1
|
Wang Y, Yao Y, Zhang Y, Qian X, Guo D, Coates BS. A chromosome-level genome assembly of the soybean pod borer: insights into larval transcriptional response to transgenic soybean expressing the pesticidal Cry1Ac protein. BMC Genomics 2024; 25:355. [PMID: 38594617 PMCID: PMC11005160 DOI: 10.1186/s12864-024-10216-2] [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: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Genetically modified (GM) crop plants with transgenic expression of Bacillus thuringiensis (Bt) pesticidal proteins are used to manage feeding damage by pest insects. The durability of this technology is threatened by the selection for resistance in pest populations. The molecular mechanism(s) involved in insect physiological response or evolution of resistance to Bt is not fully understood. RESULTS To investigate the response of a susceptible target insect to Bt, the soybean pod borer, Leguminivora glycinivorella (Lepidoptera: Tortricidae), was exposed to soybean, Glycine max, expressing Cry1Ac pesticidal protein or the non-transgenic parental cultivar. Assessment of larval changes in gene expression was facilitated by a third-generation sequenced and scaffolded chromosome-level assembly of the L. glycinivorella genome (657.4 Mb; 27 autosomes + Z chromosome), and subsequent structural annotation of 18,197 RefSeq gene models encoding 23,735 putative mRNA transcripts. Exposure of L. glycinivorella larvae to transgenic Cry1Ac G. max resulted in prediction of significant differential gene expression for 204 gene models (64 up- and 140 down-regulated) and differential splicing among isoforms for 10 genes compared to unexposed cohorts. Differentially expressed genes (DEGs) included putative peritrophic membrane constituents, orthologs of Bt receptor-encoding genes previously linked or associated with Bt resistance, and those involved in stress responses. Putative functional Gene Ontology (GO) annotations assigned to DEGs were significantly enriched for 36 categories at GO level 2, respectively. Most significantly enriched cellular component (CC), biological process (BP), and molecular function (MF) categories corresponded to vacuolar and microbody, transport and metabolic processes, and binding and reductase activities. The DEGs in enriched GO categories were biased for those that were down-regulated (≥ 0.783), with only MF categories GTPase and iron binding activities were bias for up-regulation genes. CONCLUSIONS This study provides insights into pathways and processes involved larval response to Bt intoxication, which may inform future unbiased investigations into mechanisms of resistance that show no evidence of alteration in midgut receptors.
Collapse
Affiliation(s)
- Yangzhou Wang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yao Yao
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yunyue Zhang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xueyan Qian
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Dongquan Guo
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, 532 Science II, 2310 Pammel Dr., Ames, IA, 50011, USA.
| |
Collapse
|
2
|
Li B, Yang Z. Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between
Ostrinia furnacalis
and
Ostrinia nubilalis
(Lepidoptera: Crambidae) in the Yili area, Xinjiang, China. Ecol Evol 2022; 12:e9504. [PMID: 36407909 PMCID: PMC9667411 DOI: 10.1002/ece3.9504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Tianshan Mountains provide a model for studying biological evolution and speciation. Here we assess the evolutionary history of Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB), which are sympatric in the Yili River Valley in Xinjiang, China. Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI, COII, Cytb) and four nuclear DNA (nuDNA, EF‐1α, Wingless, RPS5, CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan), and MNS (Manasi). Our results reveal that there is an asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggests that the genetic divergence between the two species in this area may have occurred in Holocene at 0.008 Mya. Neutrality tests (Tajima's D, Fu's Fs), and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past. The demographic history and gene flow pattern between ACB and ECB may follow the “mountain isolation” hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are grouped together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear for both ACB and ECB, supporting that there has been frequent gene flow among the geographic populations in the Tianshan Mountains. These findings indicate that the Tianshan Mountains are less likely a barrier to gene flow of the two species.
Collapse
Affiliation(s)
- Bing Li
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
| | - Zhaofu Yang
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
- Key Laboratory of Plant Protection Resources and Pest MangagementNorthwest A&F UniversityYanglingChina
| |
Collapse
|
3
|
Zhukovskaya MI, Frolov AN. Alternative evolutionary strategies and tactics used by polyphagous insect to inhabit agricultural environment: Ostrinia nubialis as a case. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1007532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Substantial differentiation was found between Ostrinia populations, adapted to feed on dicotyledonous and monocotyledonous host plants, which results not only in oviposition and larval survival differences but also in formation of ethological premating sex isolation mechanisms. Two strategies are surmised in warmer and colder areas, correspondingly: wide range of host plant species in combination with strict developmental stages of the plant, and alternatively, few host plant are infested during almost all the stages of their development, Inside these strategies, tactics are plastic. They are activated by the sensory stimuli, such as temperature, humidity and odorants. The tactic of dispersal flight before mating could be beneficial when the host plant is abundant, but mating before the flight is a better choice under the situation of sparse cornfields. There are still multiple questions to address for clear understanding of Ostrinia behavior and evolution.
