Genome-wide identification of expansin gene family in barley and drought-related expansins identification based on RNA-seq

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

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Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton

BMC Plant Biology ◽

10.1186/s12870-020-02362-y ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Li-Min Lv ◽

Dong-Yun Zuo ◽

Xing-Fen Wang ◽

Hai-Liang Cheng ◽

You-Ping Zhang ◽

...

Keyword(s):

Cell Growth ◽

Gene Family ◽

Fibre Cell ◽

Expansin Gene ◽

Genome Wide

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Genome-wide identification and expression analysis of the expansin gene family in tomato

Molecular Genetics and Genomics ◽

10.1007/s00438-015-1133-4 ◽

2015 ◽

Vol 291 (2) ◽

pp. 597-608 ◽

Cited By ~ 18

Author(s):

Yongen Lu ◽

Lifeng Liu ◽

Xin Wang ◽

Zhihui Han ◽

Bo Ouyang ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Expansin Gene ◽

Genome Wide

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Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

Author(s):

Yongbin Wang ◽

Lei Ling ◽

Zhenfeng Jiang ◽

Weiwei Tan ◽

Zhaojun Liu ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Genomic Data ◽

Evolutionary Analysis ◽

Rna Seq ◽

Plant Growth And Development ◽

Genome Wide ◽

Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

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Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)

Planta ◽

10.1007/s00425-018-3020-9 ◽

2018 ◽

Vol 249 (3) ◽

pp. 815-829 ◽

Cited By ~ 9

Author(s):

Lu Hou ◽

Zhiyong Zhang ◽

Suhan Dou ◽

Yadong Zhang ◽

Xiaoming Pang ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Chinese Jujube ◽

Expansin Gene ◽

Genome Wide ◽

Ziziphus Jujuba

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Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in Brassica napus

Molecules ◽

10.3390/molecules24101985 ◽

2019 ◽

Vol 24 (10) ◽

pp. 1985 ◽

Cited By ~ 3

Author(s):

Xiaoke Ping ◽

Tengyue Wang ◽

Na Lin ◽

Feifei Di ◽

Yangyang Li ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Vital Role ◽

Gene Family Evolution ◽

Rna Seq ◽

Chain Reaction ◽

Element Analysis ◽

Cis Element ◽

Genome Wide ◽

Polymerase Chain

Lignin is an important biological polymer in plants that is necessary for plant secondary cell wall ontogenesis. The laccase (LAC) gene family catalyzes lignification and has been suggested to play a vital role in the plant kingdom. In this study, we identified 45 LAC genes from the Brassica napus genome (BnLACs), 25 LAC genes from the Brassica rapa genome (BrLACs) and 8 LAC genes from the Brassica oleracea genome (BoLACs). These LAC genes could be divided into five groups in a cladogram and members in same group had similar structures and conserved motifs. All BnLACs contained hormone- and stress- related elements determined by cis-element analysis. The expression of BnLACs was relatively higher in the root, seed coat and stem than in other tissues. Furthermore, BnLAC4 and its predicted downstream genes showed earlier expression in the silique pericarps of short silique lines than long silique lines. Three miRNAs (miR397a, miR397b and miR6034) target 11 BnLACs were also predicted. The expression changes of BnLACs under series of stresses were further investigated by RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR). The study will give a deeper understanding of the LAC gene family evolution and functions in B. napus.

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Genome-Wide Analysis, Evolutionary History and Response of ALMT Family to Phosphate Starvation in Brassica napus

International Journal of Molecular Sciences ◽

10.3390/ijms22094625 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4625

Author(s):

Ismail Din ◽

Ihteram Ullah ◽

Wei Wang ◽

Hao Zhang ◽

Lei Shi

Keyword(s):

