Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea

Xuedie Liu,Yu-Ting Jiang,Meng-Jia Zhu,Xia Yu,Di-Yang Zhang,Xin-Yu Xu,Yu Zheng,Siren Lan,Xing-Yu Liao,Zhong-Jian Liu,Liang Ma

doi:10.3390/plants10010021

Xuedie Liu, Yu-Ting Jiang + Show 9 more

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https://doi.org/10.3390/plants10010021

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Abstract

The YABBY gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three lineages. However, prior to this study, information on the function of the YABBY genes in magnoliids was extremely limited to the third major clades and the early diverging lineage of Mesangiospermae. In this study, the sum of 55 YABBY genes including five genes in INO, six in CRC, eight in YAB2, 22 in YAB5, and 14 in FIL clade were identified from seven magnoliid plants. Sequence analysis showed that all encoded YABBY protein sequences possess the highly conserved YABBY domain and C2C2 zinc-finger domain. Gene and protein structure analysis indicates that a certain number of exons were highly conserved and similar in the same class, and YABBY genes encode proteins of 71–392 amino acids and an open reading frame of 216–1179 bp in magnoliids. Additionally, the predicted molecular weight and isoelectric point of YABBY proteins in three species ranged from 7689.93 to 43578.13 and from 5.33 to 9.87, respectively. Meanwhile, the YABBY gene homolog expression of Litsea was detected at a temporal and spatial level during various developmental stages of leaf and reproductive tissues. This research could provide a brief overview of YABBY gene family evolution and its differential expression in magnoliids. Therefore, this comprehensive diversification analysis would provide a new insight into further understanding of the function of genes in seven magnoliids.

Highlights

The YABBY gene family, a small class of transcription factors, belongs to the zinc-finger superfamily
Eight members of the YABBY gene family were both identified in the genome of C. micranthum and L. cubeba, seven in that of P. bournei, six in that of L. chinense and C. salicifolius, five in that of C. praecox, and 15 in that of P. nigrum
Based on sequences verified by domain identification and the classification scheme of the YABBY gene family in other plants, 55 magnoliids YABBY genes were separated into five clades, including

Summary

Introduction

The YABBY gene family, a small class of transcription factors, belongs to the zinc-finger superfamily. In Arabidopsis thaliana, the YABBY gene family has a distinct role, declared to six subclades, including CRABS CLAW (CRC), INNER NO OUTER (INO), FILAMENTOUS. CRC and INO are considered the “reproductive-specific YABBY genes”, whereas FIL, YAB2, YAB3, and YAB5 are referred to as the “vegetative YABBY genes” [10,11]. The “vegetative YABBY genes” could regulate the lateral organ polarity development, formation of margins, maturation of the leaf, and development and phyllotaxis of the shoot apical meristem and are detected both in leaf primordia and floral organs [12,13,14], whereas two other genes, CRC and INO, are restricted to developing carpels and the outer integument of the ovule, respectively. On the basis of these findings, the YABBY gene family facilitate the abaxial cell fate of lateral organs in Arabidopsis [12]

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