Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species

Abstract

Sarcophaga peregrina (flesh fly) is a frequently found fly species in Palaearctic, Oriental, and Australasian regions that can be used to estimate minimal postmortem intervals important for forensic investigations. Despite its forensic importance, the genome information of S. peregrina has not been fully described. Therefore, we generated a comprehensive gene expression dataset using RNA sequencing and carried out de novo assembly to characterize the S. peregrina transcriptome. We obtained precise sequence information for RNA transcripts using two different methods. Based on primary sequence information, we identified sets of assembled unigenes and predicted coding sequences. Functional annotation of the aligned unigenes was performed using the UniProt, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. As a result, 26,580,352 and 83,221 raw reads were obtained using the Illumina MiSeq and Pacbio RS II Iso-Seq sequencing applications, respectively. From these reads, 55,730 contigs were successfully annotated. The present study provides the resulting genome information of S. peregrina, which is valuable for forensic applications.

Temporal Expression Profiles Reveal Potential Targets during Postembryonic Development of Forensically Important Sarcophaga peregrina (Diptera: Sarcophagidae)

“…Sarcophaga peregrina is also related to parasitic diseases and intestinal infectious diseases in humans and livestock, and it can cause myiasis [ 13 , 18 , 19 ]. Due to its medical and forensic significance, a comprehensive gene expression dataset was generated using RNA sequencing, and de novo assembly was performed to characterize the S. peregrina transcriptome [ 20 ]. In a previous study, we attempted to identify four genes ( Hsp90 , A-alpha , AFP , and AFBP ) that exhibit developmental, stage-specific expression patterns during pupation [ 21 ].…”

Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies

“…Although S. peregrina is of ecological, medical and forensic importance, there are few genomic resources for the family Sarcophagidae (Agrawal, Bajpai, Tewari, & Kurahashi, 2010; Martinson et al., 2019), seriously hindering investigation of the specific mechanisms of biological phenomena from the perspective of genomics, transcriptomics and epigenetics. Fortunately, with the emergence of next‐generation sequencing technology, genomics and transcriptomic analyses have been recently developed for dipteran flies (Anstead et al., 2015; dos Santos et al., 2014; Kim et al., 2018; Scott et al., 2014), including a recently published genome assembly of S. bullata (Martinson et al., 2019), which serves as a reference for molecular studies of related species. Due to the constraint of short Illumina reads in assembling highly contiguous genomes, the combination of SMRT (single molecule real‐time) sequencing and chromosome conformation capture (Hi‐C) can anchor scaffolds into chromosomal levels (Belton et al., 2012; Roberts, Carneiro, & Schatz, 2013), leading to high‐quality and highly contiguous reference genome assemblies.…”

Genome and Ontogenetic-Based Transcriptomic Analyses of the Flesh Fly,Sarcophaga bullata

“…Previous transcriptomic and genomics studies have focused on carrion-feeding flies closely related to S. bullata . In S. crassipalpis , transcriptomes have been used to examine responses related to diapause and cold tolerance (Ragland et al , 2010; Teets et al 2012), and a transcriptome has recently been generated for S. peregrina (Kim et al 2018). Beyond the genus Sarcophaga and the family Sarcophagidae, transcriptomic and genomic resources have been developed for other related carrion-feeding flies (Sze et al 2012; Anstead et al 2015; Wang et al 2015).…”