scholarly journals The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwins finches in Galpagos

2021 ◽  
Author(s):  
Melia Romine ◽  
Sarah A Knutie ◽  
Carly M Crow ◽  
Grace J Vaziri ◽  
Jaime Chaves ◽  
...  
Keyword(s):  
Immune Responses ◽  
Insecticide Resistance ◽  
Genome Assembly ◽  
Gene Families ◽  
Mitigation Strategies ◽  
Future Research ◽  
Host Immune Responses ◽  
Philornis Downsi ◽  
Genomic Resource ◽  
Mitigation Methods

The invasive avian vampire fly (Philornis downsi) is considered one of the greatest threats to the unique and endemic avifauna of the Galpagos Islands, Ecuador. The fly parasitizes nearly every passerine species, including Darwins finches, in the Galpagos. The fly is thought to have been introduced from mainland Ecuador, although the full pathway of invasion is not yet known. The majority of research to date has focused on the effects of the fly on the fitness of avian hosts and explorations of mitigation methods. A lag in research related to the genetics of this invasion demonstrates, in part, a need to develop full-scale genomic resources with which to address further questions within this system. In this study, an adult P. downsi collected from San Cristobal Island within the Galpagos archipelago was sequenced to generate a high-quality genome assembly. We examined various features of the genome (e.g., coding regions, non-coding transposable elements) and carried out comparative genomics analysis against other dipteran genomes. We identified lists of gene families that are significantly expanding/contracting in P. downsi >that are related to insecticide resistance, detoxification, and potential feeding ecology and counter defense against host immune responses. The P. downsi genome assembly provides an important foundational resource for studying the molecular basis of its successful invasion in the Galpagos and the dynamics of its population across multiple islands. The findings of significantly changing gene families associated with insecticide resistance and immune responses highlight the need for further investigations into the role of different gene families in aiding the flys successful invasion. Furthermore, this genomic resource will also better help inform future research studies and mitigation strategies aimed at minimizing the flys impact on the birds of the Galpagos.

scholarly journals The genome sequence of the avian vampire fly (Philornis downsi), an invasive nest parasite of Darwin’s finches in Galápagos

2021 ◽  
Author(s):  
Melia Romine ◽  
Sarah A Knutie ◽  
Carly M Crow ◽  
Grace J Vaziri ◽  
Jaime Chaves ◽  
...  
Keyword(s):  
Immune Responses ◽  
Insecticide Resistance ◽  
Genome Assembly ◽  
Gene Families ◽  
Mitigation Strategies ◽  
Future Research ◽  
Avian Host ◽  
Darwin's Finches ◽  
Philornis Downsi ◽  
Darwin’S Finches

Abstract The invasive avian vampire fly (Philornis downsi, Diptera: Muscidae) is considered one of the greatest threats to the endemic avifauna of the Galápagos Islands. The fly larvae parasitize nearly every passerine species, including Darwin’s finches. Most P. downsi research to date has focused on the effects of the fly on avian host fitness and mitigation methods. A lag in research related to the genetics of this invasion demonstrates, in part, the need to develop full-scale genomic resources with which to address further questions within this system. In this study, an adult female P. downsi was sequenced to generate a high-quality genome assembly. We examined various features of the genome (e.g., coding regions, non-coding transposable elements) and carried out comparative genomics analysis against other dipteran genomes. We identified lists of gene families that are significantly expanding or contracting in P. downsi that are related to insecticide resistance, detoxification, and counter defense against host immune responses. The P. downsi genome assembly provides an important resource for studying the molecular basis of successful invasion in the Galápagos and the dynamics of its population across multiple islands. The findings of significantly changing gene families associated with insecticide resistance and immune responses highlight the need for further investigations into the role of different gene families in aiding the fly’s successful invasion. Furthermore, this genomic resource provides a necessary tool to better inform future research studies and mitigation strategies aimed at minimizing the fly’s impact on Galápagos birds.

scholarly journals Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease

2021 ◽  
Vol 17 (1) ◽  
pp. e1009254
Author(s):  
Wei Wang ◽  
Duo Peng ◽  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Jessica C. Kissinger ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Immune Responses ◽  
Gene Amplification ◽  
Gene Diversity ◽  
Gene Families ◽  
Copy Number Variations ◽  
Host Immune Responses ◽  
Large Gene ◽  
Genes Encoding ◽  
Long Read

The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome–largely a result of these same extensive families of genes–have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi. In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of the members of large gene families in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. Gene amplification events also yield significant copy number variations in a substantial number of genes presumably not required for or involved in immune evasion, thus forming a second level of strain-dependent variation in this species. The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related kinetoplastids.

scholarly journals A Scaffold-Level Genome Assembly of the Pirate Bug, Orius Laevigatus, and a Comparative Analysis of Insecticide Resistance-Related Gene Families with Hemipteran Crop Pests

2021 ◽  
Author(s):  
Emma Bailey ◽  
Linda Field ◽  
Christopher Rawlings ◽  
Rob King ◽  
Fady Mohareb ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Genome Assembly ◽  
Hybrid Approach ◽  
Gene Families ◽  
Resistance Mechanisms ◽  
Target Site ◽  
Genomic Information ◽  
Orius Laevigatus ◽  
Crop Pests ◽  
Comparative Analyses

