Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

Abstract

Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

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“…However, the number of genes within a gene family can vary among species (Rezaee et al, 2020;Song et al, 2020;Abdullah et al, 2021a;Faraji et al, 2021). The identified tcBAHDs showed high diversity based on sequence structure, physicochemical properties, functions, and distribution across the chromosome, which is in agreement with previous reports of the BAHD gene family (Moglia et al, 2016;Zhang et al, 2019;Ahmad et al, 2020b;Liu et al, 2020a). The annotation retrieved from the Ensembl indicates the identified tcBAHD enzymes have high diversity in the function of tcBAHD.…”

“…Wholegenome analyses provide information about the genetic basis of response to abiotic and biotic stresses (Motamayor et al, 2013). In particular, genome-wide studies of the BAHD family have been reported in various species, including Populus (Yu et al, 2009), Arabidopsis (Yu et al, 2009), soybean (Ahmad et al, 2020b), Cynara cardunculus (Moglia et al, 2016), and in some species of Rosaceae (Zhang et al, 2019;Liu et al, 2020a). The chromosome-level genome assembly of T. cacao (Motamayor et al, 2013;Argout et al, 2017) provides resources for the characterization of gene families, which has led to the identification and characterization of WRKY (Dayanne et al, 2017), NAC (Shen et al, 2020), GASA (Abdullah et al, 2021a), and MGT (Heidari et al, 2021a) in cacao.…”

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“…However, the number of genes within a gene family can vary among species (Rezaee et al, 2020;Song et al, 2020;Abdullah et al, 2021a;Faraji et al, 2021). The identified tcBAHDs showed high diversity based on sequence structure, physicochemical properties, functions, and distribution across the chromosome, which is in agreement with previous reports of the BAHD gene family (Moglia et al, 2016;Zhang et al, 2019;Ahmad et al, 2020b;Liu et al, 2020a). The annotation retrieved from the Ensembl indicates the identified tcBAHD enzymes have high diversity in the function of tcBAHD.…”

“…Wholegenome analyses provide information about the genetic basis of response to abiotic and biotic stresses (Motamayor et al, 2013). In particular, genome-wide studies of the BAHD family have been reported in various species, including Populus (Yu et al, 2009), Arabidopsis (Yu et al, 2009), soybean (Ahmad et al, 2020b), Cynara cardunculus (Moglia et al, 2016), and in some species of Rosaceae (Zhang et al, 2019;Liu et al, 2020a). The chromosome-level genome assembly of T. cacao (Motamayor et al, 2013;Argout et al, 2017) provides resources for the characterization of gene families, which has led to the identification and characterization of WRKY (Dayanne et al, 2017), NAC (Shen et al, 2020), GASA (Abdullah et al, 2021a), and MGT (Heidari et al, 2021a) in cacao.…”

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

“…Wholegenome analyses provide information about the genetic basis of response to abiotic and biotic stresses (Motamayor et al, 2013). In particular, genome-wide studies of the BAHD family have been reported in various species, including Populus (Yu et al, 2009), Arabidopsis (Yu et al, 2009), soybean (Ahmad et al, 2020b), Cynara cardunculus (Moglia et al, 2016), and in some species of Rosaceae (Zhang et al, 2019;Liu et al, 2020a). The chromosome-level genome assembly of T. cacao (Motamayor et al, 2013;Argout et al, 2017) provides resources for the characterization of gene families, which has led to the identification and characterization of WRKY (Dayanne et al, 2017), NAC (Shen et al, 2020), GASA (Abdullah et al, 2021a), and MGT (Heidari et al, 2021a) in cacao.…”