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Hopper KR, Wang X, Kenis M, Seehausen ML, Abram PK, Daane KM, Buffington ML, Hoelmer KA, Kingham BF, Shevchenko O, Bernberg E. Genome divergence and reproductive incompatibility among populations of Ganaspis near brasiliensis. G3 (BETHESDA, MD.) 2024; 14:jkae090. [PMID: 38718200 PMCID: PMC11228843 DOI: 10.1093/g3journal/jkae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/12/2024] [Indexed: 07/09/2024]
Abstract
During the last decade, the spotted wing drosophila, Drosophila suzukii, has spread from eastern Asia to the Americas, Europe, and Africa. This fly attacks many species of cultivated and wild fruits with soft, thin skins, where its serrated ovipositor allows it to lay eggs in undamaged fruit. Parasitoids from the native range of D. suzukii may provide sustainable management of this polyphagous pest. Among these parasitoids, host-specificity testing has revealed a lineage of Ganaspis near brasiliensis, referred to in this paper as G1, that appears to be a cryptic species more host-specific to D. suzukii than other parasitoids. Differentiation among cryptic species is critical for introduction and subsequent evaluation of their impact on D. suzukii. Here, we present results on divergence in genomic sequences and architecture and reproductive isolation between lineages of Ganaspis near brasiliensis that appear to be cryptic species. We studied five populations, two from China, two from Japan, and one from Canada, identified as the G1 vs G3 lineages based on differences in cytochrome oxidase l sequences. We assembled and annotated the genomes of these populations and analyzed divergences in sequence and genome architecture between them. We also report results from crosses to test reproductive compatibility between the G3 lineage from China and the G1 lineage from Japan. The combined results on sequence divergence, differences in genome architectures, ortholog divergence, reproductive incompatibility, differences in host ranges and microhabitat preferences, and differences in morphology show that these lineages are different species. Thus, the decision to evaluate the lineages separately and only import and introduce the more host-specific lineage to North America and Europe was appropriate.
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Affiliation(s)
- Keith R Hopper
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Marc Kenis
- CABI, Rue des Grillons 1, CH-2800 Delémont, Switzerland
| | | | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, 6947 Highway 7, PO Box 1000, Agassiz, BC V0 M 1A2, Canada
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720-3114, USA
| | - Matthew L Buffington
- United States Department of Agriculture, Agricultural Research Service, Washington, c/o Smithsonian Institution, National Museum of Natural History, 10th and Constitution NW, MRC-168, Washington, DC 20013-7012, USA
| | - Kim A Hoelmer
- United States Department of Agriculture, Agricultural Research Service, 501 South Chapel Street, Newark, DE 19713, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Olga Shevchenko
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
| | - Erin Bernberg
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, 590 Avenue 1743, Newark, DE 19713, USA
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Wan Y, Wu HJ, Yang JP, Zhang JL, Shen ZC, Xu HJ, Ye YX. Chromosome-level genome assembly of the bethylid ectoparasitoid wasp Sclerodermus sp. 'alternatusi'. Sci Data 2024; 11:438. [PMID: 38698068 PMCID: PMC11065869 DOI: 10.1038/s41597-024-03278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
The Bethylidae are the most diverse of Hymenoptera chrysidoid families. As external parasitoids, the bethylids have been widely adopted as biocontrol agents to control insect pests worldwide. Thus far, the genomic information of the family Bethylidae has not been reported yet. In this study, we crystallized into a high-quality chromosome-level genome of ant-like bethylid wasps Sclerodermus sp. 'alternatusi' (Hymenoptera: Bethylidae) using PacBio sequencing as well as Hi-C technology. The assembled S. alternatusi genome was 162.30 Mb in size with a contig N50 size of 3.83 Mb and scaffold N50 size of 11.10 Mb. Totally, 92.85% assembled sequences anchored to 15 pseudo-chromosomes. A total of 10,204 protein-coding genes were annotated, and 23.01 Mb repetitive sequences occupying 14.17% of genome were pinpointed. The BUSCO results showed that 97.9% of the complete core Insecta genes were identified in the genome, while 97.1% in the gene sets. The high-quality genome of S. alternatusi will not only provide valuable genomic information, but also show insights into parasitoid wasp evolution and bio-control application in future studies.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Jie Wu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jia-Peng Yang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Li Zhang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhi-Cheng Shen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hai-Jun Xu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yu-Xuan Ye
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China.
