Phytozome: a comparative platform for green plant genomics

By D. Goodstein, S. Shu, R. Howson, R. Neupane, Richard D. Hayes, Joni Fazo, T. Mitros, W. Dirks, U. Hellsten, Nicholas H. Putnam and 1 more. Nucleic Acids Res., 2011

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The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5a94cedb709e7c7e005f16297a4a3f134b79fcf9

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Citations in the corpus

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (2014, methodology): “Using the MapMan classification system, complete transcriptome annotations for multiple species (126 annotation files covering 48 species, including the complete Phytozome release v9.1; Goodstein et al. 2012) have been generated and are publicly available via the MapMan web site (http://mapman.”
Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive (2013, positive): “Phytozome [314]), metabolite (e.”
Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function[OPEN] (2018, background): “Even still, while Phytozome lists ;14 000 NLR-encoding genes, only 191 have been shown toact asRgenes (Goodstein et al., 2012).”
PANTHER version 10: expanded protein families and functions, and analysis tools (2015, background): “The increased coverage of plants in PANTHER 10.0, performed in collaboration with the Phytozome resource (11) is intended to better support genomic analysis in agricultural applications.”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “Bacterial, archaeal and fungal genomes were obtained from NCBI GenBank (21) while the other eukaryotic genomes were obtained from the UCSC Genome Browser (22), NCBI GenBank (21) and JGI Phytozome (23).”
PGDD: a database of gene and genome duplication in plants (2012, methodology): “0 21 491 Fragaria vesca Strawberry December 2010 34 809 Glycine max Soybean Release 1 (December 2008) 66 153 Lotus japonicus Lotus Release 2.5 42 399 Malus domestica Apple August 2010 57 386 Medicago truncatula Barrel medic Mt 3.5.1 (December 2010) 45 108 Musa acuminata Banana July 2012 36 542 Oryza”
Marker-Assisted Plant Breeding: Principles and Practices (2015, methodology): “The BioMart tool of the database allows customized construction of sequences and annotations of genes and/or gene families (Goodstein et al. 2012).”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, background): “Phytozome Comparative genomics of green plants Joint Genome Institute (JGI)/Center for Integrative Genomics (CIG), US (26)”
PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, methodology): “Other plant genomes were downloaded from the Phytozome genome database (27).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, methodology): “DLCpar [39] was used to reconcile these gene trees with the known species tree [28].”
JBrowse: a dynamic web platform for genome visualization and analysis (2016, background): “Sites that use JBrowse (or JBrowse-based tools) span plant genomics [19–25], animal genomics [12, 26–29], and disease-related databases [30–34].”
Genetic and Genomic Resources of Small Millets (2016, background): “Phytozome (http://phytozome.jgi.doe.gov/pz/por tal.html) is one of the important web portals developed by the United States DOE’s JGI to facilitate comparative genome analysis tools and retrieval of bulk and targeted genome sequence data from diverse plant genome projects (Goodstein et al., 2012).”
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “Each gene in a subfamily window has a hyperlink to its source database, i.e. RAP-DB, Phytozome, MaizeSequence or TAIR, so that users can refer to the detailed information of the genes.”