Underwater CAM photosynthesis elucidated by Isoetes genome

Wickell, David; Kuo, Li‐Yaung; Yang, Hsiao‐Pei; Ashok, Amra Dhabalia; Irisarri, Iker; Dadras, Armin; Vries, Sophie de; Vries, Jan de; Huang, Yao‐Moan; Li, Zheng; Barker, Michael S.; Hartwick, Nolan; Michael, Todd P.; Li, Fay‐Wei

doi:10.1038/s41467-021-26644-7

Cited by 82 publications

(97 citation statements)

References 143 publications

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“…In addition to the Ceratopteris richardii genome, there are many other fern genomes that have been recently published or will be available soon. Several heterosporous fern and lycophyte genomes have been published in the last few years, including the heterosporous ferns Azolla filiculoides and Salvinia cucullata ( Li et al, 2018 ), and the heterosporous lycophytes Selaginella moellendorffii ( Banks et al, 2011 ), S. lepidophylla ( VanBuren et al, 2018 ), and Isoëtes taiwanensis ( Wickell et al, 2021 ). In the near future, several additional homosporous fern genomes will be available, including Adiantum capillus-veneris (Polypodiales), Alsophila spinulosa (Cyatheales), Dipteris conjugata (Gleichinales), Ptisana robusta (Marattiales), Huperzia asiatica and Diphasiastrum complanata (Lycopodiales; Drs.…”

Section: Plant Genome Structure and Evolutionmentioning

confidence: 99%

The biology of C. richardii as a tool to understand plant evolution

Kinosian

Wolf

2022

eLife

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The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.

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Section: Plant Genome Structure and Evolutionmentioning

confidence: 99%

The biology of C. richardii as a tool to understand plant evolution

Kinosian

Wolf

2022

eLife

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“…By contrast, structure and dynamics of seed-free plant genomes are little understood (2,5,21). Comparison of the few available high-quality genomes suggests that overall genomic architectures of seed-free and seed plant genomes likely differ, which may be a consequence of their divergent genome dynamics (5,22–24).…”

Section: Introductionmentioning

confidence: 99%

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Kirbis¹,

Rahmatpour

Dong

et al. 2022

Preprint

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Background: While genome evolutionary processes of seed plants are intensively investigated, very little is known about seed-free plants in this respect. Here, we use one of the largest groups of seed-free plants, the mosses, and newly generated chromosome-scale genome assemblies to investigate three poorly known aspects of genome dynamics and their underlying processes in seed-free plants: (i) genome size variation, (ii) genomic collinearity/synteny, and (iii) gene set differentiation. Results: Comparative genomic analyses on the model moss Physcomitrium (Physcomitrella) patens and two genomes of Funaria hygrometrica reveal that, like in seed plants, genome size change (approx. 140 Mbp) is primarily due to transposable element expansion/contraction. Despite 60 million years of divergence, the genomes of P. patens and F. hygrometrica show remarkable chromosomal stability with the majority of homologous genes located in conserved collinear blocks. In addition, both genomes contain a relatively large set of lineage-specific genes with no detectible homologs in the other speciesʼ genome, suggesting a highly dynamic gene space fueled by the process of de novo gene birth and loss rather than by gene family diversification/duplication. Conclusions: These, combined with previous observations suggest that genome dynamics in mosses involves the coexistence of a collinear homologous and a highly dynamic species-specific gene sets. Besides its significance for understanding genome evolution, the presented chromosome-scale genome assemblies will provide a foundation for comparative genomic and functional studies in the Funariaceae, a family holding historical and contemporary model taxa in the evolutionary biology of mosses.

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“…Beauv.) Spring [ 32 ], and Isoëtes taiwanensis De Vol [ 33 ], numerous mysteries of lycophytes have gradually been uncovered in recent years.…”

Section: Introductionmentioning

confidence: 99%

Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes

Chen

Wang

Shu

et al. 2022

Genes

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Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.

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Underwater CAM photosynthesis elucidated by Isoetes genome

Cited by 82 publications

References 143 publications

The biology of C. richardii as a tool to understand plant evolution

The biology of C. richardii as a tool to understand plant evolution

Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space

Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes

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