Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes

Abstract Background Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. Results In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. Conclusions These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

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Evolution, Expression and Functional Analysis of Cultivated Allotetraploid Cotton DIR Genes

10.21203/rs.3.rs-100138/v1 ◽

2020 ◽

Author(s):

Zhengwen Liu ◽

Xingfen Wang ◽

Zhengwen Sun ◽

Yan Zhang ◽

Chengsheng Meng ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Rapid Evolution ◽

Gene Clusters ◽

Vital Role ◽

Fiber Development ◽

Rna Seq ◽

Evolutionarily Conserved ◽

Cell Wall Development ◽

Tandem Duplications

Abstract Background: Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton.Results: In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls.Conclusions: These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

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Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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

10.7287/peerj.preprints.27606v1 ◽

2019 ◽

Author(s):

Yongbin Wang ◽

Zhenfeng Jiang ◽

Zhenxiang Li ◽

Yuanling Zhao ◽

Weiwei Tan ◽

...

Keyword(s):

Glycine Max ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Pcr Analysis ◽

Rna Seq ◽

Biological Functions ◽

Conserved Domain ◽

Genome Wide ◽

Development Processes

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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Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family

Scientific Reports ◽

10.1038/s41598-021-96854-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Katie Emelianova ◽

Andrea Martínez Martínez ◽

Lucia Campos-Dominguez ◽

Catherine Kidner

Keyword(s):

Gene Duplication ◽

Gene Family ◽

Genome Size ◽

Stress Responses ◽

Chalcone Synthase ◽

Expression Profiles ◽

Rna Seq ◽

Biotic And Abiotic Stress ◽

Chalcone Synthase Gene ◽

Study Species

AbstractBegonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.

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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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The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

Agronomy ◽

10.3390/agronomy10030401 ◽

2020 ◽

Vol 10 (3) ◽

pp. 401

Author(s):

Zhen Liu ◽

Yuhui Liu ◽

Jeffrey A. Coulter ◽

Baoyun Shen ◽

Yuanming Li ◽

...

Keyword(s):

Abiotic Stress ◽

Solanum Tuberosum ◽

Gene Family ◽

Stress Responses ◽

Anthocyanin Biosynthesis ◽

Solanum Tuberosum L ◽

Interaction Network ◽

Purifying Selection ◽

Rna Seq ◽

Specific Expression

WD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (Solanum tuberosum L.). In the present study, 178 potato WD40 (StWD40) genes were identified and their distribution on chromosomes, gene structure, and conserved motifs were assessed. According to their structural and phylogenetic protein features, these 178 StWD40 genes were classified into 14 clusters and 10 subfamilies. Collinearity analysis showed that segmental duplication events played a major role in the expansion of the StWD40 gene family. Synteny analysis indicated that 45 and 23 pairs of StWD40 genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively, and that these gene pairs evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-specific expression and abiotic stress-responsive StWD40 genes in doubled monoploid potato (DM). Furthermore, we further analyzed the WD40 genes might be involved in anthocyanin biosynthesis and drought stress in tetraploid potato cultivars based on RNA-seq data. In addition, a protein interaction network of two homologs of Arabidopsis TTG1, which is involved in anthocyanin biosynthesis, was constructed to identify proteins that might be related to anthocyanin biosynthesis. The result showed that there were 112 pairs of proteins interacting with TTG1, with 27 being differentially expressed in pigmented tissues. This study indicates that WD40 proteins in potato might be related to anthocyanin biosynthesis and abiotic stress responses.

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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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Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.)

10.21203/rs.3.rs-108242/v1 ◽

2020 ◽

Author(s):

Yucong Xie ◽

Karl Ravet ◽

Stephen Pearce

Keyword(s):

Triticum Aestivum ◽

Plant Defense ◽

Gene Family ◽

Common Wheat ◽

Stress Responses ◽

Functional Characterization ◽

Gene Clusters ◽

High Rate ◽

Tandem Gene Duplication ◽

Duplication Events

Abstract Background Bowman-Birk inhibitors (BBI) are a family of serine-type protease inhibitors that modulate endogenous plant proteolytic activities during different phases of development. They also inhibit exogenous proteases as a component of plant defense mechanisms, and their overexpression can confer resistance to phytophagous herbivores and multiple fungal and bacterial pathogens. Dicot BBIs are multifunctional, with a “double-headed” structure containing two separate inhibitory loops that can bind and inhibit trypsin and chymotrypsin proteases simultaneously. By contrast, monocot BBIs have a non-functional chymotrypsin inhibitory loop, although they have undergone internal duplication events giving rise to proteins with multiple BBI domains.Results We used a Hidden Markov Model (HMM) profile-based search to identify 57 BBI genes in the common wheat (Triticum aestivum L.) genome. The BBI genes are unevenly distributed, with large gene clusters in the telomeric regions of homeologous group 1 and 3 chromosomes that likely arose through a series of tandem gene duplication events. The genomes of wheat progenitors also contain contiguous clusters of BBI genes, suggesting this family underwent expansion before the domestication of common wheat. However, the BBI gene family varied in size among different cultivars, showing this family remains dynamic. Because of these expansions, the BBI gene family is larger in wheat than other monocots such as maize, rice and Brachypodium.We found BBI proteins in common wheat with intragenic homologous duplications of cysteine-rich functional domains, including one protein with four functional BBI domains. This diversification may expand the spectrum of target substrates. Expression profiling suggests that some wheat BBI proteins may be involved in regulating endogenous proteases during grain development, while others were induced in response to biotic and abiotic stresses, suggesting a role in plant defense.Conclusions Genome-wide characterization reveals that the BBI gene family in wheat is subject to a high rate of homologous tandem duplication and deletion events, giving rise to a diverse set of encoded proteins. This information will facilitate the functional characterization of individual wheat BBI genes to determine their role in wheat development and stress responses and their potential application in breeding.

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

10.7287/peerj.preprints.27606 ◽

2019 ◽

Author(s):

Yongbin Wang ◽

Zhenfeng Jiang ◽

Zhenxiang Li ◽

Yuanling Zhao ◽

Weiwei Tan ◽

...

Keyword(s):

Glycine Max ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Pcr Analysis ◽

Rna Seq ◽

Biological Functions ◽

Conserved Domain ◽

Genome Wide ◽

Development Processes

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Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-03206-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Wenjing Hu ◽

Qiaoyu Ren ◽

Yali Chen ◽

Guoliang Xu ◽

Yexiong Qian

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Regulatory Network ◽

Abiotic Stresses ◽

Interaction Analysis ◽

Expression Patterns ◽

Wrky Transcription Factor ◽

Rna Seq

Abstract Background The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize. Results In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network. Conclusions Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.

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