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      The Genomic Impact of Mycoheterotrophy in Orchids

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          Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy has occurred independently in many major lineages of land plants, most frequently in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. A comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two completely mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed the unexpected retention of several genes associated with photosynthetic activities. In addition to these selected retentions, the analysis of their expression profiles showed that many orthologs had inverted underground/aboveground expression ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism but was associated primarily with function losses rather than metabolic innovations.

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          Most cited references 91

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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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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              Fast and sensitive protein alignment using DIAMOND.

              The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.

                Author and article information

                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                09 June 2021
                : 12
                1Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk , Gdańsk, Poland
                2Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, CNRS, INRAE, Univ Evry , Orsay, France
                3Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay , Orsay, France
                4Sorbonne Université, CNRS, EPHE, Muséum National d’Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité , Paris, France
                Author notes

                Edited by: Susann Wicke, Humboldt University of Berlin, Germany

                Reviewed by: Maria D. Logacheva, Skolkovo Institute of Science and Technology, Russia; Sean W. Graham, University of British Columbia, Canada; Craig Barrett, West Virginia University, United States

                *Correspondence: Etienne Delannoy, etienne.delannoy@ 123456inrae.fr

                These authors have contributed equally to this work

                This article was submitted to Plant Systematics and Evolution, a section of the journal Frontiers in Plant Science

                Copyright © 2021 Jąkalski, Minasiewicz, Caius, May, Selosse and Delannoy.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 4, Tables: 3, Equations: 0, References: 91, Pages: 16, Words: 0
                Funded by: Narodowe Centrum Nauki 10.13039/501100004281
                Funded by: Agence Nationale de la Recherche 10.13039/501100001665
                Plant Science
                Original Research


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