Systematic analysis of the OSCA family members in Vigna radiata and their involvement in osmotic resistance

Abstract Background Mung bean (Vigna radiata) is a warm-season legume crop and belongs to papilionoid subfamily of the Fabaceae. China is the leading producer of mung bean in the world. It has significant economic and health benefits and is a promising species with broad adaptation and high tolerance to stress environments. The OSCA family members play an important role in the modulation of hypertonic stresses, such as drought and salinity. However, genome-wide analysis of the OSCA family in mung bean is lacking. Results We identified a total of 13 OSCA genes in the mung bean genome and named according to their homology with AtOSCAs. All the OACAs were phylogenetically splitted into four clades. Phylogenetic relationship and synteny analyses showed that the VrOSCAs in mung bean and soybean shared a relatively conserved evolutionary history. In addition, three duplicated VrOSCA gene pairs were identified and the duplicated VrOSCA shave mainly undergone purifying selection pressure during evolution. Protein domain, motif and transmembrane analysis indicated that most of the VrOSCAs shared similar structures with their homologs. The expression pattern showed that exception of VrOSCA2.1, the other 12VrOSCAs were up-regulated expression under treatment with ABA, PEG and NaCl, among which VrOSCA1.4 showed the largest increased expression levels. The duplicated genes VrOSCA2.1/VrOSCA2.2 showed divergence expression, which might experience functionalization during subsequent evolution. The expression profiles under ABA, PEG and NaCl stress revealed a functional divergence of VrOSCA genes, which agreed with the cis-acting elements analysis in the promoter of VrOSCA genes. Conclusions Collectively, the study provided a systematic analysis of the VrOSCA family in mung bean. Our results would lay an important foundation for functional and evolutionary analysis of VrOSCAs, and provide promising genes for further investigation of abiotic stress tolerance in mung bean.

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Genome-wide analysis of OSCA gene family members in Vigna radiata and their involvement in the osmotic response

BMC Plant Biology ◽

10.1186/s12870-021-03184-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lili Yin ◽

Meiling Zhang ◽

Ruigang Wu ◽

Xiaoliang Chen ◽

Fei Liu ◽

...

Keyword(s):

Gene Family ◽

Vigna Radiata ◽

Mung Bean ◽

Expression Profiles ◽

Family Members ◽

Regulatory Elements ◽

Evolutionary Analysis ◽

Genome Wide Analysis ◽

Gene Pairs ◽

Genome Wide

Abstract Background Mung bean (Vigna radiata) is a warm-season legume crop and belongs to the papilionoid subfamily of the Fabaceae family. China is the leading producer of mung bean in the world. Mung bean has significant economic and health benefits and is a promising species with broad adaptation ability and high tolerance to environmental stresses. OSCA (hyperosmolality-gated calcium-permeable channel) gene family members play an important role in the modulation of hypertonic stress, such as drought and salinity. However, genome-wide analysis of the OSCA gene family has not been conducted in mung bean. Results We identified a total of 13 OSCA genes in the mung bean genome and named them according to their homology with AtOSCAs. All the OSCAs were phylogenetically split into four clades. Phylogenetic relationship and synteny analyses showed that the VrOSCAs in mung bean and soybean shared a relatively conserved evolutionary history. In addition, three duplicated VrOSCA gene pairs were identified, and the duplicated VrOSCAs gene pairs mainly underwent purifying selection pressure during evolution. Protein domain, motif and transmembrane analyses indicated that most of the VrOSCAs shared similar structures with their homologs. The expression pattern showed that except for VrOSCA2.1, the other 12 VrOSCAs were upregulated under treatment with ABA, PEG and NaCl, among which VrOSCA1.4 showed the largest increased expression levels. The duplicated genes VrOSCA2.1/VrOSCA2.2 showed divergent expression, which might have resulted in functionalization during subsequent evolution. The expression profiles under ABA, PEG and NaCl stress revealed a functional divergence of VrOSCA genes, which agreed with the analysis of cis-acting regulatory elements in the promoter regions of VrOSCA genes. Conclusions Collectively, the study provided a systematic analysis of the VrOSCA gene family in mung bean. Our results establish an important foundation for functional and evolutionary analysis of VrOSCAs and identify genes for further investigation of their ability to confer abiotic stress tolerance in mung bean.

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Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae

International Journal of Genomics ◽

10.1155/2020/7146701 ◽

2020 ◽

Vol 2020 ◽

pp. 1-15

Author(s):

Gongbo Lv ◽

Chunmiao Jiang ◽

Tiantian Liang ◽

Yayi Tu ◽

Xiaojie Cheng ◽

...

