The aim of the study was to investigate the population genomics of autochtonous and putative invasive yeast species of the Hanseniaspora genus in Slovenian vineyards. We focused on the species Hanseniaspora uvarum, considered native, and Hanseniaspora opuntiae, considered invasive. Using various bioinformatics tools, we analyzed the genomic sequences of 100 isolates. In the sample, we identified 73 isolates of H. uvarum and 22 isolates of H. opuntiae. We assessed the quality of the genomes obtained through short-read sequencing technology, DNBSeq. The isolates were identified by aligning genomic nucleotide sequences to reference genomes using the SppIDer tool. We identified single nucleotide polymorphisms (SNPs) in the genomic sequences using the GATK pipeline. The genetic diversity of the isolates based on SNPs in the coding regions of the genomes was visualized using phylogenetic trees and population structure for both H. uvarum and H. opuntiae. By comparing the phylogenetic trees and population structure data, we confirmed that H. uvarum is autochthonous, while H. opuntiae is an invasive species of Hanseniaspora in Slovenia, as it is present only in the wine-growing region of Primorska. In the population of H. opuntiae, we detected the presence of hybrids with H. pseudoguilliermondii. We recorded 6 hybrid isolates out of 100 Hanseniaspora isolates, or 6 hybrid isolates out of 22 H. opuntiae isolates. For H. uvarum, we identified 4 populations, while for H. opuntiae, we found 2 populations in Slovenia. These were compared with the phylogenetic tree and linked to data on geographical location and isolation origin. We found the formation of new population structures based on the presence of hybrids, the properties of rapid genetic change, and geographic and isolation origins.
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