Brassica Napus ◽

Gene Family ◽

P Availability ◽

Rna Seq ◽

Soil P ◽

Genome Wide ◽

Low Phosphorus ◽

Leaf Tissues ◽

Identification And Characterization

Low phosphorus (P) availability is one of the major constraints to plant growth, particularly in acidic soils. A possible mechanism for enhancing the use of sparsely soluble P forms is the secretion of malate in plants by the aluminum-activated malate transporter (ALMT) gene family. Despite its significance in plant biology, the identification of the ALMT gene family in oilseed rape (Brassica napus; B. napus), an allotetraploid crop, is unveiled. Herein, we performed genome-wide identification and characterization of ALMTs in B. napus, determined their gene expression in different tissues and monitored transcriptional regulation of BnaALMTs in the roots and leaves at both a sufficient and a deficient P supply. Thirty-nine BnaALMT genes were identified and were clustered into five branches in the phylogenetic tree based on protein sequences. Collinearity analysis revealed that most of the BnaALMT genes shared syntenic relationships among BnaALMT members in B. napus, which suggested that whole-genome duplication (polyploidy) played a major driving force for BnaALMTs evolution in addition to segmental duplication. RNA-seq analyses showed that most BnaALMT genes were preferentially expressed in root and leaf tissues. Among them, the expression of BnaC08g13520D, BnaC08g15170D, BnaC08g15180D, BnaC08g13490D, BnaC08g13500D, BnaA08g26960D, BnaC05g14120D, BnaA06g12560D, BnaC05g20630D, BnaA07g02630D, BnaA04g15700D were significantly up-regulated in B. napus roots and leaf at a P deficient supply. The current study analyzes the evolution and the expression of the ALMT family in B. napus, which will help in further research on their role in the enhancement of soil P availability by secretion of organic acids.

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The Hsp70 Gene family in Solanum Lycopersicum; Genome-wide Identification and Expression Analysis Under Heavy Metals Stresses

10.21203/rs.3.rs-546628/v1 ◽

2021 ◽

Author(s):

Ahmed El Sappah ◽

Manzar Abbas ◽

Ahmed S. Elrys ◽

Vivek Yadav ◽

Hamza H. El-Sappah ◽

...

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Gene Ontology ◽

Gene Family ◽

Candidate Genes ◽

Solanum Lycopersicum ◽

Expression Analysis ◽

Hsp70 Gene ◽

Rna Seq ◽

Genome Wide

Abstract The Heat shock protein-70 (Hsp70) gene family is one of the protective mechanisms; however, it has not been widely studied in tomatoes. Therefore, the current study provides the first report genome-wide analysis of the Hsp70 gene family in tomato (Solanum lycopersicum L.) under five heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+) stresses. We identified 23 candidate genes of the Hsp70 gene family based on the PF00012 domain through bioinformatics studies, including gene structure, distribution, synteny, phylogenetic tree, protein-protein interactions, gene ontology, and previous RNA-seq data analysis followed by qRT-PCR analysis. Based on the phylogenetic analysis, the 23 candidate genes were classified into five subfamilies where the same subfamily contains similar SlHsp70 proteins. Many pairs of SlHsp70 gene duplications have appeared, consisting of tandem and segment duplication. In addition, analysis of previous RNA-seq besides the gene ontology gave us significant evidence about the vital roles of these genes during tomato development and growth. The SlHsp7s showed different responses, which were varied depend on different plant tissues and types of heavy metal. Some of the SlHsp70s were up-regulated after heavy metal exposure, such as Cd2+/SlHsp70-23 and Mn2+/ SlHsp70-8. Still, down-regulated others such as Fe2+/ SlHsp70-18. Finally, our gene expression analysis revealed the significant roles of the Hsp70s, especially, SlHsp70- 3, SlHsp70-8, SlHsp70-12, SlHsp70-19, and SlHsp70-23, with the different heavy metals treatments.

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Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

PeerJ ◽

10.7717/peerj.10934 ◽

2021 ◽

Vol 9 ◽

pp. e10934

Author(s):

Ruihua Wang ◽

Taili Han ◽

Jifeng Sun ◽

Ligong Xu ◽

Jingjing Fan ◽

...

Keyword(s):

Gene Family ◽

Brassica Rapa ◽

Expression Patterns ◽

Structural Evolution ◽

Amino Acid Residues ◽

Rna Seq ◽

Cis Acting ◽

Genome Wide ◽

Genome Triplication

Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

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