The Top 10 Plant Genome Databases
Posted 10th October 2016 by Jane Williams
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you need on plant genomes is difficult when published data is spread across a vast amount of journals and the rest is unpublished.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.
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.
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.
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.
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 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.
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.
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.
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 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.