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

期刊

JOURNAL OF EXPERIMENTAL BOTANY
卷 73, 期 13, 页码 4291-4305

出版社

OXFORD UNIV PRESS
DOI: 10.1093/jxb/erac052

关键词

Bioinformatics; bryophytes; genomics; hornworts; liverworts; Marchantia polymorpha; mosses; Physcomitrium patens; transcription factors; transcriptomics

资金

  1. Deutsche Forschungsgemeinschaft (DFG) [RE 1697/19-1]
  2. Junta de Andalucia Emergia program [EMERGIA20_00286]

向作者/读者索取更多资源

Bryophytes are valuable models for various studies in plant evolution, development, stress responses, and gametogenesis. Advances in genomics research have provided a wealth of resources, including annotations, databases, and bioinformatics tools, for better understanding bryophytes. The use of bioinformatics, phylogenetics, and comparative genomics has significantly contributed to our knowledge of bryophytes and their evolution.
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 use of bioinformatics, phylogenetics, and comparative genomics, together with the recent publication of several key bryophyte genome sequences, have greatly advanced the knowledge about bryophytes and their evolution.

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