Short Communication - Biomedical Research (2019) Volume 30, Issue 2
Analyses of single nucleotide polymorphisms in Angiostrongylus cantonensis based on transcriptome sequencing.
Objective: This study aimed to reveal the SNP characters of Angiostrongylus cantonensis based on transcriptome sequencing for further using. Method: SAMtools and GATK2 were used for SNP detection. SNP frequency and transition verse transversion ratio were calculated. SNPs containing unigenes were annotated with six data bases. Results: A total number of 71,214 SNPs were predicted based on the transcriptomes of the fifth stage larvae (L5) and female adults (F). 53,019 of them were predicted as non-synonymous while another 18,195 were predicted as synonymous SNPs. Statistical analysis of all these predicted SNPs indicated that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.125. Moreover, gene function analysis including GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis of all SNPs containing unigenes were conducted for the better understanding of their functions and significances in genetics. Conclusion: The results will help us to understand the basic characters of A. cantonensis SNPs fully and the predicted SNPs will be powerful tools for species authentication development, transmission survey, as well as many other genome wide association studies (GWAS).Author(s): Liang Yu, Wenzhen Fang, Damin Luo.