A high-quality<i>de novo</i>genome assembly from a single parasitoid wasp

Ye, Xinhai; Yang, Yi; Tian, Zhaoyang; Le, Xu; Yu, Kaili; Xiao, Shan; Yin, Chuanlin; Xiong, Shijiao; Fang, Qi; Chen, Hu; Li, Fēi; Yè, Gōngyín

doi:10.1101/2020.07.13.200725

Cited by 8 publications

(16 citation statements)

References 44 publications

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“…In a recent study, we carrier out the sequencing and assembly of the H. hebetor genomem, its assembled genome is 131.6 Mb in size with a contig N50 of 1.63 Mb (Ye et al, 2020 ). Here, we prepared embryos, larvae, and other samples from the wasps for RNA-Seq analysis.…”

Section: Methodsmentioning

confidence: 99%

Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor

Xiong

et al. 2020

Front. Physiol.

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Neuropeptides are a group of signal molecules that regulate many physiological and behavioral processes by binding to corresponding receptors, most of which are G-protein-coupled receptors (GPCRs). Using bioinformatic methods, we screened genomic and transcriptomic data of the ectoparasitoid wasp, Habrobracon hebetor, and annotated 34 neuropeptide candidate precursor genes and 44 neuropeptide receptor candidate genes. The candidate neuropeptide genes were found to encode all known insect neuropeptides except allatotropin, neuropeptide F, pigment dispersing factor, and CCHamides. When compared with the endoparasitic wasp Pteromalus puparum and the ectoparasitic wasp Nasonia vitripennis, trissin and FMRFamide were found only in H. hebetor. A similar result held for the neuropeptide receptor genes, for the receptors were found in H. hebetor except the receptors of CCHamides and neuroparsin. Furthermore, we compared and analyzed the differences in neuropeptides in eight Braconidae wasps and identified natalisin in H. hebetor, Diachasma alloeum, Fopius arisanus and Microplitis demolitor, but not in the other wasps. We also analyzed the transcriptome data and qRT-PCR data from different developmental stages and tissues to reveal the expression patterns of the neuropeptides and their receptors. In this study, we revealed composition of neuropeptides and neuropeptide receptors in H. hebetor, which may contribute to future neurobiological studies.

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Section: Methodsmentioning

confidence: 99%

Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor

Xiong

et al. 2020

Front. Physiol.

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“…We comprehensively considered three factors of each species for comparative genomics analyses and phylogenomic analyses, including genome quality, popularity, and evolutionary position. OrthoFinder v2.5.1 [20] was used to identify the orthologous and paralogous genes of 13 Hymenoptera genomes including O. abietinus (RefSeq assembly accession: GCF_000612105.2), C. chilonis (http://www.insect-genome.com/), Habrobracon hebetor (Ye et al [142]), Trichogramma pertiosum (RefSeq assembly accession: GCF_000599845.2), Nasonia vitripennis (OGS2.0, Rago et al [143]), P. puparum (OGS1.0, Ye et al [13]), G. flavifemur (this study), P. dominula (RefSeq assembly accession: GCF_001465965.1), Solenopsis invicta (RefSeq assembly accession: GCF_000188075.2), Ooceraea biroi (RefSeq assembly accession: GCF_003672135.1), Megachile rotundata (RefSeq assembly accession: GCF_ 000220905.1), A. mellifera (RefSeq assembly accession: GCF_003254395.2), and A. rosae (RefSeq assembly accession: GCF_000344095.2). The basal hymenopteran A. rosae was used as an outgroup.…”

Section: Comparative Genomicsmentioning

confidence: 99%

Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation

Yang

Dang

et al. 2021

BMC Biol

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Background Hymenoptera comprise extremely diverse insect species with extensive variation in their life histories. The Dryinidae, a family of solitary wasps of Hymenoptera, have evolved innovations that allow them to hunt using venom and a pair of chelae developed from the fore legs that can grasp prey. Dryinidae larvae are also parasitoids of Auchenorrhyncha, a group including common pests such as planthoppers and leafhoppers. Both of these traits make them effective and valuable for pest control, but little is yet known about the genetic basis of its dual adaptation to parasitism and predation. Results We sequenced and assembled a high-quality genome of the dryinid wasp Gonatopus flavifemur, which at 636.5 Mb is larger than most hymenopterans. The expansion of transposable elements, especially DNA transposons, is a major contributor to the genome size enlargement. Our genome-wide screens reveal a number of positively selected genes and rapidly evolving proteins involved in energy production and motor activity, which may contribute to the predatory adaptation of dryinid wasp. We further show that three female-biased, reproductive-associated yellow genes, in response to the prey feeding behavior, are significantly elevated in adult females, which may facilitate the egg production. Venom is a powerful weapon for dryinid wasp during parasitism and predation. We therefore analyze the transcriptomes of venom glands and describe specific expansions in venom Idgf-like genes and neprilysin-like genes. Furthermore, we find the LWS2-opsin gene is exclusively expressed in male G. flavifemur, which may contribute to partner searching and mating. Conclusions Our results provide new insights into the genome evolution, predatory adaptation, venom evolution, and sex-biased genes in G. flavifemur, and present genomic resources for future in-depth comparative analyses of hymenopterans that may benefit pest control.

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“…With the development of next-generation sequencing technology, our lab has already completed the sequencing and assembly of the H. hebetor genome and transcriptome. 25,26 In the present study, we employed sgRNA and Cas9 protein by targeting the eye-pigmentation central gene white, which is involved in the transported of pigments, and tested their efficiency in H. hebetor. 27 Eye-color has been the subject of extensive studies mainly due to its ease of use as a marker for genetic transformation in some insects.…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9‐mediated mutagenesis of the white gene in an ectoparasitic wasp, Habrobracon hebetor

Bai,

Yu,

Xiong

et al. 2023

Pest Management Science

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BACKGROUNDThe ectoparasitic wasp Habrobracon hebetor (Hymenoptera, Braconidae) can parasitize various species of lepidopteran pests. To maximize its potential for biological control, it is necessary to investigate its gene function through genome engineering.RESULTSTo test the effectiveness of genome engineering system in H. hebetor, we injected the mixture of clustered regularly interspaced short palindromic repeats (CRISPR) ‐associated (Cas) 9 protein and single guide RNA(s) targeting gene white into embryos. The resulting mutants display a phenotype of eye pigment loss. The phenotype was caused by small indel and is heritable. Then, we compared some biological parameters between wildtype and mutant, and found there were no significant differences in other parameters except for the offspring female rate and adult longevity. In addition, cocoons could be used to extract genomic DNA for genotype during the gene editing process without causing unnecessary harm to H. hebetor.CONCLUSIONOur results demonstrate that the CRISPR/Cas9 system can be used for H. hebetor genome editing and it does not adversely affect biological parameters of the parasitoid wasps. We also provide a feasible non‐invasive genotype detection method using genomic DNA extracted from cocoons. Our study introduces a novel tool and method for studying gene function in H. hebetor, and may contribute to better application of H. hebetor in biocontrol. © 2023 Society of Chemical Industry.

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A high-qualityde novogenome assembly from a single parasitoid wasp

Cited by 8 publications

References 44 publications

Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor

Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor

Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation

CRISPR/Cas9‐mediated mutagenesis of the white gene in an ectoparasitic wasp, Habrobracon hebetor

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