New insights into the evolution of the SBP-box family and expression analysis of genes in the growth and development of Brassica juncea

Abstract

The SQUAMOSA promoter binding protein (SBP)-box consists of a family of transcription factors unique to plants and mediates important roles in plant growth and development. We identified 57 SBP genes in the Brassica juncea (swollen-stem mustard) genome, and analyzed the structural characteristics, evolutionary relationships, as well as their involvement in regulation and response to environmental stress. By the help of phylogenetic analysis, the SBP genes were divided into seven subgroups (G1-G7). Interestingly, most members of the same group shared conserved gene structure and motifs as well as gene duplications. This suggests that their functions are redundant highlighting evolutionary relatedness. Identification of the cis-acting elements of the promoter revealed multiple regulatory elements that responded to phytohormone or abiotic stresses. In addition, data from GO annotation indicated that BjuSBPs play a role in biological processes. Further interrogation of the expression of BjuSBPs in different stages of swollen-stem mustard showed spatiotemporal expression patterns. On the other hand, quantitative real-time polymerase chain reaction (qRT-PCR) showed that the expression levels of SBP genes at the development stage correlated with their transcriptome data but treatment with phytohormones affected their expression levels. Our study showed that the SBP-box responds to phytohormone signals and the genes might confer different functions in the development of the mustard plant. Our data lay the foundation for further studies evaluating the regulatory mechanisms of SBP-box family of genes.

The glycoside hydrolase gene family profile and microbial function of Debaryomyces hansenii Y4 during South-road dark tea fermentation

“…Debaryomyces is beneficial for the development of dark tea flavor during production ( Li M. Y. et al, 2020 ). Usually, D. hansenii discovered in protein-rich fermented products exhibits the characteristics of being metabolically versatile, non-pathogenic and tolerant to low temperatures ( Viana et al, 2011 ).…”

“…accelerate the transformation of complex compounds, produce various secondary metabolites, ultimately contribute to the unique flavor of dark tea ( Zhang et al, 2016 ). Recently, some of the functional microorganisms involved in the distinctive flavor formation of dark tea have been identified, for example, Aspergillus , Debaryomyces , and Lichtheimia were confirmed to be the primary beneficial agents of Pu-erh tea during fermentation ( Li et al, 2018 ; Ma et al, 2021 ), while Aspergillus and Debaryomyces also play an important role in the volatile metabolism of Fuzhuan tea during production ( Li M. Y. et al, 2020 ). Furthermore, Aspergillus niger M10 could significantly influence the transformation of key quality components in SSDT during fermentation via the expression of GH genes ( Zou et al, 2022 , 2023 ).…”

Genome-Wide Identification, Characterization, and Expression Profiling Analysis of SPL Gene Family During The Inflorescence Development in Trifolium Repens

“…Generally, the number of gene family is partly affected by the genome size of species. Although the genomes of Arabidopsis (125Mb) (Schneeberger et al, 2011), rice (389Mb) (Takuji et al, 2005) and apple (632.4Mb) (Xuewei et al, 2016) are much smaller than T. repens (1174Mb) (Gri ths et al, 2019), the genome of mustard (1056.53Mb) (Li et al, 2020;Kang et al, 2021) and walnut (620Mb) (Annarita et al, 2020) were also smaller than T. repens. Gene replication events are also very important in determining the evolution and expansion of gene family, and species-speci c gene replication is an important reason for determining the size of SPL gene family.…”

“…In this study, 37 TrSPL genes were identi ed in T. repens, and much more than 16 in Arabidopsis, 19 in rice (Xie, Wu et al 2006), 14 in barley (Hordeum vulgare) (Tong et al, 2020), and 27 in apple (Malus domestica Borkh.) (Li et al, 2013), but less than 56 in wheat (Ting et al, 2020), 57 in mustard (Brassica juncea) (Li et al, 2020), 48 in walnut (Juglans regia) (Zhou et al, 2019), 77 in euphorbiaceae (Li et al, 2019), and 58 in oilseed rape (Brassica napus) (Cheng et al, 2016). Generally, the number of gene family is partly affected by the genome size of species.…”