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Zheng L, Wang H, Lin J, Zhou Y, Xiao J, Li K. Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China. PLoS One 2023; 18:e0294521. [PMID: 37972203 PMCID: PMC10653512 DOI: 10.1371/journal.pone.0294521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.
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Affiliation(s)
- Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Huan Wang
- Department of Plant Science and Technology, Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Songjiang District, Shanghai, China
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2
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Cohen ZP, François O, Schoville SD. Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation. Integr Comp Biol 2022; 62:1827-1837. [PMID: 36036479 DOI: 10.1093/icb/icac137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 01/05/2023] Open
Abstract
Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA.,Insect Control and Cotton Disease Research Unit, USDA, Agricultural Research Service, College Station, TX, USA
| | | | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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3
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Villamizar LF, Barrera G, Hurst M, Glare TR. Characterization of a new strain of Metarhizium novozealandicum with potential to be developed as a biopesticide. Mycology 2021; 12:261-278. [PMID: 34900381 PMCID: PMC8654417 DOI: 10.1080/21501203.2021.1935359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The fungal species Metarhizium novozealandicum, that occurs only in New Zealand and Australia has been poorly studied. In this work, a new strain of M. novozealandicum isolated from a larva of Wiseana sp. is described based on morphology, genomic multilocus (ITS, EF-1α and β-tubulin) phylogeny, growth in different culture media and insecticidal activity. The isolate AgR-F177 was clustered in the same clade with M. novozealandicum. AgR-F177 colonies developed faster on Sabouraud Dextrose Agar (SDA) than on Potato Dextrose Agar (PDA) when incubated at 25°C, with no growth observed at 30°C on either media. Conidia yield on an oat-based medium in semisolid fermentation was 7.41 x 108conidia/g of substrate and a higher yield of 1.68 x 109conidia/g of substrate was obtained using solid fermentation on cooked rice. AgR-F177 formed microsclerotia (MS) in liquid fermentation after 7 days reaching the maximum yield of 3.3 × 103 MS/mL after 10 days. AgR-F177 caused mortality in Wiseana copularis, Costelytra giveni and Plutella xylostella larvae with efficacies up to 100%, 69.2%, and 45.7%, respectively. The ease of production of AgR-F177 with different fermentation systems and its pathogenicity against different insect pests reveal its potential as a new biopesticide.
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Affiliation(s)
| | - Gloria Barrera
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA,Bogotá, Colombia
| | - Mark Hurst
- AgResearch Ltd., Lincoln Research Centre, Christchurch, New Zealand
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Christchurch, New Zealand
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Ward CM, Perry KD, Baker G, Powis K, Heckel DG, Baxter SW. A haploid diamondback moth (Plutella xylostella L.) genome assembly resolves 31 chromosomes and identifies a diamide resistance mutation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 138:103622. [PMID: 34252570 DOI: 10.1016/j.ibmb.2021.103622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/04/2021] [Accepted: 07/04/2021] [Indexed: 05/21/2023]
Abstract
The diamondback moth, Plutella xylostella (L.), is a highly mobile brassica crop pest with worldwide distribution and can rapidly evolve resistance to insecticides, including group 28 diamides. Reference genomes assembled using Illumina sequencing technology have provided valuable resources to advance our knowledge regarding the biology, origin and movement of diamondback moth, and more recently with its sister species, Plutella australiana. Here we apply a trio binning approach to sequence and annotate a chromosome level reference genome of P. xylostella using PacBio Sequel and Dovetail Hi-C sequencing technology and identify a point mutation that causes resistance to commercial diamides. A P. xylostella population collected from brassica crops in the Lockyer Valley, Australia (LV-R), was reselected for chlorantraniliprole resistance then a single male was crossed to a P. australiana female and a hybrid pupa sequenced. A chromosome level 328 Mb P. xylostella genome was assembled with 98.1% assigned to 30 autosomes and the Z chromosome. The genome was highly complete with 98.4% of BUSCO Insecta genes identified and RNAseq informed protein prediction annotated 19,002 coding genes. The LV-R strain survived recommended field application doses of chlorantraniliprole, flubendiamide and cyclaniliprole. Some hybrids also survived these doses, indicating significant departure from recessivity, which has not been previously documented for diamides. Diamide chemicals modulate insect Ryanodine Receptors (RyR), disrupting calcium homeostasis, and we identified an amino acid substitution (I4790K) recently reported to cause diamide resistance in a strain from Japan. This chromosome level assembly provides a new resource for insect comparative genomics and highlights the emergence of diamide resistance in Australia. Resistance management plans need to account for the fact that resistance is not completely recessive.
