Finding a correct species assignment for a Metschnikowia strain: insights from the genome sequencing of strain DBT012. (5th April 2023)

• Record Type: Journal Article
• Authors: Troiano, Eleonora; Larini, Ilaria; Binati, Renato L; Gatto, Veronica; Torriani, Sandra; Buzzini, Pietro; Turchetti, Benedetta; Salvetti, Elisa; Felis, Giovanna E
• Is Part Of: FEMS yeast research. Volume 23(2023)
• Publication Date: 2023-04-05
• Subjects: Metschnikowia pulcherrima clade -- whole-genome sequencing -- taxonomy -- barcodes -- split decomposition -- phylogenomics -- orthologous genes -- average nucleotide identity; Yeast -- Periodicals; Yeasts -- Periodicals; 579.562
• DOI: 10.1093/femsyr/foad024
• Languages: English
• ISSNs: 1567-1356

Abstract

Abstract: Metschnikowia pulcherrima is an important yeast species that is attracting increased interest thanks to its biotechnological potential, especially in agri-food applications. Phylogenetically related species of the so-called ' pulcherrima clade' were first described and then reclassified in one single species, which makes the identification an intriguing issue. Starting from the whole-genome sequencing of the protechnological strain Metschnikowia sp. DBT012, this study applied comparative genomics to calculate similarity with the M. pulcherrima clade publicly available genomes with the aim to verify if novel single-copy putative phylogenetic markers could be selected, in comparison with the commonly used primary and secondary barcodes. The genome-based bioinformatic analysis allowed the identification of 85 consensus single-copy orthologs, which were reduced to three after split decomposition analysis. However, wet-lab amplification of these three genes in nonsequenced type strains revealed the presence of multiple copies, which made them unsuitable as phylogenetic markers. Finally, average nucleotide identity (ANI) was calculated between strain DBT012 and available genome sequences of the M. pulcherrima clade, although the genome dataset is still rather limited. Presence of multiple copies of phylogenetic markers as well as ANI values were compatible with the recent reclassification of the clade, allowing the identification of strain DBT012 as M. pulcherrima . Abstract : Taxonomic classification of a strain of Metschnikowia pulcherrima clade using a phylogenomics approach.