Additional Funding Sources
This research is supported by a grant from the Idaho State Board of Education’s Higher Education Research Council (HERC).
Abstract
Arabis alpine (Alpine rock-cress weed) is a flowering plant, native to mountainous environments of thenorthern hemisphere. We analyzed 1,454,931,853 next-generation sequencing (NGS) reads from 38 sequenced Arabis alpine mutant individuals which that were mutagenized using the chemical mutagen, ethyl methanesulfphonate (EMS). Using the BWA short reads mapper, BWA, 95% (1,387,167,658) of the NGS reads mapped to Arabis alpine reference genome version 4. Using the SAMtools variant- detection algorithm, SAMtools, we detected a total of 1,457,917 mutations, with an average of 38,366 mutations per sample. Overall, the predicted mutations include 971,252 high-quality single nucleotide polymorphisms (SNPs) and 168,783 high-quality insertions and deletions (INDELs).
In silico Detection of EMS-Induced Mutations in an Arabis alpina Population
Arabis alpine (Alpine rock-cress weed) is a flowering plant, native to mountainous environments of thenorthern hemisphere. We analyzed 1,454,931,853 next-generation sequencing (NGS) reads from 38 sequenced Arabis alpine mutant individuals which that were mutagenized using the chemical mutagen, ethyl methanesulfphonate (EMS). Using the BWA short reads mapper, BWA, 95% (1,387,167,658) of the NGS reads mapped to Arabis alpine reference genome version 4. Using the SAMtools variant- detection algorithm, SAMtools, we detected a total of 1,457,917 mutations, with an average of 38,366 mutations per sample. Overall, the predicted mutations include 971,252 high-quality single nucleotide polymorphisms (SNPs) and 168,783 high-quality insertions and deletions (INDELs).