scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

2021 ◽  
Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Chromosome Conformation ◽  
Important Species

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.

scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia Illucens L.)

2020 ◽  
Author(s):  
Tomas N. Generalovic ◽  
Shane A. McCarthy ◽  
Ian A. Warren ◽  
Jonathan M.D. Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Population Genomics ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Reference Sequence ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens

AbstractBackgroundHermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important mass reared entomological resource for bioconversion of organic material into animal feed.ResultsWe generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudo-chromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 17,664 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and the identification of an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This revealed a plethora of inbreeding events including recent long runs of homozygosity on chromosome five.ConclusionsRelease of this novel chromosome-scale BSF genome assembly will provide an improved platform for further genomic studies and functional characterisation of candidate regions of artificial selection. This reference sequence will provide an essential tool for future genetic modifications, functional and population genomics.

Impact of age, size, and sex on adult black soldier fly [Hermetia illucens L. (Diptera: Stratiomyidae)] thermal preference

2021 ◽  
pp. 1-12
Author(s):  
N.F. Addeo ◽  
C. Li ◽  
T.W. Rusch ◽  
A.J. Dickerson ◽  
A.M. Tarone ◽  
...  
Keyword(s):  
Life History ◽  
Thermal Gradient ◽  
Life History Traits ◽  
Animal Feed ◽  
Mass Rearing ◽  
Thermal Preference ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Surface Temperatures ◽  
The Impact

Population growth and rapid urbanisation have increased the global demand for animal feed and protein sources. Therefore, traditional animal feed production should be increased through the use of alternative nutrient sources. Insects as feed are beginning to fill this need. One such insect is the black soldier fly, Hermetia illucens L. (Diptera: Stratiomyidae). However, to more effectively mass produce the black soldier fly, a better understanding of its thermal biology is needed. Thus, the aim of this study was to evaluate the impact of age, size, and sex on adult black soldier fly thermal preference. The thermal preference of adult black soldier flies was determined by exposing flies to a thermal gradient with a range of surface temperatures and monitoring their positions over time. An aluminium plate was used to create a linear thermal gradient where surface temperatures ranged from ~15-60 °C. Flies were distinguished by age (1-d-post-emergence vs 7-d-post-emergence), size (large vs small) and sex (male vs female) to assess whether thermal preference differed by specific life-history traits. Thermal preference for 7-d-post-emergence adults was significantly lower (19.2 °C) than 1-d-post-emergence adults (28.7 °C), respectively. Similarly, small adults selected significantly cooler (21.1 °C) temperatures than large adults (26.9 °C). No significant differences in thermal preferences were found between sex, regardless of age or size. In fact, males and females had similar thermal preference of 23.8 and 24.2 °C, respectively. This study reveals that multiple life-history traits of adult black soldier fly affect their thermal preference, and thus should be taken into consideration by mass rearing facilities to optimize production.

scholarly journals SIGAR: Inferring features of genome architecture and DNA rearrangements by split read mapping

2020 ◽  
Author(s):  
Yi Feng ◽  
Leslie Y. Beh ◽  
Wei-Jen Chang ◽  
Laura F. Landweber
Keyword(s):  
Genome Assembly ◽  
Repetitive Sequences ◽  
Genome Architecture ◽  
Dna Rearrangements ◽  
High Quality ◽  
Microbial Eukaryotes ◽  
Ciliate Species ◽  
Split Read ◽  
High Level ◽  
Genome Assemblies

AbstractCiliates are microbial eukaryotes with distinct somatic and germline genomes. Post-zygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programmed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. While many high-quality somatic genomes have been assembled, a high quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline SIGAR (Splitread Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short germline DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.

scholarly journals FIRST RECORD OF HERMETIA ILLUCENS (LINNAEUS, 1758) – BLACK SOLDIER FLY, FROM NEPAL

