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      Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response

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          Abstract

          Background

          Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube ( Ziziphus jujuba Mill.) has not been investigated.

          Results

          In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature ( ZjPG1) and drought stresses ( ZjBNM7, ZjBNM8, and ZjBNM9).

          Conclusions

          These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12864-022-08907-9.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            TBtools - an integrative toolkit developed for interactive analyses of big biological data

            Chengjie Chen, Hao Chen, Yi Zhang … (2020)
            The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
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              Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

              Ivica Letunic, Peer Bork (2021)
              The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
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                Author and article information

                Contributors
                Xingang Li: xingangle@nwsuaf.edu.cn
                Journal
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 6 October 2022
                Publication date PMC-release: 6 October 2022
                Publication date Collection: 2022
                Volume: 23
                Electronic Location Identifier: 692
                Affiliations
                [1 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, , Northwest A&F University, ; Yangling, 712100 Shaanxi China
                [2 ]GRID grid.410727.7, ISNI 0000 0001 0526 1937, Agricultural Genomics Institute at Shenzhen, , Chinese Academy of Agricultural Sciences, ; Shenzhen, 518116 Guangdong China
                Article
                Publisher ID: 8907
                DOI: 10.1186/s12864-022-08907-9
                PMC ID: 9541082
                PubMed ID: 36203136
                SO-VID: 43f1dd57-6669-4b5c-8245-39651de49e1e
                Copyright © © The Author(s) 2022
                License:

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                Date received : 28 July 2022
                Date accepted : 26 September 2022
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 32001343
                Award Recipient :
                Funded by: National Key Research and Development Program of China
                Award ID: 2018YFD1000607
                Award Recipient :
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © The Author(s) 2022

                ScienceOpen disciplines: Genetics
                Keywords: ziziphus jujuba mill,burp domain-containing protein,gene expression,abiotic stress,fruit development
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: ziziphus jujuba mill, burp domain-containing protein, gene expression, abiotic stress, fruit development

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