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

BMC Genomics
Yun ZhaoChang-Jie Xu

Abstract

Single nucleotide polymorphisms (SNP) have been applied as important molecular markers in genetics and breeding studies. The rapid advance of next generation sequencing (NGS) provides a high-throughput means of SNP discovery. However, SNP development is limited by the availability of reliable SNP discovery methods. Especially, the optimum assembler and SNP caller for accurate SNP prediction from next generation sequencing data are not known. Herein we performed SNP prediction based on RNA-seq data of peach and mandarin peel tissue under a comprehensive comparison of two paired-end read lengths (125 bp and 150 bp), five assemblers (Trinity, IDBA, oases, SOAPdenovo, Trans-abyss) and two SNP callers (GATK and GBS). The predicted SNPs were compared with the authentic SNPs identified via PCR amplification followed by gene cloning and sequencing procedures. A total of 40 and 240 authentic SNPs were presented in five anthocyanin biosynthesis related genes in peach and in nine carotenogenic genes in mandarin. Putative SNPs predicted from the same RNA-seq data with different strategies led to quite divergent results. The rate of false positive SNPs was significantly lower when the paired-end read length was 150 bp compared with 125 bp. ...Continue Reading

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Citations

Apr 21, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Erin E Heyer, James Blackburn
Jun 9, 2020·Critical Reviews in Biotechnology·Ramaswamy ManimekalaiMallikarjuna Kandalam
Dec 21, 2019·Journal of Experimental & Clinical Cancer Research : CR·Yi DingXianqun Fan
Oct 11, 2020·International Journal of Molecular Sciences·Ashok Babadev JagtapGurmukh Singh Johal
Jun 13, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Chenyu WangTao Yang

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Datasets Mentioned

BETA
SRP155137

Methods Mentioned

BETA
genotyping
RNA-seq
PCR
deamination
Assay

Software Mentioned

BCFtools
freebayes
SAMtools
Trans
SOAPsnp
GATK
GBS
Trinity
IDBA
PowerPoint

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