Genome-Wide Analysis of WRKY Gene Family and the Dynamic Responses of Key WRKY Genes Involved in Ostrinia furnacalis Attack in Zea mays

WRKY transcription factors comprise one of the largest gene families and serve as key regulators of plant defenses against herbivore attack. However, studies related to the roles of WRKY genes in response to herbivory are limited in maize. In this study, a total of 128 putative maize WRKY genes (ZmWRKYs) were identified from the new maize genome (v4). These genes were divided into seven subgroups (groups I, IIa–e, and III) based on phylogenomic analysis, with distinct motif compositions in each subgroup. Syntenic analysis revealed that 72 (56.3%) of the genes were derived from either segmental or tandem duplication events (69 and 3, respectively), suggesting a pivotal role of segmental duplication in the expansion of the ZmWRKY family. Importantly, transcriptional regulation prediction showed that six key WRKY genes contribute to four major defense-related pathways: L-phenylalanine biosynthesis II and flavonoid, benzoxazinoid, and jasmonic acid (JA) biosynthesis. These key WRKY genes were strongly induced in commercial maize (Jingke968) infested with the Asian corn borer, Ostrinia furnacalis, for 0, 2, 4, 12 and 24 h in the field, and their expression levels were highly correlated with predicted target genes, suggesting that these genes have important functions in the response to O. furnacalis. Our results provide a comprehensive understanding of the WRKY gene family based on the new assembly of the maize genome and lay the foundation for further studies into functional characteristics of ZmWRKY genes in commercial maize defenses against O. furnacalis in the field.

Download Full-text

Identification and Evolution Analysis of the JAZ Gene Family in Maize

10.21203/rs.3.rs-144271/v1 ◽

2021 ◽

Author(s):

Yang Han ◽

Dawn Luthe

Keyword(s):

Gene Expression ◽

Gene Family ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Gene Families ◽

Defense Responses ◽

Maize Genome ◽

Synteny Analysis ◽

Genetic Redundancy ◽

Duplication Events

Abstract Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

Download Full-text

Identification and evolution analysis of the JAZ gene family in maize

BMC Genomics ◽

10.1186/s12864-021-07522-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yang Han ◽

Dawn Luthe

Keyword(s):

Gene Expression ◽

Gene Family ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Gene Families ◽

Defense Responses ◽

Maize Genome ◽

Synteny Analysis ◽

Genetic Redundancy ◽

Duplication Events

Abstract Background Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds. Conclusions Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

Download Full-text

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽

10.3390/genes12121867 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1867

Author(s):

Yan Li ◽

Xiang Li ◽

Jiatong Wei ◽

Kewei Cai ◽

Hongzhi Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Cold Stress ◽

Gene Family ◽

Gene Families ◽

Regulatory Function ◽

Wrky Gene ◽

Wrky Transcription Factors ◽

Biotic Stresses ◽

Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

Download Full-text

Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family, and Interaction and Functional Analysis of TaWOX9 and TaWUS in Wheat

International Journal of Molecular Sciences ◽

10.3390/ijms21051581 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1581 ◽

Cited By ~ 3

Author(s):

Zheng Li ◽

Dan Liu ◽

Yu Xia ◽

Ziliang Li ◽

Doudou Jing ◽

...

Keyword(s):

Gene Family ◽

Oryza Sativa L ◽

Dynamic Balance ◽

Functional Characterization ◽

Gene Families ◽

Triticum Aestivum L ◽

Genome Wide ◽

A Genome ◽

Paralogous Copy ◽

Duplication Events

The WUSCHEL-related homeobox (WOX) is a family of plant-specific transcription factors, with important functions, such as regulating the dynamic balance of division and differentiation of plant stem cells and plant organ development. We identified 14 distinct TaWOX genes in the wheat (Triticum aestivum L.) genome, based on a genome-wide scan approach. All of the genes under evaluation had positional homoeologs on subgenomes A, B and D except TaWUS and TaWOX14. Both TaWOX14a and TaWOX14d had a paralogous copy on the same genome due to tandem duplication events. A phylogenetic analysis revealed that TaWOX genes could be divided into three groups. We performed functional characterization of TaWOX genes based on the evolutionary relationships among the WOX gene families of wheat, rice (Oryza sativa L.), and Arabidopsis. An overexpression analysis of TaWUS in Arabidopsis revealed that it affected the development of outer floral whorl organs. The overexpression analysis of TaWOX9 in Arabidopsis revealed that it promoted the root development. In addition, we identified some interaction between the TaWUS and TaWOX9 proteins by screening wheat cDNA expression libraries, which informed directions for further research to determine the functions of TaWUS and TaWOX9. This study represents the first comprehensive data on members of the WOX gene family in wheat.

Download Full-text

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

Horticulture Research ◽

10.1038/s41438-020-00455-1 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Zhiqiang Xia ◽

Dongmei Huang ◽

Shengkui Zhang ◽

Wenquan Wang ◽

Funing Ma ◽

...

