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      Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion

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          Abstract

          The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao ( Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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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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              The Sequence Alignment/Map format and SAMtools

              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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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                September 2023
                20 June 2023
                20 June 2023
                : 13
                : 9
                : jkad125
                Affiliations
                Department of Viticulture and Enology, University of California Davis , Davis 95616, CA, USA
                Genome Center, University of California Davis , 95616 Davis, CA, USA
                Department of Viticulture and Enology, University of California Davis , Davis 95616, CA, USA
                Sustainable Perennial Crops Laboratory, USDA/ARS , Beltsville 20705, MD, USA
                Sustainable Perennial Crops Laboratory, USDA/ARS , Beltsville 20705, MD, USA
                Mars La Chola (MLCH), Mars Inc. , Guayaquil 090103, Ecuador
                Mars Center for Cocoa Science, Mars Inc., Fazenda Almirante , Caixa Postal 55, Itajuípe, BA, CEP 45630-000, Brazil
                Mars Digital Technologies, Mars Inc. , Chicago 60642, IL, USA
                Sustainable Perennial Crops Laboratory, USDA/ARS , Beltsville 20705, MD, USA
                Mars Wrigley Plant Sciences Laboratory, Mars Inc. , 95616 Davis, CA, USA
                Department of Viticulture and Enology, University of California Davis , Davis 95616, CA, USA
                Sustainable Perennial Crops Laboratory, USDA/ARS , Beltsville 20705, MD, USA
                Author notes
                Corresponding author: Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA; Genome Center, University of California Davis, 95616 Davis, CA, USA. Email: dacantu@ 123456ucdavis.edu

                Conflicts of interest The author(s) declare no conflict of interest.

                Author information
                https://orcid.org/0000-0003-2643-9209
                https://orcid.org/0000-0002-4858-1508
                Article
                jkad125
                10.1093/g3journal/jkad125
                10468315
                37337677
                e69e9376-fa69-4266-b685-fbae99560c87
                © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 27 April 2023
                : 30 May 2023
                : 17 July 2023
                Page count
                Pages: 18
                Funding
                Funded by: Mars-USDA TRUST FUND COOPERATIVE AGREEMENT;
                Award ID: 58-6038-6-004
                Funded by: Mars-UC Davis agreement;
                Award ID: A18-1698
                Funded by: USDA, DOI 10.13039/100000199;
                Categories
                Fungal Genetics and Genomics
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140

                Genetics
                cacao frosty pod,genome evolution,mating type loci,pathogenomics,theobroma cacao
                Genetics
                cacao frosty pod, genome evolution, mating type loci, pathogenomics, theobroma cacao

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