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Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis

Kim, Ju Hyeon, Roh, Jong Yul, Kwon, Deok Ho, Kim, Young Ho, Yoon, Kyungjae A, Yoo, Seungil, Noh, Seung-Jae, Park, Junhyung, Shin, E-hyun, Park, Mi-Yeoun, Lee, Si Hyeock
Parasites & vectors 2014 v.7 no.1 pp. 279
Leptotrombidium, Orientia tsutsugamushi, chiggers, evolution, flow cytometry, genome, quantitative polymerase chain reaction, reliability, scrub typhus, vector competence
BACKGROUND: Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly. METHOD: The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results. RESULTS: The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. CONCLUSIONS: The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence.