Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

Abstract

Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.

Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing

“…We identified 9 candidate genes within an interval of 50 kb up- and downstream of the SNP variant. Among those genes, it is noteworthy to mention the PH02Gene21516.t2 ( Ma et al, 2021 ) that encodes a plant-specific YABBY transcription factor (TF) ( Supplementary Table 7 ). These small zinc finger TFs are associated with plant morphogenesis, the development and polarity of lateral plant organs ( Bowman, 2000 ; Kumaran et al, 2002 ), and biotic/abiotic stress ( Yamada et al, 2011 ).…”

Identification and expression analysis of YABBY family genes in Platycodon grandiflorus

“… 29 Except for PgYABBY2 , which had only a few conserved amino acids, all P. grandiflorus YABBY proteins featured YABBY and zinc finger domains. 36 Two highly conserved motifs were found in the YABBY proteins, which were speculated to be related to the conserved domains of the YABBY transcription factor and the YABBY and zinc finger domains. PgYABBY2 contained only one conserved motif, rendering it different from other PgYABBY proteins, but the reason for this difference remains unclear.…”

Identification and expression profiles of the YABBY transcription factors in wheat

“…In the present study, 20 YABBY TFs were identified in wheat. There are more YABBY members in wheat than in rice ( Toriba et al, 2007 ), Arabidopsis ( Siegfried et al, 1999 ), soybean ( Zhao et al, 2017 ), tomato ( Huang et al, 2013 ), and Moso Bamboo ( Ma et al, 2021 ), indicating that wheat YABBY has a more complex function. This reason is because wheat is a heterozygous polyploid.…”

“…To date, identification of YABBY TFs has been performed in different plant species through genome-wide analyses. A total of six YABBY TFs have been identified in Arabidopsis ( Siegfried et al, 1999 ), 17 in soybean ( Glycine max ) ( Zhao et al, 2017 ), 9 in pineapple (Ananas comosus) ( Li & Li, 2019 ), seven in grapevine ( Vitis vinifera ) ( Zhang et al, 2019 ), nine in tomato (Solanum lycopersicum) ( Huang et al, 2013 ), 12 in Gossypium arboreum , 12 in G. raimondii , 23 in G. hirsutum ( Yang et al, 2018 ), and 16 in moso bamboo ( Phyllostachys edulis) ( Ma et al, 2021 ). As one of the most important crops worldwide, the genome of wheat has been sequenced; however, few studies have been conducted on the wheat YABBY gene family.…”