Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly

Abstract

Background Blowflies (Diptera: Calliphoridae) are the most commonly found entomological evidence in forensic investigations. Distinguished from other blowflies, Aldrichina grahami has some unique biological characteristics and is a species of forensic importance. Its development rate, pattern, and life cycle can provide valuable information for the estimation of the minimum postmortem interval. Findings Herein we provide a chromosome-level genome assembly of A. grahami that was generated by Pacific BioSciences sequencing platform and chromosome conformation capture (Hi-C) technology. A total of 50.15 Gb clean reads of the A. grahami genome were generated. FALCON and Wtdbg were used to construct the genome of A. grahami, resulting in an assembly of 600 Mb and 1,604 contigs with an N50 size of 1.93 Mb. We predicted 12,823 protein-coding genes, 99.8% of which was functionally annotated on the basis of the de novo genome (SRA: PRJNA513084) and transcriptome (SRA: SRX5207346) of A. grahami. According to the co-analysis with 11 other insect species, clustering and phylogenetic reconstruction of gene families were performed. Using Hi-C sequencing, a chromosome-level assembly of 6 chromosomes was generated with scaffold N50 of 104.7 Mb. Of these scaffolds, 96.4% were anchored to the total A. grahami genome contig bases. Conclusions The present study provides a robust genome reference for A. grahami that supplements vital genetic information for nonhuman forensic genomics and facilitates the future research of A. grahami and other necrophagous blowfly species used in forensic medicine.

Chromosome‐level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure

“…Moreover, the shared orthologous gene clusters of Dastarcus helophoroides and four species ( Pyrocoelia pectoralis , Aethina tumida , Hycleus cichorii , and Anoplophora glabripennis ) were displayed using the online utility Draw Venn Diagram (https://bioinformatics.psb.ugent.be/webtools/Venn/). 38 …”

“…Twenty insect species including Dastarcus helophoroides (Supporting Information Table S15) were selected on the basis of classification background and feeding habits (necrophagia, polyphagia, parasitism, or hematophagia) to identify the gene families, which were then clustered using OrthoMCL (version 2.0) (RRID:SCR 007839). 38 The amino acid sequences of the longest transcripts for each gene were selected from the earlier species, and they were all-to-all blasted using the BlaStp utility with a threshold of e-value < 1 e −5 . The alignment results were clustered into family groups with default parameters, and the dilatation coefficient was 1.5.…”

Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis‐causing fly of warm‐blooded vertebrates

“…A representative obstacle is that repetitive sequences or polymorphic regions cannot be straddled well, leading to a fragmented genome assembly with lower contig N50 lengths. As long‐read technologies have the inherent advantages of spanning polymorphic regions, repetitive sequences and transposable elements (TE) (Richards & Murali, 2015), at present, more and more insect genome projects are a combination of continuous long reads from PacBio/Nanopore and short reads from Illumina (Meng et al, 2020; Ren et al, 2021; Ye et al, 2021). Using the strategy, to date, a number of full and draft genomes of agricultural pests are completed and publicly available, such as Mediterranean fruit fly ( Ceratitis capitata ) (Papanicolaou et al, 2016), sheep blow fly ( L. cuprina ) (Anstead et al, 2015), and the New World screwworm fly ( C. hominivorax ) (Scott et al, 2020).…”