Phytozome: a comparative platform for green plant genomics

Abstract

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.

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…Protein-coding region identification and gene prediction were conducted through a combination of homology-based prediction, de novo prediction, and transcriptome-based prediction methods. Proteins from seven plant genomes (Arabidopsis thaliana, Carica papaya, Glycine max, G. raimondii, Populus trichocarpa, Theobroma cacao and Vitis vinifera) were downloaded from Phytozome (Release 9.1) 53 . Protein sequences were aligned to the assembly using TblastN 54 with an E-value cutoff of 1e-5.…”

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

“…The tobacco genes were taken from the TOBFAC database (Rushton et al 2008b). The soybean genes were taken from phytozome (Goodstein et al 2012) and named arbitrarily except for previously published genes. The evolutionary history was inferred using the neighbor-joining method.…”

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

“…38 Phylogenetic relationships and evolutionary features of ATG4s and ATG8s indicate the conserved mechanism of autophagosome biogenesis in the plant kingdom. To determine the cross-kingdom ATG4 processing properties, we designed synthetic substrates containing AtATG8a, 30 tomato ATG8 (SlATG8), ScAtg8, and HsLC3A and investigated the processing efficiency by ATG4s from different species in vitro and in vivo.…”