Genome/transcriptome analysis of the chigger mite Leptotrombidium pallidum, a major vector for scrub typhus, with a special focus on genes more abundantly expressed in larval stage

[Display omitted] •The genome size of L. pallidum was determined to be 193 Mb and 15,842 genes were predicted.•A total of 10,885 protein-coding genes were constitutively expressed in all four stages.•A total of 4,078 genes were differentially expressed in all four stages.•Whole genome amplification is a reliable option for genome sequencing of a single tiny individual. Leptotrombidium pallidum is the major vector mite for Orientia tsutsugamushi, the causative agent of scrub typhus, in Asian countries, including Korea. Despite its medical importance, L. pallidum has little genetic information available to date. To analyze the L. pallidum genome, we extracted genomic DNA (gDNA) from a single female of a 7-generation inbred L. pallidum colony and amplified the gDNA by whole genome amplification (WGA). The resulting amplified gDNA was used to construct paired-end and mate-pair libraries that were sequenced using Illumina platforms (HiSeq2000 and MiSeq). More than 45 Gb of sequence reads from both paired-end and mate-pair libraries of the WGA gDNA were trimmed and then de novo assembled using CLC Assembly Cell v.4.0 for contig assembly and SSPACE for scaffolding. The assembly generated approximately 6,545 scaffolds with an N50 value of 92,945 and total size of ~ 193 Mb. For gene predictions, the PASA and GeneWise models were used, and ab initio gene predictions were performed independently, resulting in the prediction of 15,842 genes. RNA-Seq expression profiles revealed constitutive expression of 11,572 unique protein-coding genes in larva, 12,364 in protonymph, 12,872 in male adult, and 12,617 in female adult stages. Of the 15,842 predicted genes, 10,885 were commonly expressed through all L. pallidum stages. Genes selectively over-transcribed in the larval stage, which is when host parasitization and disease transmission occur, were further annotated, and their putative roles were discussed.