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Young R, Ahmed KA, Court L, Castro-Vargas C, Marcora A, Boctor J, Paull C, Wijffels G, Rane R, Edwards O, Walsh T, Pandey G. Improved reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella. G3 (BETHESDA, MD.) 2024; 14:jkae070. [PMID: 38564250 DOI: 10.1093/g3journal/jkae070] [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: 12/19/2023] [Revised: 12/19/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene, and polypropylene, and therefore, the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode) for G. mellonella. This 472 Mb genome is in 221 contigs with an N50 of 6.4 Mb and contains 13,604 protein-coding genes. Genes that code for known and putative polyethylene-degrading enzymes and their similarity to proteins found in other Lepidoptera are highlighted. An analysis of secretory proteins more likely to be involved in the plastic catabolic process has also been carried out.
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Affiliation(s)
| | | | - Leon Court
- CSIRO Environment, Acton, ACT 2601, Australia
| | | | - Anna Marcora
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Joseph Boctor
- Bioplastics Innovation Hub, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Cate Paull
- CSIRO Agriculture and Food, Dutton Park, QLD 4102, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Rahul Rane
- CSIRO Health and Biosecurity, Parkville, VIC 3052, Australia
| | | | - Tom Walsh
- CSIRO Environment, Acton, ACT 2601, Australia
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2
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Mahalle RM, Bosamia TC, Chakravarty S, Srivastava K, Meena RS, Kadam US, Srivastava CP. De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer. Genes (Basel) 2023; 14:1433. [PMID: 37510337 PMCID: PMC10379186 DOI: 10.3390/genes14071433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.
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Affiliation(s)
- Rashmi Manohar Mahalle
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tejas C Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Snehel Chakravarty
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Kartikeya Srivastava
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Radhe S Meena
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chandra P Srivastava
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
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3
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Zhao M, Shu G, Hu Y, Cao G, Wang Y. Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding. BMC Genomics 2023; 24:136. [PMID: 36944913 PMCID: PMC10029318 DOI: 10.1186/s12864-023-09156-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers. The genome-wide distribution and polymorphism of SSRs are not well studied due to the lack of high-quality genome DNA sequence data. RESULTS In this study, using data from high-quality de novo-sequenced maize genomes of five representative maize inbred lines, we revealed that SSRs were more densely present in telomeric region than centromeric region, and were more abundant in genic sequences than intergenic sequences. On genic sequences, tri- and hexanucleotide motifs were more abundant in CDS sequence and some mono- and dinucleotide motifs were more abundant in UTR sequences. Median length and chromosomal density of SSRs were both narrowly range-bound, with median length of 14-18 bp and genome-wide average density of 3355.77 bp/Mbp. LTR-RTs of < 0.4 Mya had higher SSR density (4498-4992 bp/Mbp). The genome-specific and motif-specific SSR polymorphism were studied. Their potential breeding applications were discussed. CONCLUSIONS We found that the median length of SSR sequences of different SSR motifs was nearly constant. SSR density in genic regions was much higher than intergenic regions. In addition, SSR density at LTR-RTs of different evolutionary ages varied in a narrow range. The SSRs and their LTR-RT carriers evolved at an equal rate. All these observations indicated that SSR length and density were under control of yet unknown evolutionary forces. The chromosome region-specific and motif-specific SSR polymorphisms we observed supported the notion that SSR polymorphism was invaluable genome resource for developing highly informative genome and gene markers in maize genetic research and molecular breeding.
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Affiliation(s)
- Meiqi Zhao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoping Shu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Yanhong Hu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Gangqiang Cao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yibo Wang
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China.
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, 450001, China.
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4
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Shao W, Cai W, Qiao F, Lin Z, Wei L. Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera). BMC Genom Data 2023; 24:5. [PMID: 36782146 PMCID: PMC9925362 DOI: 10.1186/s12863-023-01108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS). RESULTS Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)n, (AC)n, (CAA)n, (AAAC)n, (AACAA)n and (AAACAA)n, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)n, (AC)n, (TAT)n, (TTTA)n, (AACAA)n and (GAGAGG)n, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution. CONCLUSIONS Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.
