title: Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis.
abstract: 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.
  
  
  METHODS
  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.
authors.forename: Ju Hyeon
authors.initials: JH
authors.lastname: Kim
authors.forename: Jong Yul
authors.initials: JY
authors.lastname: Roh
authors.forename: Deok Ho
authors.initials: DH
authors.lastname: Kwon
authors.forename: Young Ho
authors.initials: YH
authors.lastname: Kim
authors.forename: Kyungjae A
authors.initials: KA
authors.lastname: Yoon
authors.forename: Seungil
authors.initials: S
authors.lastname: Yoo
authors.forename: Seung-Jae
authors.initials: SJ
authors.lastname: Noh
authors.forename: Junhyung
authors.initials: J
authors.lastname: Park
authors.forename: E-Hyun
authors.initials: EH
authors.lastname: Shin
authors.forename: Mi-Yeoun
authors.initials: MY
authors.lastname: Park
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea. shlee22@snu.ac.kr.
authors.forename: Si Hyeock
authors.initials: SH
authors.lastname: Lee
mesh_terms: D000818:Animals; D003001:Cloning, Molecular; D015723:Gene Library; D059646:Genome Size; D016133:Polymerase Chain Reaction / Q000379:methods*; D013045:Species Specificity; D014324:Trombiculidae / Q000235:genetics*