2023-04-03 ノースカロライナ州立大学(NCState)
このツールは、フィトフトラの190以上の形式的に記述された種と30以上の非公式な分類群に関する豊富な情報を提供し、各種の進化的な歴史、関連性、遺伝子配列データなどを含みます。また、病原体が存在するグローバルな地域、病原体が寄生する植物、病原体が植物のホストに存在する場所などの情報も提供しています。研究者は、新しい脅威種をオープンアクセスツリーに配置し、どのグループが拡大し進化しているかを確認することができます。ツールはリアルタイムで植物病気情報を更新することができ、疫学調査や次の新しい分類群を特定するために役立つとされています。
<関連情報>
- https://news.ncsu.edu/2023/04/researchers-assemble-pathogen-tree-of-life/
- https://journals.plos.org/plosone/article
新興Phytophthora種のT-BAS系統樹をオープンアクセスで公開。 An open-access T-BAS phylogeny for emerging Phytophthora species
Allison Coomber,Amanda Saville,Ignazio Carbone,Jean Beagle Ristaino
PLOS ONE Published: April 3, 2023
DOI:https://doi.org/10.1371/journal.pone.0283540
Abstract
Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.
