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

Abstract

The flesh fly, Sarcophaga bullata , is a widely-used model for examining the physiology of insect diapause, development, stress tolerance, neurobiology, and host-parasitoid interactions. Flies in this taxon are implicated in myiasis (larval infection of vertebrates) and feed on carrion, aspects that are important in forensic studies. Here we present the genome of S. bullata , along with developmental- and reproduction-based RNA-Seq analyses. We predict 15,768 protein coding genes, identify orthology in relation to closely related flies, and establish sex and developmental-specific gene sets based on our RNA-Seq analyses. Genomic sequences, predicted genes, and sequencing data sets have been deposited at the National Center for Biotechnology Information. Our results provide groundwork for genomic studies that will expand the flesh fly’s utility as a model system.

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

“…Finally, pseudochromosomes with a total length of 548.19 Mb were exactly anchored into six chromosomes, accounting for 97.76% of the draft assembled genome (Figure 1), which was identical to the karyotype of six chromosomes based on cytological observation in S. peregrina (Agrawal et al., 2010) (Figure 2a; Table S11). Although the size of the assembled genome was more than twice that of D. melanogaster , the six pseudochromosomes in the assembled genome can be aligned against the D. melanogaster genome (Figure 2b), and the total genome size is of the order of the recently assembled S. bullata genome (522 Mb) (Martinson et al., 2019). The result of completeness of the assembly indicated that the Hi‐C genome assembly covered 98.2% of complete BUSCOs and 97.4% of single‐copy BUSCOs, with only 0.8% of duplicated BUSCOs (Table S12).…”

“…Given that this reproduction reduces the stage of larval development (the time when eggs hatch to first larvae), the species can be used very accurately to estimate the postmortem interval (PMI) of decomposed corpses, and it is therefore an important necrophagous flesh fly in the field of forensic entomology (Byrd & Castner, 2010). Similar to S. bullata , S. peregrina is also a species of medical and veterinary importance, as well as serving as a key indicator in forensic investigations (Byrd & Castner, 2010; Graczyk, Knight, Gilman, & Cranfield, 2001; Martinson et al., 2019). For instance, S. peregrina is one of the most common species of insect succession patterns on cadavers as well as at many death scenes colonizing a corpse (Guo et al., 2014; Siti Aisyah, Baha, Hiromu, David Evans, & Chin, 2015; Sukontason, Bunchu, Chaiwong, Moophayak, & Sukontason, 2010; Wang et al., 2017), and thus can provide valuable data for forensic investigations, especially floating corpse cases and indoor death‐scenes (Tomberlin, Mohr, Benbow, Tarone, & VanLaerhoven, 2011).…”

“…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.…”

“…Given that this reproduction reduces the stage of larval development (the time when eggs hatch to first larvae), the species can be used very accurately to estimate the postmortem interval (PMI) of decomposed corpses, and it is therefore an important necrophagous flesh fly in the field of forensic entomology (Byrd & Castner, 2010). Similar to S. bullata, S. peregrina is also a species of medical and veterinary importance, as well as serving as a key indicator in forensic investigations (Byrd & Castner, 2010;Graczyk, Knight, Gilman, & Cranfield, 2001;Martinson et al, 2019).…”

Transcriptomic and proteomic analyses of the mechanisms of overwintering diapause in soybean pod borer (Leguminivora glycinivorella)

“…In recent years, transcriptomic and proteomic analyses have been used to identify genes that are differentially expressed between diapausing and non-diapausing individuals. [25][26][27][28][29][30][31] The molecular mechanisms regulating diapause of several insects are well known and some genes have been found to play important roles in diapause. For example, transcriptomic and proteomic analyses of the two-spotted spider mite, Tetranychus urticae, revealed that Ca 2+ -associated genes have a substantial role in diapause regulation.…”