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A high-throughput SNP discovery strategy for RNA-seq data.

Yun Zhao1, Ke Wang1, Wen-Li Wang1

  • 1Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, China.

BMC Genomics
|March 1, 2019
PubMed
Summary
This summary is machine-generated.

Optimizing single nucleotide polymorphism (SNP) discovery from RNA-seq data is crucial. The Trinity assembler, GATK SNP caller, and 150bp paired-end reads provide 100% accurate SNP identification in plants.

Keywords:
GATKPaired-end read lengthRNA-seqSingle nucleotide polymorphism (SNP)Trinity

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Single nucleotide polymorphisms (SNPs) are vital molecular markers in genetics and breeding.
  • Next-generation sequencing (NGS) enables high-throughput SNP discovery, but reliable methods are lacking.
  • Optimal assemblers and SNP callers for accurate SNP prediction from NGS data remain unknown.

Purpose of the Study:

  • To comprehensively compare different strategies for SNP prediction from RNA-seq data.
  • To identify the optimal combination of assemblers, SNP callers, and read lengths for accurate SNP discovery.
  • To establish a reliable and efficient strategy for SNP identification in plant transcriptomes.

Main Methods:

  • RNA-seq data from peach and mandarin peel tissue were analyzed.
  • Five assemblers (Trinity, IDBA, oases, SOAPdenovo, Trans-abyss) and two SNP callers (GATK, GBS) were evaluated.
  • Paired-end read lengths of 125bp and 150bp were compared.
  • Predicted SNPs were validated against authentic SNPs identified by PCR cloning and sequencing.

Main Results:

  • SNP prediction strategies yielded divergent results.
  • A 150bp paired-end read length significantly reduced false positive SNPs compared to 125bp.
  • Trinity and GATK demonstrated superior performance over other methods.
  • The combination of Trinity, GATK, and 150bp reads achieved 100% accuracy in SNP discovery for both peach and mandarin.

Conclusions:

  • A reliable and efficient strategy (Trinity-GATK with 150bp reads) for SNP discovery from RNA-seq data was identified.
  • This optimized strategy achieved 100% accuracy in peach and mandarin.
  • The findings may be applicable to SNP discovery in a wide range of plant species and other organisms.