Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

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.

Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

“…Our case study of YABBY genes indicates some of the strengths and limitations of genome-wide orthology inference. For instance, the Brassica rapa homologs recovered for each YABBY are the same with those found in a phylogenetic study on the YABBY gene family (Lu et al, 2021). We were unable to recover the Aethionema ortholog of YAB3 (AT4G00180.1; Fig 5), but the phylogenetic study considered Aa31LG2G250 as the YAB3 ortholog.…”

Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis

“…YABBYs, both C2C2 zinc finger and YABBY domain-containing TRs, are widely involved in lateral organ development in higher plants and the identification of YABBY gene family has made progress in many plants ( Lu et al, 2021 ; Xia et al, 2021 ; Yin et al, 2022 ; Zeng et al, 2022 ). However, systematic investigation of the OsYABBYs-interacting proteins have been poorly reported.…”