Dataset Information

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

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.

SUBMITTER: Kong W

PROVIDER: S-EPMC6803601 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Kong Weilong W Zhang Yue Y Deng Xiaoxiao X Li Shuangmiao S Zhang Chenhao C Li Yangsheng Y

Frontiers in plant science 20191015

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 i ...[more]

PMID: 31681387

Similar Datasets

Project description:Sugar transporter proteins (STPs), such as H+/sugar symporters, play essential roles in plants' sugar transport, growth, and development, and possess an important potential to enhance plants' performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

Project description:Polyol transporters (PLTs), also called polyol/monosaccharide transporters, is of significance in determining plant development and sugar transportation. However, the diverged evolutionary patterns of the PLT gene family in Gramineae crops are still unclear. Here a micro-evolution analysis was performed among the seven Gramineae representative crops using whole-genome sequences, i.e., Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm), leading to the identification of 12, 11, 12, 15, 20, 24, and 20 PLT genes, respectively. In this study, all PLT genes were divided into nine orthogroups (OGs). However, the number of PLT genes and the distribution of PLT OGs were not the same in these seven Gramineae species, and different OGs were also subject to different purification selection pressures. These results indicated that the PLT OGs of the PLT gene family have been expanded or lost unevenly in all tested species. Then, our results of gene duplication events confirmed that gene duplication events promoted the expansion of the PLT gene family in some Gramineous plants, namely, Bd, Or, Os, Si, Sb, and Zm, but the degree of gene family expansion, the type of PLT gene duplication, and the differentiation time of duplicate gene pairs varied greatly among these species. In addition, the sequence alignment and the internal repeat analysis of all PLTs protein sequences implied that the PLT protein sequences may originate from an internal repeat duplication of an ancestral six transmembrane helical units. Besides that, the protein motifs result highlighted that the PLT protein sequences were highly conserved, whereas the functional differentiation of the PLT genes was characterized by different gene structures, upstream elements, as well as co-expression analysis. The gene expression analysis of rice and maize showed that the PLT genes have a wide range of expression patterns, suggesting diverse biological functions. Taken together, our finding provided a perspective on the evolution differences and the functional characterizations of PLT genes in Gramineae representative crops.

Project description:The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs' biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C19-GA2ox, C20-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C19-GA2ox, and C20-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes' evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets