Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development

Abstract

18 · Background 19Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. 20However, the regulatory genes of these two processes are largely unexplored. 21 GATA factors regulate many developmental processes, but its role in plant height 22 control and rhizome development remains unclear. 23 · Results 24Here, we found that bamboo GATA factors (PeGATAs) are involved in the 25 growth regulation of bamboo shoots and rhizomes. Bioinformatics and 26 evolutionary analysis showed that there are 31 PeGATA factors in bamboo, which 27 can be divided into three subfamilies. Light, hormone, and stress-related 28 cis-elements were found in the promoter region of the PeGATA genes. Gene 29 expression of 12 PeGATA genes was regulated by phytohormone-GA but there 30 was no correlation between auxin and PeGATA gene expression. More than 27 31PeGATA genes were differentially expressed in different tissues of rhizomes, and 32 almost all PeGATAs have dynamic gene expression level during the rapid-growth 33 3 of bamboo shoots. These results indicate that PeGATAs regulate rhizome 34 development and bamboo shoot growth partially via GA signaling pathway. In 35 addition, PeGATA26, a rapid-growth negative regulatory candidate gene 36 modulated by GA treatment, was overexpressed in Arabidopsis, and 37 over-expression of PeGATA26 significantly repressed Arabidopsis primary root 38 length and plant height. The PeGATA26 overexpressing lines were also resistant 39 to exogenous GA treatment, further emphasizing that PeGATA26 inhibits plant 40 height from Arabidopsis to moso bamboo via GA signaling pathway. 41 · Conclusions 42Our results provide an insight into the function of GATA transcription factors in 43 regulating shoot rapid-growth and rhizome development, and provide genetic 44 resources for engineering plant height. 45Running title: GATA family in moso bamboo 46

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

“…edulis and two GATA genes (TaGATA-A2 and TaGATA-A11) from T . aestivum contain two or three GATA domains [ 79 , 87 ], which should be classified into subfamily VI based on the study of Oryza sativa [ 73 ], indicating that new criteria for classifying subfamilies of GATA genes should be established again against available hundreds of plant genomes.…”

“…Even though many genome-wide identifications of GATA TFs in plant species [73,[79][80][81][82][83][84][85][86][87], there is no investigation of intraspecific variations of GATA TFs, which may be fundamental data for understanding subtle differences among natural isolates. Fortunately, the genome project of resequencing A. thaliana with Illumina technology provided a gene model of 18 A. thaliana genomes [52].…”

“…Seven subfamilies of GATA genes were identified based on the most previous studies of the plant GATA gene family [73], among which three (V, VI, and VII) are monocot-specific and the rest four are common. Based on many genome-wide identification studies of GATA genes in plant genomes [73,[79][80][81][82][84][85][86][87], the number of GATA genes in subfamily I has the largest except Brassica napus [107] and that of subfamily IV is the smallest in dicot species (Table 3). Interestingly, GATA genes from two more monocot genomes, Triticum aestivum [79] and Phyllostachys PLOS ONE edulis [87] have been identified, presenting that only three or four subfamilies identified from dicots were mentioned (Table 3).…”

“…Based on many genome-wide identification studies of GATA genes in plant genomes [73,[79][80][81][82][84][85][86][87], the number of GATA genes in subfamily I has the largest except Brassica napus [107] and that of subfamily IV is the smallest in dicot species (Table 3). Interestingly, GATA genes from two more monocot genomes, Triticum aestivum [79] and Phyllostachys PLOS ONE edulis [87] have been identified, presenting that only three or four subfamilies identified from dicots were mentioned (Table 3). Two GATA genes (PeGATA6 and PeGATA11) from P. edulis and two GATA genes (TaGATA-A2 and TaGATA-A11) from T. aestivum contain two or three GATA domains [79,87], which should be classified into subfamily VI based on the study of Oryza sativa [73], indicating that new criteria for classifying subfamilies of GATA genes should be established again against available hundreds of plant genomes.…”

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

“…(2019) found that it played a prominent role in hormone regulation. Thirty‐one GATA‐binding TFs were reported to regulate bamboo shoot and rhizome growth, as observed from the repression of primary root length and plant height in Arabidopsis , when one of the genes PeGATA26 was overexpressed (Wang, Yang et al., 2019).…”