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An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes.

Authors
  • Fernandez-Pozo, Noe1, 2
  • Haas, Fabian B1
  • Gould, Sven B3
  • Rensing, Stefan A1, 4, 5
  • 1 Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany. , (Germany)
  • 2 Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain. , (Spain)
  • 3 Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany. , (Germany)
  • 4 BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany. , (Germany)
  • 5 LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany. , (Germany)
Type
Published Article
Journal
Journal of Experimental Botany
Publisher
Oxford University Press
Publication Date
Jul 16, 2022
Volume
73
Issue
13
Pages
4291–4305
Identifiers
DOI: 10.1093/jxb/erac052
PMID: 35148385
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools. © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: [email protected]

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