Keyword(s):

Gene Family ◽

Genome Assembly ◽

Metabolic Pathways ◽

Repetitive Sequences ◽

Gene Families ◽

Passion Fruit ◽

Integrated Analysis ◽

Alpha Linolenic Acid ◽

Passiflora Edulis ◽

Duplication Events

AbstractPassion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that ‘alpha-linolenic acid metabolism’, ‘metabolic pathways’, and ‘secondary metabolic pathways’ were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

Download Full-text

Aldehyde Dehydrogenase 3 Is an Expanded Gene Family with Potential Adaptive Roles in Chickpea

Plants ◽

10.3390/plants10112429 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2429

Author(s):

Rocío Carmona-Molero ◽

Jose C. Jimenez-Lopez ◽

Cristina Caballo ◽

Juan Gil ◽

Teresa Millán ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Target Genes ◽

Grain Legume ◽

Breeding Programs ◽

Aldehyde Dehydrogenases ◽

Duplication Events ◽

Sequence Similarities ◽

Study Offer ◽

Comprehensive Study

Legumes play an important role in ensuring food security, improving nutrition and enhancing ecosystem resilience. Chickpea is a globally important grain legume adapted to semi-arid regions under rain-fed conditions. A growing body of research shows that aldehyde dehydrogenases (ALDHs) represent a gene class with promising potential for plant adaptation improvement. Aldehyde dehydrogenases constitute a superfamily of proteins with important functions as ‘aldehyde scavengers’ by detoxifying aldehydes molecules, and thus play important roles in stress responses. We performed a comprehensive study of the ALDH superfamily in the chickpea genome and identified 27 unique ALDH loci. Most chickpea ALDHs originated from duplication events and the ALDH3 gene family was noticeably expanded. Based on the physical locations of genes and sequence similarities, our results suggest that segmental duplication is a major driving force in the expansion of the ALDH family. Supported by expression data, the findings of this study offer new potential target genes for improving stress tolerance in chickpea that will be useful for breeding programs.

Download Full-text

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis

10.7287/peerj.preprints.2167 ◽

2016 ◽

Author(s):

Changwei Bi ◽

Yiqing Xu ◽

Qiaolin Ye ◽

Tongming Yin ◽

Ning Ye

Keyword(s):

Gene Family ◽

Zinc Finger ◽

Large Scale ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Wrky Gene ◽

Manual Search ◽

Group I ◽

Genome Wide

WRKY proteins are the plant-specific zinc finger transcription factors. They can specifically interact with the W-box ([C/T]TGAC[T/C]), which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to the present studies, plentiful WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing in Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I - III), with five subgroups (IIa - IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events played the prominent roles in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants.

Download Full-text

Genome-wide identification and characterization of WRKY gene family in Salix suchowensis

10.7287/peerj.preprints.2167v1 ◽

2016 ◽

Author(s):

Changwei Bi ◽

Yiqing Xu ◽

Qiaolin Ye ◽

Tongming Yin ◽

Ning Ye

Keyword(s):

Gene Family ◽

Zinc Finger ◽

Large Scale ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Wrky Gene ◽

Manual Search ◽

Group I ◽

Genome Wide

Download Full-text

Genome-wide identification and characterization of WRKY gene family inSalix suchowensis

PeerJ ◽

10.7717/peerj.2437 ◽

2016 ◽

Vol 4 ◽

pp. e2437 ◽

Cited By ~ 19

Author(s):

Changwei Bi ◽

Yiqing Xu ◽

Qiaolin Ye ◽

Tongming Yin ◽

Ning Ye

Keyword(s):

Gene Family ◽

Zinc Finger ◽

Large Scale ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Wrky Gene ◽

Manual Search ◽

Group I ◽

Genome Wide

WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing ofSalix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I–III), with five subgroups (IIa–IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon–intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants.

Download Full-text

Genome-Wide Identification and Characterization of WRKY Gene Family in Camelina Sativa

10.21203/rs.3.rs-36113/v1 ◽

2020 ◽

Author(s):

Yanan Song ◽

Hongli Cui ◽

Ying Shi ◽

Jinai Xue ◽

Chunli Ji ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Evolutionary Process ◽

Camelina Sativa ◽

Wrky Gene ◽

Biological Functions ◽

Genome Wide ◽

Duplication Events ◽

Characteristic Sequences

Abstract Background: WRKY gene family is one of the largest transcription factor families and WRKY proteins (WRKYs) have the complex biological functions to regulate plant metabolic processes. Although the WRKY genes were identified in many species and the functions were verified, there were no reports of Camelina sativa WRKY genes.Results: In this investigation, a total of 202 CsWRKY genes were identified and encoded 242 CsWRKYs. The CsWRKYs were further classified into three major groups according to their structure and phylogeny. The comprehensive analysis showed the characteristic sequences of CsWRKYs were conserved in the evolutionary process. In addition, the 137 segmental duplication events were the major force to expand the CsWRKY members in evolution. Compared with other reported plant species, CsWRKYs family as the largest WRKY gene family had maximum members. Furthermore, expression profiling indicated that different CsWRKY members exhibited differently in shoots and roots, and some CsWRKY genes were also up-regulated to varying degrees under salt stress in shoots.Conclusions: In this research, a detailed overview of CsWRKY family genes and expression patterns offered precious information for understanding the potential evolutionary process and the biological functions of CsWRKY genes, which was useful for the further characteristic research of CsWRKY genes and the development of high-quality Camelina sativa varieties.

Download Full-text