Genome-Wide GRAS Gene Family Analysis Reveals the Classification, Expression Profiles in Melon (Cucumis melo L.)

Abstract Background: GRAS proteins comprise a large family of transcription factors that experienced extensive replication, and play important roles in many aspects of growth regulatory and environmental signals. However, limited information was available about the GRAS genes in sea buckthorn of Elaeagnaceae. We perform a genome-wide investigation into the expansion model and tissue expression profiling of sea buckthorn GRAS genes based on the comparative genomes methods.Results: In this study, 62 sea buckthorn GRAS (HrGRAS) genes were identified and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were further classified into nine subgroups and three HrGRASs did not belong to any of the subfamilies according to their phylogenetic features. HrGRAS genes tend to have a representative GRAS domain, few introns and unevenly distributed on chromosomes. Collinear homology dotplot and the median synonymous substitution sites of collinearity blocks distinguished gene pairs with different duplication models and found that segmental duplication was the main driver of the GRAS gene family expansion in sea buckthorn, followed by whole genome duplication and tandem duplication. The all gene pairs from the different duplication models may experience strong purifying selection pressure during evolution processes according to the Ka/Ks ratios. Expression profiles derived from transcriptome data exhibited distinct expression patterns of HrGRAS genes in various tissues and fruit developmental stages. The interaction network analysis of HrGRAS protein found that some HrGRAS proteins interacted with more proteins and retained more copies in sea buckthorn, which indicate that the products of these genes play more important roles in the growth and development of sea buckthorn.Conclusions: Sea buckthorn GRAS gene family was first comprehensively analyzed in this study. This systematic analysis provided a foundation to further understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.

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Genome-wide identification, characterization, interaction network and expression profile of GRAS gene family in sweet orange (Citrus sinensis)

Scientific Reports ◽

10.1038/s41598-018-38185-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Hua Zhang ◽

Limin Mi ◽

Long Xu ◽

Changxiu Yu ◽

Chen Li ◽

...

Keyword(s):

Gene Family ◽

Expression Profile ◽

Citrus Sinensis ◽

Sweet Orange ◽

Interaction Network ◽

Genome Wide ◽

Gras Gene

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Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01873-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhixuan Du ◽

Qitao Su ◽

Zheng Wu ◽

Zhou Huang ◽

Jianzhong Bao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Tandem Repeats ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Regulatory Elements ◽

Genome Wide ◽

Comprehensive Information ◽

Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽

10.7717/peerj.10617 ◽

2021 ◽

Vol 9 ◽

pp. e10617

Author(s):

Jie Li ◽

Xinhao Liu ◽

Qingmei Wang ◽

Junyan Sun ◽

Dexian He

Keyword(s):

Gene Family ◽

Seed Development ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Seed Formation ◽

Aphid Infestation ◽

Genome Wide ◽

A Genome ◽

Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

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