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Affiliation(s)
- C M Ward
- School of Biological Sciences, University of Adelaide, 5005, Australia
| | - K D Perry
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - G Baker
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - K Powis
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - D G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - S W Baxter
- Bio21 Institute, School of BioSciences, University of Melbourne, 3052, Australia.
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Chen MZ, Cao LJ, Li BY, Chen JC, Gong YJ, Yang Q, Schmidt TL, Yue L, Zhu JY, Li H, Chen XX, Hoffmann AA, Wei SJ. Migration trajectories of the diamondback moth Plutella xylostella in China inferred from population genomic variation. PEST MANAGEMENT SCIENCE 2021; 77:1683-1693. [PMID: 33200882 DOI: 10.1002/ps.6188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/15/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The diamondback moth (DBM), Plutella xylostella (Lepidoptera: Plutellidae), is a notorious pest of cruciferous plants. In temperate areas, annual populations of DBM originate from adult migrants. However, the source populations and migration trajectories of immigrants remain unclear. Here, we investigated migration trajectories of DBM in China using genome-wide single nucleotide polymorphisms (SNPs) genotyped using double-digest RAD (ddRAD) sequencing. We first analyzed patterns of spatial and temporal genetic structure among southern source and northern recipient populations, then inferred migration trajectories into northern regions using discriminant analysis of principal components (DAPC), assignment tests, and spatial kinship patterns. RESULTS Temporal genetic differentiation among populations was low, indicating that sources of recipient populations and migration trajectories are stable. Spatial genetic structure indicated three genetic clusters in the southern source populations. Assignment tests linked northern populations to the Sichuan cluster, and central-eastern populations to the southern and Yunnan clusters, indicating that Sichuan populations are sources of northern immigrants and southern and Yunnan populations are sources of central-eastern populations. First-order (full-sib) and second-order (half-sib) kin pairs were always found within populations, but ~ 35-40% of third-order (cousin) pairs were found in different populations. Closely related individuals in different populations were found at distances of 900-1500 km in ~ 35-40% of cases, while some were separated by > 2000 km. CONCLUSION This study unravels seasonal migration patterns in the DBM. We demonstrate how careful sampling and population genomic analyses can be combined to help understand cryptic migration patterns in insects. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Ming-Zhu Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qiong Yang
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas L Schmidt
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Lei Yue
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Schlum KA, Lamour K, de Bortoli CP, Banerjee R, Meagher R, Pereira E, Murua MG, Sword GA, Tessnow AE, Viteri Dillon D, Linares Ramirez AM, Akutse KS, Schmidt-Jeffris R, Huang F, Reisig D, Emrich SJ, Jurat-Fuentes JL. Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations. BMC Genomics 2021; 22:179. [PMID: 33711916 PMCID: PMC7953542 DOI: 10.1186/s12864-021-07492-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/26/2021] [Indexed: 11/12/2022] Open
Abstract
Background The fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of > 80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). The population genomics of the United States (USA) fall armyworm remains poorly characterized to date despite its agricultural threat. Results In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and USA were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest a panmictic S. frugiperda population, with only a minor reduction in gene flow between the two overwintering populations in the continental USA, also corresponding to distinct host strains at the mitochondrial level. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Conclusions Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations. Based on the genomic similarities found between host strains and laboratory vs. field samples, our findings validate the experimental use of laboratory strains and the host strain differentiation based on mitochondria and sex-linked genetic markers extends to minor genome wide differences with some exceptions showing mixture between host strains is likely occurring in field populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07492-7.
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Affiliation(s)
- Katrina A Schlum
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN, 37996, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Rahul Banerjee
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert Meagher
- USDA-ARS Center for Medical, Agricultural and Veterinary Entomology (CMAVE), Insect Behavior and Biocontrol Research Unit, Gainesville, FL, 32608, USA
| | - Eliseu Pereira
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570, Brazil
| | - Maria Gabriela Murua
- Estación Experimental Agroindustrial Obispo Colombres, T4101XAC, Las Talitas, Tucumán, Argentina
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Ashley E Tessnow
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Diego Viteri Dillon
- Department of Agro-Environmental Sciences, Isabel Research Substation, University of Puerto Rico, Isabela, PR, 00662, USA
| | - Angela M Linares Ramirez
- Department of Agro-Environmental Sciences, Lajas Research Substation, University of Puerto Rico, Lajas, PR, 00667, USA
| | - Komivi S Akutse
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | | | - Fangneng Huang
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Dominic Reisig
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Scott J Emrich
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN, 37996, USA. .,Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA.
| | - Juan Luis Jurat-Fuentes
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN, 37996, USA. .,Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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