Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum)
subject: k-mer-based method, taxon-specific k-mers, plant taxon identification, raw sequencing reads, Solanum lycopersicum
description: Polymerase chain reaction and different barcoding methods commonly used for plant identification from metagenomics samples are based on the amplification of a limited number of pre-selected barcoding regions. These methods are often inapplicable due to DNA degradation, low amplification success or low species discriminative power of selected genomic regions. Here we introduce a method for the rapid identification of plant taxon-specific k-mers, that is applicable for the fast detection of plant taxa directly from raw sequencing reads without aligning, mapping or assembling the reads. We identified more than 800 Solanum lycopersicum specific k-mers (32 nucleotides in length) from 42 different chloroplast genome regions using the developed method. We demonstrated that identified k-mers are also detectable in whole genome sequencing raw reads from S. lycopersicum. Also, we demonstrated the usability of taxon-specific k-mers in artificial mixtures of sequences from closely related species. Developed method offers a novel strategy for fast identification of taxon-specific genome regions and offers new perspectives for detection of plant taxa directly from sequencing raw reads.
creator: Kairi Raime, Maido Remm
source: Frontiers in Plant Science
publisher: Frontiers Media S.A.
date: 2018
language: EN
identifier: DOI: 10.3389/fpls.2018.00006
coverage: Plant culture