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

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

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.01297

DOI=10.3389/fpls.2019.01297

ISSN=1664-462X

ABSTRACT=<p><italic>Glycoside hydrolase 3</italic> (<italic>GH3</italic>) 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 <italic>GH3</italic> 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 <italic>GH3</italic> gene family in six representative Gramineae crops, namely, <italic>Setaria italica</italic> (Si), <italic>Zea mays</italic> (Zm), <italic>Sorghum bicolor</italic> (Sb), <italic>Hordeum vulgare</italic> (Hv), <italic>Brachypodium distachyon</italic> (Bd), and <italic>Oryza sativa</italic> ssp. <italic>japonica</italic> (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 <italic>GH3</italic> genes in the same groups have been differentiated. Obvious differences in total numbers of <italic>GH3</italic> genes, Ors, and duplication events among these six tested Gramineae crops reflected lineage-specific expansions and homologous gene loss/gain of <italic>GH3</italic> gene family during the evolutionary process. In addition, selective force and expression analyses indicated that all <italic>GH3</italic> genes were constrained by strong purifying selection, and <italic>GH3</italic> genes in conserved Ors showed higher expression levels than that in unconserved Ors. The current study highlighted different evolutionary patterns of <italic>GH3</italic> genes in Gramineae crops resulted from different evolutionary rates and duplication events and provided a vital insight into the functional divergence of <italic>GH3</italic> genes.</p>