How to Conduct Phylogenetic Endoglucanase (egl) Inference Using the Reference Ralstonia solanacearum Species Complex Curated Database.

Abstract

The phytopathogenic Ralstonia solanacearum species complex (RSSC) was recently divided into three distinct species, after long-standing research. In 2005, phylotype-based classification was introduced to mark the beginning of DNA-based taxonomy within the RSSC. Within each phylotype, the "sequevar" classification further refines subspecies designations, based on variations in the endoglucanase (egl) gene sequence, and these sequevars are unique to each phylotype. Whereas a single-gene approach such as egl is less comprehensive than multi-gene or whole-genome analysis, egl phylogenetic inferences provides a robust and cost-effective RSSC strain typing assessment. Curated and public egl reference sequences are essential for accurate sequevar assignment of unknown RSSC strains and help prevent issues related to incorrect sequevar assignment or trimming errors that could compromise the quality of RSSC diversity research. Our research sought to fill the gap by providing such a database to the RSSC community (https://doi.org/10.18167/DVN1/CUWA5P or https://tinyurl.com/sequevar), along with a proper methodology to perform reproducible and reliable phylogenetic inferences for publishing sequevar assignation.