Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species

TY - JOUR

T1 - Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species

AU - Lindner, Melanie

AU - Gawehns, Fleur

AU - te Molder, Sebastiaan

AU - Visser, Marcel E.

AU - van Oers, Kees

AU - Laine, Veronika N.

N1 - 7306, AnE; Data archiving: data in NCBI and Dryad

PY - 2022

Y1 - 2022

N2 - The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulphite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulphite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non-model species, which often lack genomic references. Here, we used whole-genome bisulphite sequencing (WGBS) data from four female great tits (Parus major) to evaluate the performance of seven tools for SNP calling from bisulphite sequencing data. We used SNPs from whole-genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (Bis-SNP), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.

AB - The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulphite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulphite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but there is no independent evaluation of such tools for non-model species, which often lack genomic references. Here, we used whole-genome bisulphite sequencing (WGBS) data from four female great tits (Parus major) to evaluate the performance of seven tools for SNP calling from bisulphite sequencing data. We used SNPs from whole-genome resequencing data of the same samples as baseline SNPs to assess common performance metrics like sensitivity, precision, and the number of true positive, false positive, and false negative SNPs for the full range of variant and genotype quality values. We found clear differences between the tools in either optimizing precision (Bis-SNP), sensitivity (biscuit), or a compromise between both (all other tools). Overall, the choice of SNP caller strongly depends on which performance parameter should be maximized and whether ascertainment bias should be minimized to optimize downstream analysis, highlighting the need for studies that assess such differences.

KW - DNA methylation

KW - great tit (Parus major)

KW - single nucleotide polymorphism

KW - whole-genome sequencing

KW - NIOO

KW - Plan_S-Compliant-OA

UR - https://www.ncbi.nlm.nih.gov/sra/SRR15365281/

UR - https://www.ncbi.nlm.nih.gov/sra/SRR15365284/

UR - https://www.ncbi.nlm.nih.gov/sra/SRR15410225/

UR - https://www.ncbi.nlm.nih.gov/sra/SRR15410232/

UR - https://doi.org/10.5061/dryad.ttdz08kzt

UR - https://github.com/MLindner0/lindner_et_al-2021-mer-snps_from_bs_data

U2 - 10.1111/1755-0998.13493

DO - 10.1111/1755-0998.13493

M3 - Article

C2 - 34435438

AN - SCOPUS:85114328387

SN - 1755-098X

VL - 22

SP - 834

EP - 846

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 2

ER -