Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies

Abstract

BackgroundExpansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited.ResultsA total of 75 expansin genes were identified in the soybean genome, and grouped into four subfamilies based on their phylogenetic relationships. Structural analysis revealed that the expansin genes are conserved in each subfamily, but are divergent among subfamilies. Furthermore, in soybean and Arabidopsis, the expansin gene family has been mainly expanded through tandem and segmental duplications; however, in rice, segmental duplication appears to be the dominant process that generates this superfamily. The transcriptome atlas revealed notable differential expression in either transcript abundance or expression patterns under normal growth conditions. This finding was consistent with the differential distribution of the cis-elements in the promoter region, and indicated wide functional divergence in this superfamily. Moreover, some critical amino acids that contribute to functional divergence and positive selection were detected. Finally, site model and branch-site model analysis of positive selection indicated that the soybean expansin gene superfamily is under strong positive selection, and that divergent selection constraints might have influenced the evolution of the four subfamilies.ConclusionThis study demonstrated that the soybean expansin gene superfamily has expanded through tandem and segmental duplication. Differential expression indicated wide functional divergence in this superfamily. Furthermore, positive selection analysis revealed that divergent selection constraints might have influenced the evolution of the four subfamilies. In conclusion, the results of this study contribute novel detailed information about the molecular evolution of the expansin gene superfamily in soybean.

In silicoidentification, phylogeny and expression analysis of expansin superfamily inMedicago truncatula

“…They play important roles in the regulation of plant growth and development processes, such as root development, leaf growth, fruit ripening, seed germination, penetration of pollen tubes, etc. In this study, we identified 42 MtEXP genes from M. truncatula genome by bioinformatics analysis, which was similar to previous reports in Arabidopsis, [3] rice, [27] soybean [28] and poplar, [29] and indicated that expansin genes are highly conservative in plants. [17,30] …”

Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication

“…Expansin genes were distributed on the ten chromosomes (A) of B. rapa with different densities. Two unmapped genes BrEXPA39 and BrEXPB9 were located on Scaffold000317 (gene position: 22,499-24,350) The Arabidopsis, poplar, rice, and last common ancestor data were obtained from ; the soybean, common bean, and Medicago truncatula data were obtained from Zhu et al (2014); and the grapevine data were obtained from DeSanto et al and Scaffold000111 (gene position: 290,653-291,849), respectively. The maximum number of expansin genes was found on A03 (n = 8), followed by A02 (n = 7) and A05 (n = 7).…”

“…Whole genome screening has been applied to explore several species-specific structural features of expansins in A. thaliana , rice (Oryza sativa; , poplar (Populus trichocarpa; Sampedro et al 2006), grapevine (Vitis vinifera;DeSanto et al 2013) and soybean (Glycine max; Zhu et al 2014). These genome-wide identifications and comparisons among different species have provided rich resources for the evolutionary analysis of expansins.…”

Overexpression of a soybean expansin gene, GmEXP1, improvesdrought tolerance in transgenic tobacco

“…They are 768 bp in length, encoding 255 amino acids. When compared with the classification system proposed by Zhu et al (2014), GmEXP1 is identical to GmEXPA37, an α-expansin subfamily, which is located on chromosome 17. This result is consistent with the soybean mRNA genetic map constructed by Libault et al (2010).…”

“…The GmEXP1 from chromosome 17 is 1491 nucleotides long, containing 3 exons and 2 introns. The coding region is 768 nucleotides in length, encoding α-expansin with 255 amino acids (Kende et al, 2004;Zhu et al, 2014), and consists of three regions: a signaling region, an active region similar to endoglucanase, and the pollen allergen region for substrate adhesion (Wu et al, 2001). When the cell wall reaches a pH growth level of 4.5-6.0 and the ratio of expansin and cell wall (on a dry mass basis) is 1:10,000, the expansin will cause cellular structural changes by sticking, breaking links between polysaccharide components (including pectin and hemicellulose), and loosening the polymer network.…”