In recent years, high-throughput next-generation sequencing (NGS) techniques have provided fascinating opportunities to understand the biology of non-model organisms, especially insect species. The decrease in sequencing costs and extensive sequencing services from NGS providers has brought many entomologists to be involved in genome sequencing. However, poor planning can lead to extremely fragmented genome assemblies which prevents high quality gene annotation and other desired analyses. Insect genomes can be problematic to assemble, due to combinations of high polymorphism, inability to breed for genome homozygosity, and small physical sizes limiting the quantity of DNA able to be isolated from a single individual. Given to the rapid development of host resistance to multiple classes of insecticides, it is indispensable to study the comprehensive genomic information of insects. Recent advances in sequencing technology and assembly strategies can able to fetch breakthroughs in deciphering the genetic information of insects. Here, we present the cost effective high throughput genome sequencing and assembly strategies for insect species in respects to taxonomy, evolutionary history, immune response, drug development, insect host-virus interactions and pest management etc.

Leptotrombidium pallidum is the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. To understand the molecular mechanism of L. pallidum, we sequenced the whole genome using Illumina sequencing technology. Totally four genomic libraries with different insert sizes ranging from 280 bp to 8 kb were used to generate 45.1 Gb of genome in the combination of paired-end and mate-pairs sequencing reads. Quality filtering and correction of paired-end reads for very small and/or bad-quality sequences yielded 26.9 Gb of high-quality sequences, which are used to estimate the genome size as 175 Mbusing kmer methods and assembled into a 193.7 Mb genomic sequence scaffolds with N50 length of 92,945 bp. Furthermore, 94% of CEGMA completeness score were obtained from genome scaffold assembly. To facilitate gene annotation, we used a combination of de novo and homology based tools to predict gene models in the chigger mite genome. A combination of evidence-based and de novo approaches predicted 15,842 high-confidence protein-coding genes with an average transcript length of 1,511 bp and 2.4 exons per gene which corresponds to about 12.4% total gene length. Bacterial endosymbiosis are very common in mite species and can range from mutualistic to pathogenic associations. Henceforth, the endosymbionts in L. pallidum were predicted using the NCBI microbial draft genomes and mitochondrial genome. Besides, this L. pallidum draft genome can be used as a significant reference for comparative genomic studies across mite species.