Keyword(s):

Gene Family ◽

Aspergillus Oryzae ◽

Expression Profiles ◽

Protein Domain ◽

Growth Stages ◽

Sugar Transporter ◽

Motif Analysis ◽

Comprehensive Overview ◽

Systematic Analysis ◽

Functional Features

Sugar transporter (SUT) genes are associated with multiple physiological and biochemical processes in filamentous fungi, such as the response to various stresses. However, limited systematic analysis and functional information of SUT gene family have been available on Aspergillus oryzae (A. oryzae). To investigate the potential roles of SUTs in A. oryzae, we performed an integrative analysis of the SUT gene family in this study. Based on the conserved protein domain search, 127 putative SUT genes were identified in A. oryzae and further categorized into eight distinct subfamilies. The result of gene structure and conserved motif analysis illustrated functional similarities among the AoSUT proteins within the same subfamily. Additionally, expression profiles of the AoSUT genes at different growth stages elucidated that most of AoSUT genes have high expression levels at the stationary phase while low in the adaptive phase. Furthermore, expression profiles of AoSUT genes under salt stress showed that AoSUT genes may be closely linked to salt tolerance and involved in sophisticated transcriptional process. The protein-protein interaction network of AoSUT propounded some potentially interacting proteins. A comprehensive overview of the AoSUT gene family will offer new insights into the structural and functional features as well as facilitate further research on the roles of AoSUT genes in response to abiotic stresses.

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Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms21010351 ◽

2020 ◽

Vol 21 (1) ◽

pp. 351

Author(s):

Liru Cao ◽

Pengyu Zhang ◽

Xiaomin Lu ◽

Guorui Wang ◽

Zhenhua Wang ◽

...

Keyword(s):

Drought Tolerance ◽

Abiotic Stresses ◽

Family Members ◽

Proline Content ◽

Protein Domain ◽

Bimolecular Fluorescence Complementation ◽

Systematic Analysis ◽

Over Expression ◽

Core Elements ◽

Positive Correlations

OSCAs are hyperosmolality-gated calcium-permeable channel proteins. In this study, two co-expression modules, which are strongly associated with maize proline content, were screened by weighted correlation network analysis, including three ZmOSCA family members. Phylogenetic and protein domain analyses revealed that 12 ZmOSCA members were classified into four classes, which all contained DUF221 domain. The promoter region contained multiple core elements responsive to abiotic stresses and hormones. Colinear analysis revealed that ZmOSCAs had diversified prior to maize divergence. Most ZmOSCAs responded positively to ABA, PEG, and NaCl treatments. ZmOSCA2.3 and ZmOSCA2.4 were up-regulated by more than 200-fold under the three stresses, and showed significant positive correlations with proline content. Yeast two-hybrid and bimolecular fluorescence complementation indicated that ZmOSCA2.3 and ZmOSCA2.4 proteins interacted with ZmEREB198. Over-expression of ZmOSCA2.4 in Arabidopsis remarkably improved drought resistance. Moreover, over-expression of ZmOSCA2.4 enhanced the expression of drought tolerance-associated genes and reduced the expression of senescence-associated genes. We also found that perhaps ZmOSCA2.4 was regulated by miR5054.The results provide a high-quality molecular resource for selecting resistant breeding, and lay a foundation for elucidating regulatory mechanism of ZmOSCA under abiotic stresses.

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Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ ◽

10.7717/peerj.11052 ◽

2021 ◽

Vol 9 ◽

pp. e11052

Author(s):

Sushma Naithani ◽

Daemon Dikeman ◽

Priyanka Garg ◽

Noor Al-Bader ◽

Pankaj Jaiswal

Keyword(s):

Gene Ontology ◽

Abiotic Stress ◽

Differential Expression ◽

Functional Annotation ◽

Expression Profiles ◽

Abiotic Stress Tolerance ◽

Family Members ◽

Gene Families ◽

Structural Features ◽

Response Expression

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

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Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.632155 ◽

2021 ◽

Vol 12 ◽

Author(s):

Muhammad Waheed Riaz ◽

Jie Lu ◽

Liaqat Shah ◽

Liu Yang ◽

Can Chen ◽

...

Keyword(s):

Triticum Aestivum ◽

Gene Family ◽

Expression Profiles ◽

Functional Divergence ◽

Triticum Aestivum L ◽

Vital Role ◽

Systematic Analysis ◽

Wheat Seedlings ◽

A Genome ◽

Duplication Events

The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.

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