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      Editing melon eIF4E associates with virus resistance and male sterility

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          Summary

          The cap‐binding protein eIF4E, through its interaction with eIF4G, constitutes the core of the eIF4F complex, which plays a key role in the circularization of mRNAs and their subsequent cap‐dependent translation. In addition to its fundamental role in mRNA translation initiation, other functions have been described or suggested for eIF4E, including acting as a proviral factor and participating in sexual development. We used CRISPR/Cas9 genome editing to generate melon eif4e knockout mutant lines. Editing worked efficiently in melon, as we obtained transformed plants with a single‐nucleotide deletion in homozygosis in the first eIF4E exon already in a T0 generation. Edited and non‐transgenic plants of a segregating F2 generation were inoculated with Moroccan watermelon mosaic virus (MWMV); homozygous mutant plants showed virus resistance, while heterozygous and non‐mutant plants were infected, in agreement with our previous results with plants silenced in eIF4E. Interestingly, all homozygous edited plants of the T0 and F2 generations showed a male sterility phenotype, while crossing with wild‐type plants restored fertility, displaying a perfect correlation between the segregation of the male sterility phenotype and the segregation of the eif4e mutation. Morphological comparative analysis of melon male flowers along consecutive developmental stages showed postmeiotic abnormal development for both microsporocytes and tapetum, with clear differences in the timing of tapetum degradation in the mutant versus wild‐type. An RNA‐Seq analysis identified critical genes in pollen development that were down‐regulated in flowers of eif4e/eif4e plants, and suggested that eIF4E‐specific mRNA translation initiation is a limiting factor for male gametes formation in melon.

          Abstract

          Resistance to MWMV is associated with eIF4E editing and eif4e knock‐out plants show a post‐meiotic, sporophytic male sterility phenotype.

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          Most cited references80

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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              Mfold web server for nucleic acid folding and hybridization prediction.

              M Zuker (2003)
              The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.
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                Author and article information

                Contributors
                m.aranda@cebas.csic.es
                Journal
                Plant Biotechnol J
                Plant Biotechnol J
                10.1111/(ISSN)1467-7652
                PBI
                Plant Biotechnology Journal
                John Wiley and Sons Inc. (Hoboken )
                1467-7644
                1467-7652
                25 July 2022
                October 2022
                : 20
                : 10 ( doiID: 10.1111/pbi.v20.10 )
                : 2006-2022
                Affiliations
                [ 1 ] Department of Stress Biology and Plant Pathology Centro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSIC Murcia Spain
                Author notes
                [*] [* ] Correspondence (Tel +34 968 396 200; Fax +34 968 396 213; email m.aranda@ 123456cebas.csic.es )
                Author information
                https://orcid.org/0000-0003-3457-9156
                https://orcid.org/0000-0002-5454-2994
                https://orcid.org/0000-0001-5989-7148
                https://orcid.org/0000-0002-8504-4541
                https://orcid.org/0000-0002-3648-5666
                https://orcid.org/0000-0001-8221-2434
                https://orcid.org/0000-0002-0828-973X
                Article
                PBI13885 PBI-00489-2022.R2
                10.1111/pbi.13885
                9491454
                35778883
                7faf402a-41e8-4b4d-9ac3-aa202971e9e7
                © 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 19 June 2022
                : 28 April 2022
                : 23 June 2022
                Page count
                Figures: 8, Tables: 1, Pages: 2022, Words: 14832
                Funding
                Funded by: Consejería de empleo, universidades y empresa, Region de Murcia
                Award ID: 2I16SA000057
                Funded by: Fundación Seneca, Region de Murcia
                Award ID: 20800/PI/18
                Funded by: Ministerio de Ciencia e Innovación , doi 10.13039/501100004837;
                Award ID: AGL2015‐65838
                Award ID: BES‐2016‐077826
                Award ID: PLEC2021‐007715
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                October 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.8 mode:remove_FC converted:21.09.2022

                Biotechnology
                cucurbit,pollen,potyvirus resistance,resistance breaking,sexual development,translation initiation

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