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      The bZIP gene family in watermelon: genome-wide identification and expression analysis under cold stress and root-knot nematode infection

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          Abstract

          The basic leucine zipper (bZIP) family transcription factors play crucial roles in regulating plant development and stress response. In this study, we identified 62 ClabZIP genes from watermelon genome, which were unevenly distributed across the 11 chromosomes. These ClabZIP proteins could be classified into 13 groups based on the phylogenetic relationships, and members in the same group showed similar compositions of conserved motifs and gene structures. Transcriptome analysis revealed that a number of ClabZIP genes have important roles in the melatonin (MT) induction of cold tolerance. In addition, some ClabZIP genes were induced or repressed under red light (RL) or root-knot nematode infection according to the transcriptome data, and the expression patterns of several ClabZIP genes were further verified by quantitative real-time PCR, revealing their possible roles in RL induction of watermelon defense against nematode infection. Our results provide new insights into the functions of different ClabZIP genes in watermelon and their roles in response to cold stress and nematode infection.

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          The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

          Steven Cannon, Arvind Mitra, Andrew Baumgarten … (2004)
          Background Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. Results Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. Conclusions Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.
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            Roles of melatonin in abiotic stress resistance in plants.

            Na Zhang, Qianqian Sun, Haijun Zhang … (2015)
            In recent years melatonin has emerged as a research highlight in plant studies. Melatonin has different functions in many aspects of plant growth and development. The most frequently mentioned functions of melatonin are related to abiotic stresses such as drought, radiation, extreme temperature, and chemical stresses. This review mainly focuses on the regulatory effects of melatonin when plants face harsh environmental conditions. Evidence indicates that environmental stress can increase the level of endogenous melatonin in plants. Overexpression of the melatonin biosynthetic genes elevates melatonin levels in transgenic plants. The transgenic plants show enhanced tolerance to abiotic stresses. Exogenously applied melatonin can also improve the ability of plants to tolerate abiotic stresses. The mechanisms by which melatonin alleviates abiotic stresses are discussed.
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              Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice.

              Aashima Nijhawan, Mukesh Jain, Akhilesh K. Tyagi … (2008)
              The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.
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                Author and article information

                Contributors
                Yong Zhou:
                ORCID: http://orcid.org/0000-0002-8432-6678
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (pmc): PeerJ
                Journal ID (publisher-id): PeerJ
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 16 October 2019
                Publication date Collection: 2019
                Volume: 7
                Electronic Location Identifier: e7878
                Affiliations
                [1 ]Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University , Nanchang, Jiangxi, China
                [2 ]Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University , Nanchang, Jiangxi, China
                [3 ]State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University , Yangling, Shaanxi, China
                [4 ]Department of Biochemistry and Molecular Biology, College of Bioscience and Bioengineering, Jiangxi Agricultural University , Nanchang, Jiangxi, China
                Author information
                http://orcid.org/0000-0002-8432-6678
                Article
                Publisher ID: 7878
                DOI: 10.7717/peerj.7878
                PMC ID: 6800529
                PubMed ID: 31637131
                SO-VID: 40b757d6-ccdd-4fb3-a51c-62635f966a75
                Copyright © © 2019 Yang et al.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                Date received : 12 February 2019
                Date accepted : 12 September 2019
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31560572
                Funded by: Natural Science Foundation of Jiangxi Province, China
                Award ID: 20171BAB214030
                Funded by: Youth Science Foundation of Jiangxi Provincial Department of Education, China
                Award ID: GJJ160393 and GJJ180172
                Funded by: Jiangxi Province Postdoctoral Science Foundation, China
                Award ID: 2016KY06
                This work was funded by the National Natural Science Foundation of China (31560572), Natural Science Foundation of Jiangxi Province, China (20171BAB214030), the Youth Science Foundation of Jiangxi Provincial Department of Education, China (GJJ160393 and GJJ180172), and the Jiangxi Province Postdoctoral Science Foundation, China (2016KY06). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Agricultural Science
                Subject: Biochemistry
                Subject: Bioinformatics
                Subject: Genomics
                Subject: Plant Science

                Keywords: watermelon (citrullus lanatus),bzip transcription factor,cold stress,genome-wide analysis,root-knot nematode,expression pattern
                Data availability:
                Keywords: watermelon (citrullus lanatus), bzip transcription factor, cold stress, genome-wide analysis, root-knot nematode, expression pattern

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