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The Top 10 Plant Genome Databases

Plant Genome Database

Finding the information that you need on plant genomes is difficult when published data is spread across a vast amount of journals and the rest is unpublished. So we gathered together 10 of the best plant genome databases to make your job easier.

Brassica.info

Brassica.info database
Brassica.info brings together information from various studies to provide approximate genome size information for the various Brassica species.

Ensembl Plants

Ensembl Plants database
Ensembl Plants is a genome-centric portal for plants of scientific interest, providing statistics (for example, base pairs and genome size) and information on assembly, annotation, regulation, variation and sequences. Data can be searched by gene identifier or by BLAST sequence search.

Genome Size in Asteraceae Database

Genome Size in Asteraceae Database
The Genome Size in Asteraceae Database is an exhaustive catalogue of genome size data for the family Asteraceae, making Asteraceae genome size data easily accessible to scientists. Genome sizes are currently available for 1,219 species based on 2,768 records from 133 publications, covering approximately 5% of species, 10% of genera, 40% of tribes and 50% of subfamilies.

NCBI

NCBI database
The National Center for Biotechnology Information provides access to genomic information in order to advance science. The genome database currently comprises of 16,326 species and can be sorted by kingdom, group and subgroup.

PGDJ DNA Marker and Linkage Database

PGDJ DNA Marker and Linkage database
The Plant Genome Database Japan’s DNA Marker and Linkage Database brings together information from smaller databases and literature. Information on the organism, genome (for example, chromosome number and genome size), markers and genome specific databases can be accessed.

Phytozome

Phytozome database
Phytozome is a plant comparative genomics portal wherein families of related genes representing the modern descendants of ancestral genes are constructed at key phylogenetic nodes. Currently Phytozome provides access to 58 sequenced and annotated green plant genomes.

Plant DNA C-Values Database

Plant DNA C-Values database
Kew Royal Botanic Garden’s Plant DNA C-values database contains C-values for 8,510 angiosperm, gymnosperm, pteridopghyte, bryophyte and algal species. Users can choose between analysing C-value data across different groups of plants, or searching just part of the database by selecting the specific plant group of interest.

Plant rDNA Database

Plant rDNA database
The Plant rDNA Database comprises of data from over 600 publications and approximately 3000 plant species. It provides information on the numbers and positions of ribosomal DNA signals and their structures. Where possible, information on ploidy level, chromosome number, genome size and life cycle is also available.

PlantGDB Genome Browser

PlantGDB Genome Browser database
The Plant GDB Genome Browser displays current gene structure models and transcript evidence from spliced alignments of EST and cDNA sequences. If applicable, matched GSS contigs, community annotations, similar proteins, and microarray probes are displayed.

PTGBase

PTGBase database
PTGBase is an integrated database to study tandem repeated genes in plants. Currently PTGBase comprises of 39 plant species arrayed in 54,130 tandem repeat gene clusters containing 129,652 genes. Scientists can extract the full list of repeat genes, their coding sequences and protein sequences, as well as whole genome sets about sequenced plant species. A search function can be used to find a target gene, tandem array name and gene numbers of tandem array in a specific species.

Do you work in plant science? Check out our plant genomics events.

2 Responses to “The Top 10 Plant Genome Databases”

  1. please suggest me a database or software to download a sequence of (MORINGA OLEIFERA
    )

    Reply
  2. The Plant DNA C-values database has just been updated and now includes C-value data for 12,273 species comprising 10,770 angiosperms, 421 gymnosperms, 303 pteridophytes (246 ferns and fern allies and 57 lycophytes), 334 bryophytes, and 445 algae.

    Citation: Plant DNA C-values Database
    Leitch IJ, Johnston E, Pellicer J, Hidalgo O, Bennett MD. Plant DNA C-values database (Release 7.1, April 2019). https://cvalues.science.kew.org/

    Reply

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