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Kim J, Rahman MM, Han C, Shin J, Ahn SJ. Chromosome-level genome assembly and comparative genomics shed light on Helicoverpa assulta ecology and pest management. PEST MANAGEMENT SCIENCE 2024. [PMID: 38942610 DOI: 10.1002/ps.8273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND The Oriental tobacco budworm, Helicoverpa assulta, a specialist herbivorous insect that exclusively feeds on plants of the Solanaceae family, causes considerable damage to crops, such as tobacco and hot pepper. The absence of a genome sequence for this species hinders further research on its pest management and ecological adaptation. RESULTS Here, we present a high-quality chromosome-level genome of a Korean strain of H. assulta (Pyeongchang strain, K18). The total assembly spans 424.4 Mb with an N50 length of 14.54 Mb and 37% GC content. The assembled genome (ASM2961881v1) comprises 31 chromosomes, similar to other congeneric generalist species including H. armigera and H. zea. In terms of genomic assembly quality, the complete BUSCOs and repeat content accounted for 98.3% and 33.01% of the genome, respectively. Based on this assembly, 19 485 protein-coding genes were predicted in the genome annotation. A comparative analysis was conducted using the identified number of protein-coding genes in H. armigera (24154) and H. zea (23696). Out of the 19 485 predicted genes, 137 genes in 15 orthogroups were found to have expanded significantly in H. assulta, while 149 genes in 95 orthogroups contracted rapidly. CONCLUSION This study revealed specific gene expansions and contractions in H. assulta compared to those in its close relatives, indicating potential adaptations related to its specialized feeding habits. Also, the comparative genome analysis provides valuable insights for the integrated pest management of H. assulta and other globally significant pests in the Heliothinae subfamily. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Juil Kim
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon, Republic of Korea
- Interdisciplinary Graduate Program in Smart Agriculture, Kangwon National Unversity, Chuncheon, Republic of Korea
| | - Md-Mafizur Rahman
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon, Republic of Korea
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, Bangladesh
| | - Changhee Han
- Interdisciplinary Graduate Program in Smart Agriculture, Kangwon National Unversity, Chuncheon, Republic of Korea
| | - Jiyeong Shin
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon, Republic of Korea
| | - Seung-Joon Ahn
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, USA
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Guo R, Papanicolaou A, Fritz ML. Validation of reference-assisted assembly using existing and novel Heliothine genomes. Genomics 2022; 114:110441. [PMID: 35931274 DOI: 10.1016/j.ygeno.2022.110441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran family with few genomic resources. We then examined the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa and applied it to our Heliothine genomes. Our work demonstrates that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. We conclude by discussing both the potential and pitfalls of reference-assisted assembly according to the intended downstream assembly application.
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Affiliation(s)
- Rong Guo
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia.
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA.
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Cong Y, Ye X, Mei Y, He K, Li F. Transposons and Non-coding Regions Drive the Intrafamily Differences of Genome Size in Insects. iScience 2022; 25:104873. [PMID: 36039293 PMCID: PMC9418806 DOI: 10.1016/j.isci.2022.104873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein–Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution. The most comprehensive variation pattern of insects genome size (GS) to date GS evolution of the Insecta was reflected by the adaptive Ornstein–Uhlenbeck model Ancestral state of insect GS was estimated to be ∼1 Gb Intrafamily GS variations were driven by recent transpositions and non-coding regions
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Lata D, Coates BS, Walden KKO, Robertson HM, Miller NJ. Genome size evolution in the beetle genus Diabrotica. G3 (BETHESDA, MD.) 2022; 12:jkac052. [PMID: 35234880 PMCID: PMC8982398 DOI: 10.1093/g3journal/jkac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 and 1.64 gigabase pairs and between 2.26 and 2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of the fucata group and the virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements and gypsy-like long terminal repeat retroelements.
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Affiliation(s)
- Dimpal Lata
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Nicholas J Miller
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
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Benowitz KM, Allan CW, Degain BA, Li X, Fabrick JA, Tabashnik BE, Carrière Y, Matzkin LM. Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea. Genetics 2022; 221:6540856. [PMID: 35234875 PMCID: PMC9071530 DOI: 10.1093/genetics/iyac037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bacillus thuringiensis toxins can improve resistance monitoring, resistance management, and the design of new insecticides. Here, we investigated the genetic basis of resistance to Bacillus thuringiensis toxin Cry1Ac in the lepidopteran Helicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus on chromosome 13 that was strongly associated with resistance in a strain of Helicoverpa zea that had been selected for resistance in the field and lab. The mutation in this quantitative trait locus contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This quantitative trait locus contains no genes with a previously reported role in resistance or susceptibility to Bacillus thuringiensis toxins. However, in resistant insects, this quantitative trait locus has a premature stop codon in a kinesin gene, which is a primary candidate as a mutation contributing to resistance. We found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance.
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Affiliation(s)
- Kyle M Benowitz
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA,Department of Biology, Austin Peay State University, Clarksville, TN 37040, USA,Corresponding author: Department of Biology, Austin Peay State University, Sundquist Science Center, 681 Summer St., Clarksville, TN 37040, USA.
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
| | - Benjamin A Degain
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
| | - Xianchun Li
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
| | - Jeffrey A Fabrick
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138, USA
| | - Bruce E Tabashnik
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
| | - Yves Carrière
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA,Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Transcriptional response to host chemical cues underpins the expansion of host range in a fungal plant pathogen lineage. THE ISME JOURNAL 2022; 16:138-148. [PMID: 34282282 PMCID: PMC8692328 DOI: 10.1038/s41396-021-01058-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 06/26/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum has been reported to parasitize more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in two representative strains of broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Comparative analyses revealed a lack of transcriptional response to camalexin in the S. trifoliorum strain and suggest that regulatory variation in detoxification and effector genes at the population level may associate with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work proposes transcriptional plasticity and the co-existence of signatures for generalist and polyspecialist adaptive strategies in the genome of a plant pathogen.
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Genome Size Estimation of Callipogon relictus Semenov (Coleoptera: Cerambycidae), an Endangered Species and a Korea Natural Monument. INSECTS 2021; 12:insects12020111. [PMID: 33513896 PMCID: PMC7910860 DOI: 10.3390/insects12020111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary The longhorned beetle Calipogon relictus has been considered as a class I endangered species since 2012 in Korea. In an attempt towards beetle conservation, we estimated its genome size at 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes. This study provides useful insight at the genome level and facilitates the development of an effective conservation strategy. Abstract We estimated the genome size of a relict longhorn beetle, Callipogon relictus Semenov (Cerambycidae: Prioninae)—the Korean natural monument no. 218 and a Class I endangered species—using a combination of flow cytometry and k-mer analysis. The two independent methods enabled accurate estimation of the genome size in Cerambycidae for the first time. The genome size of C. relictus was 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes studied to date. An accurate estimation of genome size of a critically endangered longhorned beetle is a major milestone in our understanding and characterization of the C. relictus genome. Ultimately, the findings provide useful insight into insect genomics and genome size evolution, particularly among beetles.
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The relationship between genome size, morphological parameters and diet breadth in insect species. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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