Dataset Information

Dynamic genome evolution in a model fern.

ABSTRACT: The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

SUBMITTER: Marchant DB

PROVIDER: S-EPMC9477723 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Dynamic genome evolution in a model fern.

Marchant D Blaine DB Chen Guang G Cai Shengguan S Chen Fei F Schafran Peter P Jenkins Jerry J Shu Shengqiang S Plott Chris C Webber Jenell J Lovell John T JT He Guifen G Sandor Laura L Williams Melissa M Rajasekar Shanmugam S Healey Adam A Barry Kerrie K Zhang Yinwen Y Sessa Emily E Dhakal Rijan R RR Wolf Paul G PG Harkess Alex A Li Fay-Wei FW Rössner Clemens C Becker Annette A Gramzow Lydia L Xue Dawei D Wu Yuhuan Y Tong Tao T Wang Yuanyuan Y Dai Fei F Hua Shuijin S Wang Hua H Xu Shengchun S Xu Fei F Duan Honglang H Theißen Günter G McKain Michael R MR Li Zheng Z McKibben Michael T W MTW Barker Michael S MS Schmitz Robert J RJ Stevenson Dennis W DW Zumajo-Cardona Cecilia C Ambrose Barbara A BA Leebens-Mack James H JH Grimwood Jane J Schmutz Jeremy J Soltis Pamela S PS Soltis Douglas E DE Chen Zhong-Hua ZH

Nature plants 20220901 9

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-g ...[more]

PMID: 36050461

Similar Datasets

Project description:BACKGROUND: Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae). RESULTS: The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. CONCLUSION: By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.

Dataset Information

Dynamic genome evolution in a model fern.

Publications

Dynamic genome evolution in a model fern.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets