A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms.

BACKGROUND: While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. RESULTS: We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. CONCLUSIONS: Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies.

Structural and Genetic Investigation of the Egg and First-Instar Larva of an Egg-Laying Population of Blaesoxipha plinthopyga (Diptera: Sarcophagidae), a Species of Forensic Importance.

Flies in the family Sarcophagidae incubate their eggs and are known to be ovoviviparous (i.e., ovolarviparous), but a laboratory-maintained colony of Blaesoxipha plinthopyga (Wiedemann) deposited clutches of viable eggs over 10 generations. A description of the egg and first-instar larva of this species is provided along with genetic data (genome size and cytochrome oxidase I sequences). The egg is similar to previously described eggs of other Sarcophagidae but differs in the configuration of the micropyle. In the first-instar larva, the oral ridges are much more developed than has been described for other species. B. plinthopyga has forensic importance, and the present descriptive information is critical for proper case management.

Identification and Characterization of Small RNA Markers of Age in the Blow Fly Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae).

Blow fly development is important in decomposition ecology, agriculture, and forensics. Much of the impact of these species is from immature samples, thus knowledge of their development is important to enhance or ameliorate their effects. One application of this information is the estimation of immature insect age to provide temporal information for death investigations. While traditional markers of age such as stage and size are generally accurate, they lack precision in later developmental stages. We used miRNA sequencing to measure miRNA expression, throughout development, of the secondary screwworm, Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae) and identified 217 miRNAs present across the samples. Ten were identified to be significantly differentially expressed in larval samples and seventeen were found to be significantly differentially expressed in intrapuparial samples. Twenty-eight miRNAs were identified to be differentially expressed between sexes. Expression patterns of two miRNAs, miR-92b and bantam, were qPCR-validated in intrapuparial samples; these and likely food-derived miRNAs appear to be stable markers of age in C. macellaria. Our results support the use of miRNAs for developmental markers of age and suggest further investigations across species and under a range of abiotic and biotic conditions.

An Analysis of Forensically Important Insects Associated with Human Remains in Indiana, U.S.A.

Research documenting insect colonization of human remains is limited in North America, and currently nonexistent for the American Midwest. Such research is essential for forensic entomologists to identify species of research interest in a region. In this study, we collected insects from human remains in 24 cases across Indiana from June 2016 through September 2018. We analyzed species composition across scene type and season. Eight species of blow flies were collected as larvae from human remains, with Phormia regina and Lucilia sericata as the two predominant colonizers. Phormia regina was the most numerous species collected from outdoor scenes (73.6% of total collections) while L. sericata was the most numerous from the indoor scenes (60.4% of total collections). With scene types pooled, Calliphora vicina and Cochliomya macellaria were the predominant species in the fall (55.6% and 42.2%, respectively); P. regina was the dominant colonizer in the spring (68.6%); and P. regina and L. sericata were the predominant colonizers (46.5% and 44.4%, respectively) in the summer. In addition to these findings, we confirmed the first record of Lucilia cuprina colonizing human remains in Indiana having collected this species from three cases. A single adult Chrysomya megacephala was collected from an indoor scene in southern Indiana, which represents its second collection in the state. Beetles belonging to the families Staphylinidae, Silphidae, Histeridae, Cleridae, Trogidae, Dermestdae, and Nitidulidae were also collected from two outdoor scenes. This study provides important baseline data for forensic entomologists in Indiana, as well as surrounding states with similar environments.

Facultative Viviparity in a Flesh Fly (Diptera: Sarcophagidae): Forensic Implications of High Variability in Rates of Oviparity in Blaesoxipha plinthopyga (Diptera: Sarcophagidae).

Flesh flies are major primary consumers of carrion and are commonly found on human remains. Due to this latter feeding habit, their development rates can be used to provide temporal information in forensic investigations. This is usually done by referencing published flesh fly development datasets. Flesh flies are typically assumed to be strictly viviparous and datasets reporting their development rates therefore start at the first larval instar. However, an increasing number of studies has identified oviposition by flesh flies, including the forensically relevant species Blaesoxipha plinthopyga Wiedemann. To assess the impact of egg-laying behavior on casework, oviparity rates and time before larval hatching were assessed under controlled laboratory conditions that reflect common casework conditions in Harris County, Texas. We demonstrated systematic deposition of viable eggs but at a very variable rate between samples. Similarly, the duration between oviposition and larval hatching was highly variable, with some eggs taking more than a day to hatch after deposition. These results highlight the need to account for embryonic development in forensic investigations including B. plinthopyga and advocates for the re-evaluation of the assumed strict viviparity of the Sarcophagidae.

Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera.

Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.