF was analyzed in the leaves, reproductive developmental stages such as the bud, and the pre-anthesis and anthesis stages in B. sinuspersici, A. thaliana, and B. rapa. CRC and INO possessed conserved floral-specific expression. Temporal and perpetual changes in the expression of YGF orthologs were observed in the leaves and reproductive developmental stages. The results of this study provide an overview of YGF evolution, copy number, and its differential expression in B. sinuspersici. Further studies are required to shed light on the roles of YABBY genes in the evolution of SCC₄ plants and their distinct physiologies.

Keywords: Bienertia sinuspersici; Genome sequencing; Whole genome duplication (WGD); YABBY gene family (YGF); diversification.

Figure 1

Phylogenetic tree of the YABBY gene family in Vitis vinefera, Arabidopsis thaliana, Brassica rapa, Bienertia sinuspersici, and Chenopodium quinoa constructed by the maximum likelihood method using MEGA v. 6.0. Light green down triangle, V. vinefera; Brown circle, A. thaliana; Dark green square, B. rapa; Blue diamond, B. sinuspersici; and Red up triangle, C. quinoa.

Figure 2

Motif of the YABBY gene family in Vitis vinefera, Arabidopsis thaliana, Brassica rapa, Bienertia sinuspersici, and Chenopodium quinoa, identified using the MULTIPLE EM for MOTIF ELICITATION (MEME) server. Details of the motifs are shown in Table S1. Motif numbers.

Figure 3

(a) Leaf and reproductive developmental stages of Arabidopsis thaliana (A-D), Brassica rapa (E-H), and Bienertia sinuspersici (I-L). The floral stage images were taken using a microscope (www.dimis.co.kr). Orange bar, 100×; White bar, 50×. (b) Real-time quantitative-polymerase chain reaction analysis of YABBY gene expression in Arabidopsis thaliana (At), Brassica rapa (Br), and Bienertia sinuspersici (Bs). Legends: L, Leaf; F, Floral bud stage; P, Pre-anthesis elongation stage; and A, Anthesis stage. Bars indicate mean ± standard error.