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      The chromosome-scale genome and the genetic resistance machinery against insect herbivores of the Mexican toloache, Datura stramonium

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          Abstract

          Plant resistance refers to the heritable ability of plants to reduce damage caused by natural enemies, such as herbivores and pathogens, either through constitutive or induced traits like chemical compounds or trichomes. However, the genetic architecture—the number and genome location of genes that affect plant defense and the magnitude of their effects—of plant resistance to arthropod herbivores in natural populations remains poorly understood. In this study, we aimed to unveil the genetic architecture of plant resistance to insect herbivores in the annual herb Datura stramonium (Solanaceae) through quantitative trait loci mapping. We achieved this by assembling the species’ genome and constructing a linkage map using an F 2 progeny transplanted into natural habitats. Furthermore, we conducted differential gene expression analysis between undamaged and damaged plants caused by the primary folivore, Lema daturaphila larvae. Our genome assembly resulted in 6,109 scaffolds distributed across 12 haploid chromosomes. A single quantitative trait loci region on chromosome 3 was associated with plant resistance, spanning 0 to 5.17 cM. The explained variance by the quantitative trait loci was 8.44%. Our findings imply that the resistance mechanisms of D. stramonium are shaped by the complex interplay of multiple genes with minor effects. Protein–protein interaction networks involving genes within the quantitative trait loci region and overexpressed genes uncovered the key role of receptor-like cytoplasmic kinases in signaling and regulating tropane alkaloids and terpenoids, which serve as powerful chemical defenses against D. stramonium herbivores. The data generated in our study constitute important resources for delving into the evolution and ecology of secondary compounds mediating plant–insect interactions.

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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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            Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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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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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                February 2024
                19 December 2023
                19 December 2023
                : 14
                : 2
                : jkad288
                Affiliations
                Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México , Mexico City 04510, Mexico
                Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Lomma, Alnarp 230 53, Sweden
                Escuela Nacional de Estudios Superiores (ENES), Universidad Nacional Autónoma de México (UNAM), Campus Morelia , Morelia, Michoacán 8701, Mexico
                Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México , Mexico City 04510, Mexico
                Author notes
                Corresponding author: Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico. Email: farfan@ 123456unam.mx
                Corresponding author: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 5, Lomma, Alnarp 230 53, Sweden. Email: ivan.de.la.cruz.arguello@ 123456slu.se

                Conflicts of interest The authors declare no conflicts of interest.

                Author information
                https://orcid.org/0000-0001-5829-8338
                Article
                jkad288
                10.1093/g3journal/jkad288
                10849327
                38113048
                999cda0a-bca8-4b7a-9f9a-a4bb45b5d35d
                © 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
                : 21 September 2023
                : 11 December 2023
                : 09 January 2024
                Page count
                Pages: 15
                Funding
                Funded by: CONACyT, DOI 10.13039/501100003141;
                Award ID: 283799
                Funded by: Fronteras de la Ciencia;
                Funded by: CONACyT Mexico;
                Award ID: 2016-2/1527
                Funded by: PAPIIT-DGAPA;
                Award ID: AG200717
                Categories
                Investigation
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                Genetics/136

                Genetics
                genomics of plant defense,herbivory,plant resistance,solanaceae,quantitative trait loci (qtls) of plant resistance,plant genetics and genomics

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