Collapse
|
4
|
Enos AN, Kozak GM. Elevated temperature increases reproductive investment in less preferred mates in the invasive European corn borer moth. Ecol Evol 2021; 11:12064-12074. [PMID: 34522361 PMCID: PMC8427566 DOI: 10.1002/ece3.7972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/10/2021] [Accepted: 07/14/2021] [Indexed: 01/26/2023] Open
Abstract
Rapidly changing environments may weaken sexual selection and lead to indiscriminate mating by interfering with the reception of mating signals or by increasing the costs associated with mate choice. If temperature alters sexual selection, it may impact population response and adaptation to climate change. Here, we examine how differences in temperature of the mating environment influence reproductive investment in the European corn borer moth (Ostrinia nubilalis). Mate preference in this species is known to be related to pheromone usage, with assortative mating occurring between genetically distinct E and Z strains that differ in the composition of female and male pheromones. We compared egg production within and between corn borer lines derived from four different populations that vary in pheromone composition and other traits. Pairs of adults were placed in a mating environment that matched the pupal environment (ambient temperature) or at elevated temperature (5°C above the pupal environment). At ambient temperature, we found that within-line pairs produced eggs sooner and produced more egg clusters than between-line pairs. However, at elevated temperature, between-line pairs produced the same number of egg clusters as within-line pairs. These results suggest that elevated temperature increased investment in matings with typically less preferred, between-line mates. This increased investment could result in changes in gene flow among corn borer populations in warming environments.
Collapse
Affiliation(s)
- Arielle N. Enos
- Department of BiologyUniversity of Massachusetts‐DartmouthDartmouthMassachusettsUSA
| | - Genevieve M. Kozak
- Department of BiologyUniversity of Massachusetts‐DartmouthDartmouthMassachusettsUSA
| |
Collapse
|
5
|
Wang Y, Kim KS, Li Q, Zhang Y, Wang Z, Coates BS. Influence of voltine ecotype and geographic distance on genetic and haplotype variation in the Asian corn borer. Ecol Evol 2021; 11:10244-10257. [PMID: 34367572 PMCID: PMC8328404 DOI: 10.1002/ece3.7829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 11/09/2022] Open
Abstract
Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in Ostrinia furnacalis may influence adult mating generation number (voltinism) across different local environments. The degree to which voltine ecotype, geographic distance, or other ecological factors influence O. furnacalis population genetic structure remains uncertain. Genetic differentiation was estimated between voltine ecotypes collected from 8 locations. Mitochondrial haplotypes were significantly different between historically allopatric univoltine and bivoltine locations, but confounded by a strong correlation with geographic distance. In contrast, single nucleotide polymorphism (SNP) genotypes show low but significant levels of variation and a lack of influence of geographic distance between allopatric voltine locations. Regardless, 11 of 257 SNP loci were predicted to be under selection, suggesting population genetic homogenization except at loci proximal to factors putatively under selection. These findings provide evidence of haplotype divergent voltine ecotypes that may be maintained in allopatric and sympatric areas despite relatively high rates of nuclear gene flow, yet influence of voltinism on maintenance of observed haplotype divergence remains unresolved.
Collapse
Affiliation(s)
- Yangzhou Wang
- Northeast Agricultural Research Center of ChinaJilin Academy of Agricultural SciencesChangchunChina
| | - Kyung Seok Kim
- Natural Resource Ecology and ManagementIowa State UniversityAmesIAUSA
| | - Qiyun Li
- Northeast Agricultural Research Center of ChinaJilin Academy of Agricultural SciencesChangchunChina
| | - Yunyue Zhang
- Northeast Agricultural Research Center of ChinaJilin Academy of Agricultural SciencesChangchunChina
| | - Zhen‐Ying Wang
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | | |
Collapse
|
6
|
Fisher KE, Bradbury SP, Coates BS. Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts. Sci Rep 2020; 10:19123. [PMID: 33154458 PMCID: PMC7645498 DOI: 10.1038/s41598-020-76088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.
Collapse
Affiliation(s)
- Kelsey E Fisher
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
| | - Steven P Bradbury
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- Department of Agriculture, Agriculture Research Station, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| |
Collapse
|
7
|
Adams SA, Tsutsui ND. The evolution of species recognition labels in insects. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190476. [PMID: 32420852 PMCID: PMC7331023 DOI: 10.1098/rstb.2019.0476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
The evolution of pre-zygotic reproductive isolation is a key step in the process of speciation. In many organisms, particularly insects, chemical labels are used as pheromones for species-specific mate recognition. Although an enormous body of knowledge exists regarding the patterns of pheromone chemical ecology, much less is known about the evolutionary processes that underlie the origin of new mating pheromones. Here, we examine case studies that have illuminated the origins of species-specific mating pheromones and suggest future directions for productive research. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.
