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      Identification of TIFY gene family in walnut and analysis of its expression under abiotic stresses

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          Abstract

          Background

          Walnuts ( Juglans regia L.) are known for their nutrient-rich nuts and are one of the important economic tree species in the world. However, due to global warming and soil salinization, walnuts suffer from various abiotic stresses. TIFY (TIF[F/Y]XG) proteins play an essential role in the growth and development of plants, signal transduction, and stress response in plants. At present, although the TIFY gene family of a number of plants has been identified and studied, how TIFY takes part in stress tolerance remains obscure and many functions of TIFY require further investigation.

          Result

          In this study, twenty-one TIFY transcription factors were identified in the walnut genome database, and they were divided into four subfamilies (TIFY, JAZ, ZML, and PPD) by bioinformatics analysis. Chromosome location revealed tandem duplication of some genes. Phylogenetic tree analysis showed JrTIFYs were closely related to the TIFY gene family of Arabidopsis thaliana ( A. thaliana). qRT-PCR (quantitative real-time PCR) analysis revealed the TIFY genes have different expression patterns in ‘Qingxiang’ and ‘Xiangling’ walnut varieties under drought, heat, and salt stress. JAZ subfamily was more expressed in different abiotic stress than other subfamilies. The expressions of JrTIFY14 under heat and salt stress were significantly higher than those under drought stress. However, the expression of JrTIFYs was not significant in ‘Xiangling’.

          Conclusion

          This study reveals the TIFY gene family plays an important role in walnuts facing abiotic stresses and provides a theoretical basis for walnut breeding.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12864-022-08416-9.

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          Most cited references53

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          BLAST+: architecture and applications

          Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              Clustal W and Clustal X version 2.0.

              The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
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                Author and article information

                Contributors
                475370128@qq.com
                3209768372@qq.com
                yangguiyan@nwsuaf.edu.cn
                jacava@163.com
                pshaobing@nwsuaf.edu.cn
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                7 March 2022
                7 March 2022
                2022
                : 23
                : 190
                Affiliations
                [1 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, Laboratory of Walnut Research Center, College of Forestry, , Northwest A & F University, ; Yangling, 712100 Shaanxi China
                [2 ]GRID grid.13291.38, ISNI 0000 0001 0807 1581, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, , Sichuan University, ; Chengdu, 610065 Sichuan China
                [3 ]GRID grid.144022.1, ISNI 0000 0004 1760 4150, Department of Foreign Languages, , Northwest A & F University, ; Yangling, 712100 Shaanxi China
                Article
                8416
                10.1186/s12864-022-08416-9
                8903722
                35255828
                b760dccb-f93b-4c6b-b04e-39a568455943
                © The Author(s) 2022

                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
                : 7 October 2021
                : 21 February 2022
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31670650
                Funded by: Ministry of Science and Technology of the People’s Republic of China
                Award ID: 2017YFD0600103-4-2
                Funded by: Northwest A & F University
                Award ID: TGZX2020-05
                Categories
                Research
                Custom metadata
                © The Author(s) 2022

                Genetics
                walnut,tify gene family,evolution,phylogeny,stress expression analysis
                Genetics
                walnut, tify gene family, evolution, phylogeny, stress expression analysis

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