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

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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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

10.21203/rs.3.rs-537204/v1 ◽

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.

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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 ◽

10.1186/s12864-021-08249-y ◽

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.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.728418 ◽

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.

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A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection

10.1101/668384 ◽

2019 ◽

Cited By ~ 3

Author(s):

Mats E. Pettersson ◽

Christina M. Rochus ◽

Fan Han ◽

Junfeng Chen ◽

Jason Hill ◽

...

Keyword(s):

Genetic Differentiation ◽

Genome Assembly ◽

Large Scale ◽

De Novo ◽

Hybrid Approach ◽

Ecological Adaptation ◽

Atlantic Herring ◽

Total Size ◽

Bony Fishes ◽

Chromosome Level

ABSTRACTThe Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining ade novoPacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.

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Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

GigaScience ◽

10.1093/gigascience/giab070 ◽

2021 ◽

Vol 10 (10) ◽

Author(s):

Mi Ou ◽

Rong Huang ◽

Cheng Yang ◽

Bin Gui ◽

Qing Luo ◽

...

Keyword(s):

Comparative Analysis ◽

Low Temperature ◽

Gene Families ◽

Temperature Adaptation ◽

Fish Family ◽

Transcription Factor Genes ◽

Immune Related Genes ◽

Genome Assemblies ◽

Temperature Adaptability ◽

Chromosome Level

Abstract Background Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different. Results In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P < 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P < 0.01). Conclusions C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.

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

10.1101/2021.06.09.447800 ◽

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.

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Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

Frontiers in Genetics ◽

10.3389/fgene.2021.730255 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wu Gan ◽

Chenxi Zhao ◽

Xinran Liu ◽

Chao Bian ◽

Qiong Shi ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Mechanisms ◽

Gene Families ◽

Northwestern Pacific ◽

Draft Assembly ◽

Genome Wide ◽

Long Reads ◽

The Family ◽

Collichthys Lucidus ◽

Chromosome Level

Spiny head croaker (Collichthys lucidus), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23 Mb, with a contig N50 of 74.92 kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24 Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24 Mb, with an improved scaffold N50 of 26.58 Mb. Based on our phylogenetic analysis, we observed that C. lucidus is much closer to Larimichthys crocea than Miichthys miiuy. We also predicted that many gene families were significantly expanded (p-value <0.05) in spiny head croaker; among them, some are associated with “calcium signaling pathway” and potential “inner ear functions.” In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae.

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A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

Nature Communications ◽

10.1038/s41467-019-12175-9 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 18

Author(s):

Fanghao Wan ◽

Chuanlin Yin ◽

Rui Tang ◽

Maohua Chen ◽

Qiang Wu ◽

...

Keyword(s):

Insecticide Resistance ◽

Genome Assembly ◽

Association Studies ◽

Receptor Gene ◽

Cydia Pomonella ◽

Codling Moth ◽

Invasive Pest ◽

Z Chromosome ◽

Genome Wide Association Studies ◽

Chromosome Level

Abstract The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.

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Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae

Scientific Data ◽

10.1038/s41597-019-0238-8 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 7

Author(s):

Dian-Chang Zhang ◽

Liang Guo ◽

Hua-Yang Guo ◽

Ke-Cheng Zhu ◽

Shang-Qi Li ◽

...

Keyword(s):

Comparative Analysis ◽

Genome Assembly ◽

Protein Coding ◽

Trachinotus Ovatus ◽

Golden Pompano ◽

Protein Coding Genes ◽

Wide Geographical Distribution ◽

The Family ◽

Conserved Genes ◽

Chromosome Level

Abstract Golden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family.

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

Genome Biology and Evolution ◽

10.1093/gbe/evab094 ◽

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.

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