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Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.

Dan Wang1,2, Liu Yang1, Chao Ning1,2

  • 1National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.

BMC Genomics
|October 13, 2021
PubMed
Summary
This summary is machine-generated.

Using breed-specific reference sequences (BS-ref) significantly improves mitochondrial DNA (mtDNA) mapping accuracy and efficiency in next-generation sequencing (NGS) analyses. This approach enhances SNP calling accuracy for diverse populations.

Keywords:
MappingMitochondrial genomePigReference sequenceSNP calling

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Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Reference sequences are crucial for next-generation sequencing (NGS) mapping quality in genome analyses.
  • Existing reference genomes often lack the full genetic diversity of a species due to population divergence.
  • Optimizing mitochondrial genome (mitogenome) reference sequences can improve alignment accuracy and efficiency.

Purpose of the Study:

  • To compare the accuracy of mitogenome alignment and SNP calling using three types of reference sequences: commonly used (CU-ref), breed-specific (BS-ref), and sample-specific (SS-ref).
  • To identify the optimal reference sequence for mitochondrial DNA (mtDNA) analyses in specific populations.

Main Methods:

  • High-throughput sequencing of four pigs from three breeds.
  • Mapping sequencing reads to CU-ref, BS-ref, and SS-ref.
  • Evaluating mapping ratio, coverage depth, and running time.
  • Performing single nucleotide polymorphism (SNP) calling using 18 strategies with SAMtools, VarScan, and GATK on BS-ref mapped data.

Main Results:

  • Mapping reads to BS-ref yielded the largest mapping ratio and deepest coverage without increasing running time.
  • All 18 SNP calling strategies demonstrated high specificity and sensitivity when using BS-ref.
  • High accuracy of mitogenome alignment with BS-ref was indicated by the low requirement for specific SNP calling tools and parameters.

Conclusions:

  • The choice of reference sequence significantly impacts mitogenome alignment in NGS data.
  • Breed-specific reference sequences (BS-ref) are optimal for mitogenome analyses of specific populations.
  • This study offers a refined perspective for processing NGS data, particularly for mtDNA analyses.