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      A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

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          Abstract

          Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species.Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogs and alleles of the recognized effector, facilitating durable resistance against P. infestans.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          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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            The Sequence Alignment/Map format and SAMtools

            Heng Li, Bob Handsaker, Alec Wysoker … (2009)
            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              Fast and accurate short read alignment with Burrows–Wheeler transform

              Heng Li, Richard Durbin (2009)
              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
              Article 0 comments Cited 10466 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101651677
                Journal ID (nlm-ta): Nat Plants
                Journal ID (iso-abbrev): Nat Plants
                Title: Nature plants
                ISSN (Electronic): 2055-0278
                Publication date Nihms-submitted: 27 January 2021
                Publication date (Print): 01 February 2021
                Publication date (Electronic): 11 February 2021
                Publication date PMC-release: 11 August 2021
                Volume: 7
                Issue: 2
                Pages: 198-208
                Affiliations
                [1 ]The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
                [2 ]John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
                [3 ]Phytopathology, Technical University Munich, 85354 Freising, Germany
                [4 ]School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
                [5 ]Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
                [6 ]University of Hull, Hull, HU6 7RX, UK
                [7 ]Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
                Author notes
                [* ]Corresponding author: Jonathan D. G. Jones ( jonathan.jones@ 123456tsl.ac.uk )
                [$]

                Current addresses:

                HSK: U.S. Department of Agriculture-Agricultural Research Service, Madison, WI 53706, U.S.A

                FJ: Bayer Crop Science, Chesterfield, MO, USA

                WB: The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand

                CHW: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

                TS: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P. R. China

                Article
                Manuscript ID: EMS114913
                DOI: 10.1038/s41477-021-00854-9
                PMC ID: 7116783
                PubMed ID: 33574576
                SO-VID: f5089c1b-31e0-48ff-9c26-8c6e807d5bec
                License:

                Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

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