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Single‐nucleotide polymorphism discovery in L eptographium longiclavatum , a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing
Author(s) -
Ojeda Dario I.,
Dhillon Braham,
Tsui Clement K. M.,
Hamelin Richard C.
Publication year - 2014
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12191
Subject(s) - biology , genotyping , single nucleotide polymorphism , genetics , genome , genomics , population genomics , population , reference genome , sequence assembly , whole genome sequencing , computational biology , genotype , gene , transcriptome , demography , gene expression , sociology
Single‐nucleotide polymorphisms ( SNP s) are rapidly becoming the standard markers in population genomics studies; however, their use in nonmodel organisms is limited due to the lack of cost‐effective approaches to uncover genome‐wide variation, and the large number of individuals needed in the screening process to reduce ascertainment bias. To discover SNP s for population genomics studies in the fungal symbionts of the mountain pine beetle ( MPB ), we developed a road map to discover SNP s and to produce a genotyping platform. We undertook a whole‐genome sequencing approach of Leptographium longiclavatum in combination with available genomics resources of another MPB symbiont, Grosmannia clavigera . We sequenced 71 individuals pooled into four groups using the Illumina sequencing technology. We generated between 27 and 30 million reads of 75 bp that resulted in a total of 1, 181 contigs longer than 2 kb and an assembled genome size of 28.9 Mb (N 50 = 48 kb, average depth = 125x). A total of 9052 proteins were annotated, and between 9531 and 17 266 SNP s were identified in the four pools. A subset of 206 genes (containing 574 SNP s, 11% false positives) was used to develop a genotyping platform for this species. Using this roadmap, we developed a genotyping assay with a total of 147 SNP s located in 121 genes using the Illumina ® Sequenom iPLEX Gold. Our preliminary genotyping (success rate = 85%) of 304 individuals from 36 populations supports the utility of this approach for population genomics studies in other MPB fungal symbionts and other fungal nonmodel species.