Genome-Wide Identification, Expansion, and Evolution Analysis of Homeobox Gene Family Reveals TALE Genes Important for Secondary Cell Wall Biosynthesis in Moso Bamboo (Phyllostachys edulis)

Abstract

The TALE gene family is a subfamily of the homeobox gene family and has been implicated in regulating plant secondary growth. However, reports about the evolutionary history and function of the TALE gene family in bamboo are limited. Here, the homeobox gene families of moso bamboo Olyra latifolia and Bonia amplexicaulis were identified and compared. Many duplication events and obvious expansions were found in the TALE family of woody bamboo. PhTALEs were found to have high syntenies with TALE genes in rice. Through gene co-expression analysis and quantitative real-time PCR analysis, the candidate PhTALEs were thought to be involved in regulating secondary cell wall development of moso bamboo during the fast-growing stage. Among these candidate PhTALEs, orthologs of OsKNAT7, OSH15, and SH5 in moso bamboo may regulate xylan synthesis by regulating the expression of IRX-like genes. These results suggested that PhTALEs may participate in the secondary cell wall deposition in internodes during the fast-growing stage of moso bamboo. The expansion of the TALE gene family may be implicated in the increased lignification of woody bamboo when divergent from herbaceous bamboos.

Genome-wide identification of three-amino-acid-loop-extension gene family and their expression profile under hormone and abiotic stress treatments during stem development of Prunus mume

“…For example, Que. et al found that the TALE genes of Moso Bamboo and the TALE genes of rice have a high collinearity relationship (Que et al, 2022). In this study, we used the inter-species collinearity analysis to study the collinearity of TALE genes between P. mume and four other Prunus species.…”

“…Studies have shown that evolution caused by gene duplication events is prevalent in angiosperms. For example, there is obvious expansion phenomenon in woody bamboo TALE gene family, which is caused by many duplication events (Que et al, 2022). Whole-genome duplication events occurred in G. raimondii and G. arboretum (Huang et al, 2020), and there were 34 gene pairs with fragment duplication in the TALE genes of G. hirsutum obtained by crossing the above two species, and also selected by purification (Zhang et al, 2021b).…”

“…Downregulated expression of cotton TALE gene family member GhSTM3 affects flowering time (Zhang et al, 2021b). During the rapid growth period of Phyllostachys edulis, members of the TALE gene family may affect the formation of secondary cell walls in internodes by regulating the synthesis of xylan (Que et al, 2022). Nearly half of (17) TALE genes in poplar are highly expressed in stem, which may play a key regulatory role in wood formation (Zhao et al, 2019).…”

“…Previous reports have shown that TALE genes are involved in stem development of plants (Testone et al, 2012;Zhao et al, 2019;Que et al, 2022). In this study, in order to preliminarily explore the effect of TALE genes on P. mume stem development, we selected 11 members highly expressed in the P. mume stem to perform further expression pattern analysis in three different developmental stages of stem.…”

Genome-wide analysis of the KNOX gene family in Moso bamboo: Insights into their role in promoting the rapid shoot growth

“…However, only a limited number of studies have delved into the downstream targets of KNOX genes. KNOX is a TF and has been shown to modulate hormone levels, particularly cytokinin and auxin [23][24][25], to inhibit gibberellin synthesis [26], and to participate in secondary cell wall formation [27]. Consequently, KNOX genes emerge as pivotal contributors to plant growth and development [28].…”