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Zhong YW, Fan YY, Zuo ZQ, Shu RG, Liu YQ, Luan JB, Li F, Liu SS. A chromosome-level genome assembly of the parasitoid wasp Eretmocerus hayati. Sci Data 2023; 10:585. [PMID: 37673910 PMCID: PMC10482854 DOI: 10.1038/s41597-023-02450-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Hymenoptera is an order accounting for a large proportion of species in Insecta, among which Chalcidoidea contains many parasitoid species of biocontrol significance. Currently, some species genomes in Chalcidoidea have been assembled, but the chromosome-level genomes of Aphelinidae are not yet available. Using Illumina, PacBio HiFi and Hi-C technologies, we assembled a genome assembly of Eretmocerus hayati (Aphelinidae, Hymenoptera), a worldwide biocontrol agent of whiteflies, at the chromosome level. The assembled genome size is 692.1 Mb with a contig N50 of 7.96 Mb. After Hi-C scaffolding, the contigs was assembled onto four chromosomes with a mapping rate of > 98%. The scaffold N50 length is 192.5 Mb, and Benchmarking Universal Single-Copy Orthologues (BUSCO) value is 95.9%. The genome contains 370.8 Mb repeat sequences and total of 24471 protein coding genes. P450 gene families were identified and analyzed. In conclusion, our chromosome-level genome assembly provides valuable support for future research on the evolution of parasitoid wasps and the interaction between hosts and parasitoid wasps.
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Affiliation(s)
- Yu-Wei Zhong
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yun-Yun Fan
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Zhang-Qi Zuo
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Run-Guo Shu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yin-Quan Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jun-Bo Luan
- College of Plant Protection, Shenyang Agricultural University, 110866, Shenyang, China
| | - Fei Li
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Shu-Sheng Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 310058, Hangzhou, China.
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Comparative Karyotype Analysis of Parasitoid Hymenoptera (Insecta): Major Approaches, Techniques, and Results. Genes (Basel) 2022; 13:genes13050751. [PMID: 35627136 PMCID: PMC9141968 DOI: 10.3390/genes13050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
A comprehensive review of main approaches, techniques and results of the chromosome study of parasitic wasps is given. In this group, the haploid chromosome number ranges from n = 3 to 23. Distribution of parasitic wasp species by the chromosome number is bimodal, with two obvious modes at n = 6 and 11. Karyotype analysis based on routinely stained preparations of mitotic chromosomes can be used to identify members of taxonomically complicated parasitoid taxa and to distinguish between them. Morphometric study effectively reveals subtle differences between similar chromosome sets of parasitic wasps. If combined with meiotic analysis and/or cytometric data, information on mitotic karyotypes can highlight pathways of the genome evolution in certain parasitoid taxa. C- and AgNOR-banding as well as staining with base-specific fluorochromes detected important interspecific differences within several groups of parasitic wasps. Fluorescence in situ hybridization (FISH) is successfully used for physical mapping of various DNA sequences on parasitoid chromosomes. These techniques demonstrate that heterochromatic segments are usually restricted to pericentromeric regions of chromosomes of parasitic wasps. Haploid karyotypes carrying one or two nucleolus organizing regions (NORs) are the most frequent among parasitoid Hymenoptera. In combination with chromosome microdissection, FISH could become a powerful tool exploring the genome evolution of parasitic wasps. Perspectives of the comparative cytogenetic study of parasitoid Hymenoptera are outlined.
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