DOI: 10.5061/dryad.q83bk3jr8
title: Single Nucleotide Polymorphisms (SNPs) data of Metarhizium species for Taxonomic Elucidation of M. anisopliae sensu lato

description: Metarhizium anisopliae (Clavicipitaceae, Hypocreales) is a globally
 distributed entomopathogenic fungus, which has been largely studied and
 used in agriculture for its potent entomopathogenicity. Since its
 taxonomic establishment as a member of Metarhizium, many closely related
 taxa have been described with highly similar morphology (cryptic species).
 A holotype specimen of M. anisopliae is not extant, and the ex-neotype
 strain (CBS 130.71) does not form a monophyletic clade with other strains,
 up to now, recognized as M. anisopliae sensu stricto. In this study, we
 have conducted an integrative taxonomic treatment of M. anisopliae sensu
 lato by including the ex-neotype strain of M. anisopliae, other unknown
 strains from our collections identified as M. anisopliae s. lat., as well
 as other known species that have been previously delimited as closely
 related but distinct to M. anisopliae. By including whole-genome
 sequencing, morphometric analysis, LC–MS based metabolomics, and virulence
 assays, we have demonstrated that M. anisopliae s. str. should also
 include M. lepidiotae (synonym), and that M. anisopliae s. str.
 differentiates from the other species of the complex by its metabolome and
 less severe entomopathogenicity. New taxa, namely M. hybridum, M.
 neoanisopliae and M. parapingshaense spp. nov., are proposed. The novel
 taxa proposed here have strong phylogenomics support, corroborated by
 fine-scale differences in the length/width of conidia/phialides, while the
 metabolomics and virulence data still largely overlap. We have also
 demonstrated via population genomics data the existence of local clonal
 lineages, particularly the one corresponding to the persistence of a
 biocontrol candidate strain that has been used in the field application
 for three years. This study showcases the utility of combining various
 data sources for accurate delimitation of species within an important
 group of fungal biocontrol agents against pest insects.
description: # Single Nucleotide Polymorphisms (SNPs) data of *Metarhizium* species for
 Taxonomic Elucidation of *M. anisopliae sensu lato*
 [https://doi.org/10.5061/dryad.q83bk3jr8](https://doi.org/10.5061/dryad.q83bk3jr8) The dataset contains 98,085 single nucleotide polymorphisms (SNPs) data of 70 strains of *Metarhizium* spp. Seventy strains of *Metarhizium* spp. were grown on a fungal culture media (PDA), and harvested for DNA extraction. The DNA were used for whole-genome sequencing using MGISeq-2000 platform. The raw data were quality controlled and mapped to a reference genome of *M. anisopliae* strain JEF-290 (Lee et al. 2019) and SNPs were inferred using GATK pipeline. Lee MR, Li D, Lee SJ, et al (2019) Use of *Metarhizum aniopliae s.l.* to control soil-dwelling longhorned tick, *Haemaphysalis longicornis*. J Invertebr Pathol 166:. [https://doi.org/10.1016/j.jip.2019.107230](https://doi.org/10.1016/j.jip.2019.107230) ## Description of the data and file structure Two files are given: 1) Metarhizium_SNPs_data.vcf.gz, 2) Metarhizium_Samples_list.xlsx. The main data file is a VCF file (Metarhizium_SNPs_data.vcf.gz) containing SNPs data of 70 samples of *Metarhizium *spp. The VCF format is consisted of two parts: headers and data. The header lines start with ‘#’ describe the upstream filtering and SNP calling procedures that were used until the final results. The last header line correspond to 79 field headers as following:  #CHROM      POS   ID    REF   ALT   QUAL  FILTER      INFO  FORMAT      &lt;*Sample1&gt;   *      .     .      . CHROM=Chromosome name where SNPs are found, POS = SNP position, ID = SNP identity, REF = Nucleotide identity of the reference genome, ALT = Alternative nucleotides as found by SNPs calling pipeline, QUAL = Quality score, FILTER = Name of filter applied (PASS means the SNPs have passed filtering criteria), INFO = Additional information (‘.’ signifies no additional information), FORMAT = Genotype information format (GT:AD:DP:GQ:PGT:PID:PL:PS = Genotype:Allele depth:Depth across samples:Genotype quality:Pre-implantation genetic testing:Physical phasing ID:Phred-scaled likelihood:Phrasing set). The information on the samples are in the file “Metarhizium_Samples_list.xlsx”.