Abstract Background: The pirate bug, Orius laevigatus, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs).Methods and findings: In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649bp and a total genome size of 150.98Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 15,102 protein-coding genes - 87% of which were assigned a putative function - and the resultant gene set achieved a completeness of 84.5%. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. Conclusion and significance: This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by effectively controlling pests in a sustainable and environmentally-friendly manner, without impacting beneficial predator populations.

scholarly journals Chromosomal-level reference genome of the neotropical tree Jacaranda mimosifolia D. Don

2021 ◽  
Author(s):  
Mingcheng Wang ◽  
Lei Zhang ◽  
Zhiqiang Wang
Keyword(s):  
Genome Assembly ◽  
Morphological Characteristics ◽  
Gene Families ◽  
Deciduous Tree ◽  
Protein Coding ◽  
Neotropical Tree ◽  
A Genome ◽  
Genomic Resource ◽  
Jacaranda Mimosifolia ◽  
Chromosome Level

Abstract Jacaranda mimosifolia D. Don is a deciduous tree widely cultivated in the tropics and subtropics of the world. It is famous for its beautiful blue flowers and pinnate compound leaves. In addition, this tree has great potential in environmental monitoring, soil quality improvement, and medicinal applications. However, a genome resource for J. mimosifolia has not been reported to date. In this study, we constructed a chromosome-level genome assembly of J. mimosifolia using PacBio sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼707.32 Mb in size, 688.76 Mb (97.36%) of which could be grouped into 18 pseudochromosomes, with contig and scaffold N50 values of 16.77 and 39.98 Mb, respectively. A total of 30,507 protein-coding genes were predicted, 95.17% of which could be functionally annotated. Phylogenetic analysis among 12 plant species confirmed the close genetic relationship between J. mimosifolia and Handroanthus impetiginosus. Gene family clustering revealed 481 unique, 103 significantly expanded, and 16 significantly contracted gene families in the J. mimosifolia genome. This chromosome-level genome assembly of J. mimosifolia will provide a valuable genomic resource for elucidating the genetic bases of the morphological characteristics, adaption evolution, and active compounds biosynthesis of J. mimosifolia.

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

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Fanming Meng ◽  
Zhuoying Liu ◽  
Han Han ◽  
Dmitrijs Finkelbergs ◽  
Yangshuai Jiang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Gene Families ◽  
Development Rate ◽  
Future Research ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Chromosome Level

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.

scholarly journals A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Emma Bailey ◽  
Linda Field ◽  
Christopher Rawlings ◽  
Rob King ◽  
Fady Mohareb ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Genome Assembly ◽  
Gene Families ◽  
Resistance Mechanisms ◽  
Target Site ◽  
Genomic Information ◽  
Orius Laevigatus ◽  
Crop Pests ◽  
Comparative Analyses ◽  
Minute Pirate Bug

Abstract Background Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs). Methods and findings In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649 bp and a total genome size of 150.98 Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1658 core insect genes present as full-length genes. Genome annotation identified 15,102 protein-coding genes - 87% of which were assigned a putative function. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. Conclusion and significance This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably, environmentally-friendly and effectively control pests without impacting beneficial predator populations.

scholarly journals Host Immune Responses to Clostridioides difficile: Toxins and Beyond

2021 ◽  
Vol 12 ◽  
Author(s):  
Britt Nibbering ◽  
Dale N. Gerding ◽  
Ed J. Kuijper ◽  
Romy D. Zwittink ◽  
Wiep Klaas Smits
Keyword(s):  
Immune Responses ◽  
Bacterial Infections ◽  
Plasma Cells ◽  
Current Knowledge ◽  
Treatment Options ◽  
T Cell Response ◽  
Medical Community ◽  
Future Research ◽  
Host Immune Responses ◽  
Clostridioides Difficile

Clostridioides difficile is often resistant to the actions of antibiotics to treat other bacterial infections and the resulting C. difficile infection (CDI) is among the leading causes of nosocomial infectious diarrhea worldwide. The primary virulence mechanism contributing to CDI is the production of toxins. Treatment failures and recurrence of CDI have urged the medical community to search for novel treatment options. Strains that do not produce toxins, so called non-toxigenic C. difficile, have been known to colonize the colon and protect the host against CDI. In this review, a comprehensive description and comparison of the immune responses to toxigenic C. difficile and non-toxigenic adherence, and colonization factors, here called non-toxin proteins, is provided. This revealed a number of similarities between the host immune responses to toxigenic C. difficile and non-toxin proteins, such as the influx of granulocytes and the type of T-cell response. Differences may reflect genuine variation between the responses to toxigenic or non-toxigenic C. difficile or gaps in the current knowledge with respect to the immune response toward non-toxigenic C. difficile. Toxin-based and non-toxin-based immunization studies have been evaluated to further explore the role of B cells and reveal that plasma cells are important in protection against CDI. Since the success of toxin-based interventions in humans to date is limited, it is vital that future research will focus on the immune responses to non-toxin proteins and in particular non-toxigenic strains.

scholarly journals A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

2021 ◽  
Author(s):  
Emma Bailey ◽  
Linda Field ◽  
Christopher Rawlings ◽  
Rob King ◽  
Fady Mohareb ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Insecticide Resistance ◽  
Genome Assembly ◽  
Crop Yields ◽  
Hybrid Approach ◽  
Gene Families ◽  
Genomic Information ◽  
Predator Species ◽  
Crop Pests ◽  
Chromosome Level

Abstract Background: Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). Methods and findings: In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily levels between S. rueppellii and some crop pests. Conclusion and significance: This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.

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