2020 ◽  
Vol 5 (1) ◽  
pp. 21-23
Author(s):  
Biplov Sapkota ◽  
Shristi Upadhyaya ◽  
Anuj Lamichhane ◽  
Rajendra Regmi ◽  
Kuldip Ghimire ◽  
...  
Keyword(s):  
Organic Waste ◽  
Animal Feed ◽  
Morphological Characteristics ◽  
First Record ◽  
Feed Ingredient ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Animal Feeding ◽  
Simple Systems ◽  
First Time

Hermetia illucens (Linnaeus, 1758)- Black soldier fly is a beneficial insect which has been used in simple systems, to treat organic waste efficiently and rapidly, and to produce animal feed ingredient and fertilizer as end products. These flies are naturally found in warmer parts of the globe. The incidence of Black soldier fly was recorded for the first time in Nepal in between April and May 2020 in the sub urban area of Chitwan District, Nepal. Identification of the insect was done in the Laboratory of Department of Entomology, Faculty of Agriculture, Agriculture and Forestry University, Nepal. Both adult and larval forms of the insect were identified based on the study of morphological characteristics of captured specimens using simple microscope and stereomicroscope. The record of this insect in Nepal opens up a new dimension for its use in bio-systems to treat organic waste and produce more sustainable ingredient for animal feeding, and rich fertilizer to be used in agriculture.

scholarly journals Effects of insecticides on mortality, growth and bioaccumulation in black soldier fly (Hermetia illucens) larvae

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249362
Author(s):  
Nathan Meijer ◽  
Theo de Rijk ◽  
Joop J. A. van Loon ◽  
Lisa Zoet ◽  
H. J. van der Fels-Klerx
Keyword(s):  
Animal Feed ◽  
Accumulation Factor ◽  
The European Union ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Growth And Survival ◽  
Maximum Residue Level ◽  
Sequential Experiments ◽  
Food And Feed ◽  
Black Soldier Fly Larvae

Residues of persistent insecticides may be present in the substrates on which insects are reared for food and feed, which may affect insect growth or survival. In addition, insecticidal substances may bio-accumulate in reared insects. The objective of this study was to assess potential effects of selected insecticides on the growth and survival of black soldier fly larvae (BSFL, Hermetia illucens) and on their safety when used as animal feed. Six insecticides (chlorpyrifos, propoxur, cypermethrin, imidacloprid, spinosad, tebufenozide) with different modes of action were tested in two sequential experiments. Cypermethrin was also tested with the synergist piperonyl butoxide (PBO). Standard BSFL substrate was spiked to the respective maximum residue level (MRL) of each insecticide allowed by the European Union to occur in feed; and BSFL were reared on these substrates. Depending on the observed effects in the first experiment, spiked concentrations tested in the second experiment were increased or reduced. At the concentrations applied (1 and 10 times MRL), three of the six tested substances (chlorpyrifos, propoxur, tebufenozide) did not affect the survival or biomass growth of BSFL, compared to the control (non-spiked) treatments. At MRL, imidacloprid stimulated the growth of BSFL compared to the controls. Spinosad and cypermethrin at the MRL level negatively affected growth and survival. The effects of cypermethrin appeared to be augmented by addition of PBO. A mean bio-accumulation factor of ≤0.01 was found in both experiments for all substances–except for cypermethrin, which was comparatively high, but still below 1 (0.79 at 0.1 mg/kg). The lack of accumulation of insecticides in the larvae suggests that there is no risk of larval products being uncompliant with feed MRLs. However, we conclude that insecticides present in substrates may affect growth and survival of BSFL. More research on a larger variety of substances and insect species is recommended.

scholarly journals The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

2020 ◽  
Author(s):  
Zeyuan Chen ◽  
Özgül Doğan ◽  
Nadège Guiglielmoni ◽  
Anne Guichard ◽  
Michael Schrödl
Keyword(s):  
Transposable Elements ◽  
Genome Assembly ◽  
De Novo ◽  
Repetitive Sequences ◽  
Land Snails ◽  
Whole Genome ◽  
Pest Species ◽  
High Quality ◽  
Genome Duplication Event ◽  
Arion Vulgaris

