Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops.

Weilong Kong,Xiaoxiao Deng,Yue Zhang,Yangsheng Li,Shuangmiao Li,Chenhao Zhang

doi:10.3389/fpls.2019.01297

Abstract

Glycoside hydrolase 3 (GH3) gene family belongs to auxin-responsive gene families and is tightly linked with hormone homeostasis and signaling pathways. However, our knowledge about the evolutionary dynamic of GH3 genes in Gramineae crops is limited. In this study, a comparative genomic and transcriptomic analysis was conducted to study evolutionary patterns and the driving selective forces of GH3 gene family in six representative Gramineae crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa ssp. japonica (Os). A total of 17, 13, 11, 9, 8, and 11 GH3 proteins (GH3s) were identified in Si, Zm, Sb, Hv, Bd, and Os, respectively. Phylogenetic, conserved motif, and gene structural analyses could divide all GH3s into two groups (I and II), and all GH3s consisted of seven orthogroups (Ors) on the basis of Or identification result. We further found that genes in the same Or showed similar sequence and structural features, whereas genes in the same groups exhibited intrinsic differences in exon numbers and intron lengths. These results revealed GH3 genes in the same groups have been differentiated. Obvious differences in total numbers of GH3 genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of GH3 gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all GH3 genes were constrained by strong purifying selection, and GH3 genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of GH3 genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of GH3 genes.

Highlights

Auxin, one of the most important hormones in plants, plays essential roles in embryogenesis, vascular differentiation, phototropism, and plant morphology (Jain et al, 2006; Terol et al, 2006)
We investigated a total of 69 nonredundant Glycoside hydrolase 3 (GH3) genes from the six studied species, with 17 in S. italica, 13 in Z. mays, 11 in S. bicolor, 9 in H. vulgare, 8 in B. distachyon, and 11 in Oryza sativa ssp. japonica (Os). sativa ssp. japonica (Table S1)
Or1 showed four to six genes in S. italica, Z. mays, and S. bicolor, whereas only two to three genes in H. vulgare, B. distachyon, and O. sativa ssp. japonica. These results indicated that the GH3 gene family has lineage-specific expansions and homologous gene loss/gain in Gramineae crops during the evolutionary process

Summary

Introduction

One of the most important hormones in plants, plays essential roles in embryogenesis, vascular differentiation, phototropism, and plant morphology (Jain et al, 2006; Terol et al, 2006). Plant GH3 proteins played important roles in signaling pathways, organ developments, and plant architecture (Fu et al, 2011; Singh et al, 2015; Cano et al, 2018). OsGH3-1, OsGH3-2, OsGH3-8, and OsGH3-13 are associated with crosstalk modulation between the IAA, JA, and SA signaling pathways under biotic or/and abiotic stresses (Ding et al, 2008; Domingo et al, 2009; Zhang et al, 2009). Another study reported that “auxin-miR167ARF8-OsGH3-2” signaling pathway responses to exogenous auxin (Yang et al, 2006). “miR156f-OsSPL7OsGH3-8” signaling pathway modulates the plant architecture (Dai et al, 2018)

Methods

Results

Discussion

Conclusion