scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Xiaoxuan Hu ◽  
Chenyu Hao ◽  
Zong-Ming Cheng ◽  
Yan Zhong
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Analysis ◽  
Gene Pair ◽  
Expression Patterns ◽  
Protein Motifs ◽  
Genome Wide ◽  
Copper Zinc ◽  
Essential Enzyme ◽  
Sod Gene Family

Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.

Genome-wide identification and expression analysis of the superoxide dismutase (SOD) gene family in Salvia miltiorrhiza

Gene ◽  
2020 ◽  
Vol 742 ◽  
pp. 144603 ◽  
Author(s):  
Li-min Han ◽  
Wen-ping Hua ◽  
Xiao-yan Cao ◽  
Jun-an Yan ◽  
Chen Chen ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Analysis ◽  
Salvia Miltiorrhiza ◽  
Genome Wide ◽  
Sod Gene Family

Genome-wide characterization and expression profiling of the MAPKKK genes in Gossypium arboreum L.

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 609-622 ◽  
Author(s):  
Weidong Zhu ◽  
Wei Tan ◽  
Qiulin Li ◽  
Xiugui Chen ◽  
Junjuan Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Gossypium Arboreum ◽  
Developmental Processes ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stresses

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of MAPK cascades, which have different functions during developmental processes and stress responses. To date, there has been no systematic investigation of this gene family in the diploid cotton Gossypium arboreum L. In this study, a genome-wide survey was performed that identified 78 MAPKKK genes in G. arboreum. Phylogenetic analysis classified these genes into three subgroups: 14 belonged to ZIK, 20 to MEKK, and 44 to Raf. Chromosome location, phylogeny, and the conserved protein motifs of the MAPKKK gene family in G. arboreum were analyzed. The MAPKKK genes had a scattered genomic distribution across 13 chromosomes. The members in the same subfamily shared similar conserved motifs. The MAPKKK expression patterns were analyzed in mature leaves, stems, roots, and at different ovule developmental stages, as well as under salt and drought stresses. Transcriptome analysis showed that 76 MAPKKK genes had different transcript accumulation patterns in the tested tissues and 38 MAPKKK genes were differentially expressed in response to salt and drought stresses. These results lay the foundation for understanding the complex mechanisms behind MAPKKK-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

scholarly journals Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shutao He ◽  
Xiaomeng Hao ◽  
Shuli He ◽  
Xiaoge Hao ◽  
Xiaonan Chen
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Sweet Potato ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Promoters ◽  
Biotic And Abiotic Stress ◽  
Protein Motifs ◽  
Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

scholarly journals The Hsp70 Gene Family in Boleophthalmus pectinirostris: Genome-Wide Identification and Expression Analysis under High Ammonia Stress

Animals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 36
Author(s):  
Zhaochao Deng ◽  
Shanxiao Sun ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Large Body ◽  
Hypoxic Condition ◽  
Hsp70 Gene ◽  
High Concentration ◽  
Genome Wide ◽  
Boleophthalmus Pectinirostris ◽  
Shock Proteins

Heat shock proteins 70 have triggered a remarkable large body of research in various fishes; however, no genome-wide identification and expression analysis has been performed on the Hsp70 gene family of Boleophthalmus pectinirostris. In this study, we identified 20 Hsp70 genes within the genome of B. pectinirostris and provided insights into their response to high environmental ammonia (HEA) stress. Positive selection on stress response genes and expansion of hspa1a and hspa1a-like genes might be related to terrestrial adaptations in this species. The expression patterns of the Hsp70 gene family in the gill and liver of B. pectinirostris under HEA stress were studied by examining transcriptome data. The results showed that most Hsp70 genes were downregulated after high concentration ammonia exposure. The downregulation may be related to the hypoxic condition of the tissues.

scholarly journals Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family inGossypium

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Jingbo Zhang ◽  
Bo Li ◽  
Yang Yang ◽  
Wenran Hu ◽  
Fangyuan Chen ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Distribution Analysis ◽  
Gossypium Arboreum ◽  
Genome Wide ◽  
A Genome ◽  
Gossypium Raimondii ◽  
Sod Gene Family

Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated inArabidopsisand rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified inGossypium arboreumandGossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are distributed across 7 chromosomes inGossypium arboreumand 8 chromosomes inGossypium raimondii. Segmental duplication is predominant duplication event and major contributor for expansion of SOD gene family. Gene structure and protein structure analysis showed that SOD genes have conserved exon/intron arrangement and motif composition. Microarray-based expression analysis revealed that SOD genes have important function in abiotic stress. Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. Taken together, this study has imparted new insights into the putative functions of SOD gene family in cotton. Findings of the present investigation could help in understanding the role of SOD gene family in various aspects of the life cycle of cotton.

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