AbstractBackgroundThe “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe. It is common and invasive to at least northern and eastern parts of Europe, probably benefitting from climate change and the modern human lifestyle. The origin and expansion of this species, the mechanisms behind its outstanding adaptive success and ability to outcompete other land slugs are worth to be explored on a genomic level. However, a high-quality chromosome-level genome is still lacking.FindingsThe final assembly of A. vulgaris was obtained by combining short reads, linked reads, Nanopore long reads, and Hi-C data. The genome assembly size is 1.54 Gb with a contig N50 length of 8.6 Mb. We found a recent expansion of transposable elements (TEs) which results in repetitive sequences accounting for more than 75% of the A. vulgaris genome, which is the highest among all known gastropod species. We identified 32,518 protein coding genes, and 2,763 species specific genes were functionally enriched in response to stimuli, nervous system and reproduction. With 1,237 single-copy orthologs from A. vulgaris and other related mollusks with whole-genome data available, we reconstructed the phylogenetic relationships of gastropods and estimated the divergence time of stylommatophoran land snails (Achatina) and Arion slugs at around 126 million years ago, and confirmed the whole genome duplication event shared by them.ConclusionsTo our knowledge, the A. vulgaris genome is the first land slug genome assembly published to date. The high-quality genomic data will provide valuable genetic resources for further phylogeographic studies of A. vulgaris origin and expansion, invasiveness, as well as molluscan aquatic-land transition and shell formation.

scholarly journals Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

2021 ◽  
Vol 12 ◽  
Author(s):  
Jielong Zhou ◽  
Peifu Wu ◽  
Zhongping Xiong ◽  
Naiyong Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Thaumetopoea Pityocampa ◽  
High Quality ◽  
Protein Coding ◽  
Peptidoglycan Recognition Protein ◽  
Recognition Protein ◽  
Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

scholarly journals A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Qingzhen Wei ◽  
Jinglei Wang ◽  
Wuhong Wang ◽  
Tianhua Hu ◽  
Haijiao Hu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Specific Gene ◽  
High Quality ◽  
Total Size ◽  
Protein Coding ◽  
Fruit Length ◽  
Protein Coding Genes

Abstract Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

Legislative landscape of black soldier fly (Hermetia illucens) as feed

2021 ◽  
pp. 1-14
Author(s):  
S. Alagappan ◽  
D. Rowland ◽  
R. Barwell ◽  
S.M.O. Mantilla ◽  
D. Mikkelsen ◽  
...  
Keyword(s):  
Animal Feed ◽  
Amino Acid Profile ◽  
Nutritional Composition ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Suitable Material ◽  
Regulatory Frameworks ◽  
Agricultural Household ◽  
Different Types ◽  
Black Soldier Fly Larvae

The demand for animal-based protein sources is increasing rapidly. The rearing of insects on bioproducts and their subsequent use as feedstock for animals has been receiving a lot of attention lately. Hermetia illucens, black soldier flies are highly investigated insects owing to their ability to reduce and transform different types of wastes, such as agricultural, household, municipal wastes, and human sludge. The nutritional composition and amino acid profile of black soldier fly larvae (BSFL) raised on these organic wastes is similar to that of several feed constituents making it a suitable material for feed. However, the commercialisation of BSFL is limited due to prevailing unclear legislative requirements regarding their use as feed. In this paper, the legislative landscape involved in using BSFL as feed in different regions is addressed. European Union, Australia, Canada and USA specifically allow the trade and manufacture of BSFL as feed under specific conditions. Interestingly, most countries where entomophagy is a tradition, lack specific regulations concerning their use as feed and are currently drafting regulatory frameworks. Understanding the legislative layout is essential for harmonising the industrial upscaling of BSFL as animal feed.

Sign in / Sign up

Export Citation Format

Share Document