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PubPlant - a continuously updated resource for sequenced and published plant genomes

This website attempts to track sequenced plant genomes which have been published in peer-reviewed journals. It is updated on a monthly basis.
The graph below displays the quarterly increase of published sequenced plant genomes in the past decade. Light green bars  show the number of plant species having their genome published at least once. Green bars  refer to genomes which have been published at least twice and  dark green bars  to genomes published three or more times.

Cladogram

The overview diagram displays the phylogenetic position of each seed plant family, the numbers of known species and the number of species with sequenced genomes. The two major groups of seed plants are gymnosperms (classified into 8 taxonomic orders and 13 families) and angiosperms (64 taxonomic orders and over 400 families).

The cladogram views arrange published plant genomes also according to the phylogenetic position of the plant species. In contrast to the overview, here the lowest taxonomic rank taken into account is the species rank. Genomes of different subspecies or varieties are pooled into a single species. The cladograms for flowering plants and non-flowering plants (including primary algae) are displayed separately.

Resources used to evaluate the phylogenetic positions

Flowering plants
• Angiosperm Phylogeny Group, APG version IV (Angiosperm Phylogeny Group 2016)
• Phylogenomics and the rise of the angiosperms. (Zuntini et al. 2024)

Gymnosperms
• Recent advances on phylogenomics of gymnosperms and a new classification. (Yang Y et al. 2022)

Ferns and lycophytes
• A community-derived classification for extant lycophytes and ferns. (Pteridophyte Phylogeny Group 2016)

Bryophytes
• Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. (Bechteler J et al. 2023)

Algae
• AlgaeBase. Guiry MD & Guiry GM 2024. University of Galway. www.algaebase.org

Other
• Catalogue of Life (CoL). Catalogue of Life partners, Banki O et al. 2024. www.checklistbank.org
• NCBI Taxonomy. Schoch et al. 2020, National Library of Medicine (US). www.ncbi.nlm.nih.gov/taxonomy

Cross-checking scientific names

• Plants of the World Online. Govaerts et al. 2021, facilitated by the Royal Botanic Gardens, Kew. powo.science.kew.org

Timeline

The timeline views display published plant genomes according to the chronology of their first publication. If there are more than one publication for an individual plant species on the exact same date, the publication with the earliest date of acceptance is listed.
If a single publication describes several species of the same genus, the genus and spp. (for species pluralis) is displayed on the timeline and the corresponding mouse-over tooltip lists the individual species from the publication.

Criteria

The criteria for being listed as a published plant genome are...

• the publication has been released in a recognized peer-reviewed journal
• the organism belongs to an eukaryote of the Archaeplastida group (comprised of land plants, green algae, glaucophytes, red algae and Rhodelphidia)
• the genome has been fully sequenced
• the sequences have been assembled to a high quality reference genome level (e.g. scaffolds/long-read contigs and/or pseudo-chromosome level)
• the assembly underwent structural gene annotation

Terms of Use

Usage of this site follows the GDPR Privacy Notice of Plant Biotechnology Information (plantBI), IBG-4, Jülich Research Centre (FZJ). The detailed GDPR Privacy Notice is available at GDPR Privacy Notice. In accordance with that policy, we use Matomo Analytics software to collect anonymised data on visits to this site.

The views display scientific names of plant species and their phylogenetic position for illustration purpose only. They do not claim to be an authoritative source for correct plant nomenclature and classification. The curators have attempted to the best of their ability to include all published plant genomes (with some minimal criteria). Inclusion of a published plant genome should not be interpreted as an endorsement of the quality of the genome assembly.

Feel free to contact us (plabipd@fz-juelich.de) if you see any omissions or errors.

Acknowlegdements

We gratefully acknowledge the Javascript code libraries that are used on this website.