Evolutionary Analysis of the YABBY Gene Family in Brassicaceae.

Yun-Hai Lu,Intikhab Alam,Li-Xi Jiang,Wen-Chao Chi,Ya-Cen Yu,Boulos Chalhoub,Song-Biao Chen,Yan-Qing Yang

doi:10.3390/plants10122700

Abstract

The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.

Highlights

The YABBY gene family contains several transcription factor members present in all seed plants [1,2]
Six YABBY genes were identified in the model plant A. thaliana genome, including FILAMENTOUS FLOWER (FIL), YAB2, YAB3, YAB5, INNER NO OUTER (INO), and CRABS CLAW (CRC), where FIL and YAB3 represent the most recent gene duplication within the family [8]
FIL, YAB2, YAB3, and YAB5 are called “vegetative” and shown to be preferentially expressed in leaves and leaf-derived organs, whereas INO and CRC are expressed in developing floral organs that are evolutionarily derived from leaves [5,6,7,9,10,11,12]

Summary

Introduction

The YABBY gene family contains several transcription factor members present in all seed plants [1,2]. FIL, YAB2, YAB3, and YAB5 are called “vegetative” and shown to be preferentially expressed in leaves and leaf-derived organs (i.e., cotyledons, sepals, petals, stamens, and carpels), whereas INO and CRC are expressed in developing floral organs (i.e., ovules and carpels respectively) that are evolutionarily derived from leaves [5,6,7,9,10,11,12] These YABBY genes were initially and extensively studied in Arabidopsis, and they were shown to play important roles in the specification of abaxial cell fates in lateral organs produced by apical and flower meristems in both distinct and redundant manners [8]. CRC is required for normal carpel development by suppressing radial growth of the developing gynoecium but promoting its longitudinal growth, in addition to being important for nectary development; its mutation (crc) generates shorter and wider gynoecia with the two carpels being unfused at the apex and flowers lacking nectaries [5,17]

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