Collapse
Affiliation(s)
| | - Neil Durie Tsutsui
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, #3114, Berkeley, CA 94720-3114, USA
| |
Collapse
|
8
|
Corrêa AS, Cordeiro EM, Omoto C. Agricultural insect hybridization and implications for pest management. PEST MANAGEMENT SCIENCE 2019; 75:2857-2864. [PMID: 31124266 DOI: 10.1002/ps.5495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Biological invasions, the expansion of agricultural frontiers, and climate change favor encounters of divergent lineages of animals and plants, increasing the likelihood of hybridization. However, hybridization of insect species and its consequences for agroecosystems have not received sufficient attention. Gene exchange between distinct and distant genetic pools can improve the survival and reproduction of insect pests, and threaten beneficial insects in disturbed agricultural environments. Hybridization may be the underlying explanation for the recurrent pest outbreaks and control failures in putative hybrid zones, as suspected for bollworm, corn borer, whiteflies, and stink bugs. Reliable predictions of the types of changes that can be expected in pest insect genomes and fitness, and of their impacts on the fate of species and populations remain elusive. Typical steps in pest management, such as insect identification, pest monitoring, and control are likely affected by gene flow and adaptive introgression mediated by hybridization, and we do not have ways to respond to or mitigate the problem. To address the adverse effects of farming intensification and global trade, we must ensure that current integrated pest management programs incorporate up-to-date monitoring and diagnostic tools. The rapid identification of hybrids, quantification of levels of introgression, and in-depth knowledge of what genes have been transferred may help to explain and predict insect population outbreaks and control failures in the future. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
- Alberto S Corrêa
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Erick Mg Cordeiro
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Celso Omoto
- Department of Entomology and Acarology, University of São Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| |
Collapse
|
9
|
Coates BS, Kozak GM, Seok Kim K, Sun J, Wang Y, Fleischer SJ, Dopman EB, Sappington TW. Influence of host plant, geography and pheromone strain on genomic differentiation in sympatric populations of Ostrinia nubilalis. Mol Ecol 2019; 28:4439-4452. [PMID: 31495004 DOI: 10.1111/mec.15234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/19/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
Abstract
Patterns of mating for the European corn borer (Ostrinia nubilalis) moth depend in part on variation in sex-pheromone blend. The ratio of (E)-11- and (Z)-11-tetradecenyl acetate (E11- and Z11-14:OAc) in the pheromone blend that females produce and males respond to differs between strains of O. nubilalis. Populations also vary in female oviposition preference for and larval performance on maize (C4) and nonmaize (C3) host plants. The relative contributions of sexual and ecological trait variation to the genetic structure of O. nubilalis remains unknown. Host-plant use (13 C/14 C ratios) and genetic differentiation were estimated among sympatric E and Z pheromone strain O. nubilalis males collected in sex-pheromone baited traps at 12 locations in Pennsylvania and New York between 2007 and 2010. Among genotypes at 65 single nucleotide polymorphism marker loci, variance at a position in the pheromone gland fatty acyl-reductase (pgfar) gene at the locus responsible for determining female pheromone ratio (Pher) explained 64% of the total genetic differentiation between males attracted to different pheromones (male response, Resp), providing evidence of sexual inter-selection at these unlinked loci. Principal coordinate, Bayesian clustering, and distance-based redundancy analysis (dbRDA) demonstrate that host plant history or geography does not significantly contribute to population variation or differentiation among males. In contrast, these analyses indicate that pheromone response and pgfar-defined strain contribute significantly to population genetic differentiation. This study suggests that behavioural divergence probably plays a larger role in driving genetic variation compared to host plant-defined ecological adaptation.
Collapse
Affiliation(s)
- Brad S Coates
- Corn Insects & Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts-Dartmouth, Dartmouth, MA, USA.,Department of Biology, Tufts University, Medford, MA, USA
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Jing Sun
- Department of Entomology, Iowa State University, Ames, IA, USA
| | - Yangzhou Wang
- Jilin Academy of Agricultural Sciences, Changchun, China
| | | | - Erik B Dopman
- Department of Biology, Tufts University, Medford, MA, USA
| | | |
Collapse
|
10
|
Chen YH, Schoville SD. Editorial overview: Ecology: Ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary biology and agricultural entomology. CURRENT OPINION IN INSECT SCIENCE 2018; 26:iv-viii. [PMID: 29764669 DOI: 10.1016/j.cois.2018.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI, USA
| |
Collapse
|