ArticleGenome biology and evolution2021
A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 39 citations in OpenAlex.
- The post-fertilization archegonium gene network of seedless plants contributed to the origin of seeds.Nature communications · 2026Article
- Sex-type specification and meristem development in fern gametophytes.Discover developmental biology · 2026Review
- Non-seed plant research in the spotlight.Biology open · 2025Article
- Cellular basis of ABA-induced de novo meristem formation and sex-type conversion in Ceratopteris gametophytes.The Plant journal : for cell and molecular biology · 2025Article
- The genome of the vining fernProceedings of the National Academy of Sciences of the United States of America · 2025Article
- A BRASSINOSTEROID INSENSISTIVE 1 receptor kinase ortholog is required for sex determination in Ceratopteris richardii.The Plant cell · 2025Article
- HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.BMC bioinformatics · 2025Article
- Functions and Regulation of HAM Family Genes in Meristems During Gametophyte and Sporophyte Generations.Plant, cell & environment · 2025Review
- The cellular basis of meristem development in fern gametophytes.Biochemical Society transactions · 2025Review
- Single cell-derived multicellular meristem: insights into male-to-hermaphrodite conversion and de novo meristem formation in Ceratopteris.Development (Cambridge, England) · 2025Article
- A conserved GRAS-domain transcriptional regulator links meristem indeterminacy to sex determination in Ceratopteris gametophytes.Current biology : CB · 2024Article
- Conserved autophagy and diverse cell wall composition: unifying features of vascular tissues in evolutionarily distinct plants.Annals of botany · 2024Article
- Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii.Annals of botany · 2024Article
- Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae.Plants (Basel, Switzerland) · 2024Article
- Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered FernGenes · 2023Article
- Cell Division and Meristem Dynamics in Fern Gametophytes.Plants (Basel, Switzerland) · 2023Article
- Cell growth dynamics in two types of apical meristems in fern gametophytes.The Plant journal : for cell and molecular biology · 2022Article
- Positional cues and cell division dynamics drive meristem development and archegonium formation in Ceratopteris gametophytes.Communications biology · 2022Article
- The biology ofeLife · 2022Article
- Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing.International journal of molecular sciences · 2022Review
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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