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Affiliation(s)
- Weiwei Shao
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Wei Cai
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Fen Qiao
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Zhihua Lin
- grid.440824.e0000 0004 1757 6428College of Ecology, Lishui University, Lishui, 323000 Zhejiang People’s Republic of China
| | - Li Wei
- College of Ecology, Lishui University, Lishui, 323000, Zhejiang, People's Republic of China.
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Tay WT, Meagher RL, Czepak C, Groot AT. Spodoptera frugiperda: Ecology, Evolution, and Management Options of an Invasive Species. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:299-317. [PMID: 36198399 DOI: 10.1146/annurev-ento-120220-102548] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera, Noctuidae), is a well-known agricultural pest in its native range, North and South America, and has become a major invasive pest around the globe in the past decade. In this review, we provide an overview to update what is known about S. frugiperda in its native geographic ranges. This is followed by discussion of studies from the invaded areas to gain insights into S. frugiperda's ecology, specifically its reproductive biology, host plant use, status of insecticide resistance alleles, and biocontrol methods in native and invasive regions. We show that reference to host strains is uninformative in the invasive populations because multidirectional introduction events likely underpinned its recent rapid spread. Given that recent genomic analyses show that FAW is much more diverse than was previously assumed, and natural selection forces likely differ geographically, region-specific approaches will be needed to control this global pest.
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Affiliation(s)
- Wee Tek Tay
- CSIRO Black Mountain Laboratories, Australian Capital Territory, Australia;
| | - Robert L Meagher
- Agricultural Research Service, United States Department of Agriculture, Gainesville, Florida, USA;
| | - Cecilia Czepak
- Escola de Agronomia, Campus Samambaia, Universidade Federal de Goiás, Goiânia, Brazil;
| | - Astrid T Groot
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherlands;
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6
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Kanyesigye D, Alibu VP, Tay WT, Nalela P, Paparu P, Olaboro S, Nkalubo ST, Kayondo IS, Silva G, Seal SE, Otim MH. Population Genetic Structure of the Bean Leaf Beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda. INSECTS 2022; 13:543. [PMID: 35735880 PMCID: PMC9225125 DOI: 10.3390/insects13060543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/26/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022]
Abstract
Bean leaf beetle (BLB) (Ootheca mutabilis) has emerged as an important bean pest in Uganda, leading to devastating crop losses. There is limited information on the population genetic structure of BLB despite its importance. In this study, novel microsatellite DNA markers and the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequences were used to analyze the spatial population genetic structure, genetic differentiation and haplotype diversity of 86 O. mutabilis samples from 16 (districts) populations. We identified 19,356 simple sequence repeats (SSRs) (mono, di-, tri-, tetra-, penta-, and hexa-nucleotides) of which 81 di, tri and tetra-nucleotides were selected for primer synthesis. Five highly polymorphic SSR markers (4-21 alleles, heterozygosity 0.59-0.84, polymorphic information content (PIC) 50.13-83.14%) were used for this study. Analyses of the 16 O. mutabilis populations with these five novel SSRs found nearly all the genetic variation occurring within populations and there was no evidence of genetic differentiation detected for both types of markers. Also, there was no evidence of isolation by distance between geographical and genetic distances for SSR data and mtCOI data except in one agro-ecological zone for mtCOI data. Bayesian clustering identified a signature of admixture that suggests genetic contributions from two hypothetical ancestral genetic lineages for both types of markers, and the minimum-spanning haplotype network showed low differentiation in minor haplotypes from the most common haplotype with the most common haplotype occurring in all the 16 districts. A lack of genetic differentiation indicates unrestricted migrations between populations. This information will contribute to the design of BLB control strategies.
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Affiliation(s)
- Dalton Kanyesigye
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Vincent Pius Alibu
- College of Natural Sciences (CoNAS), Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Wee Tek Tay
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia;
| | - Polycarp Nalela
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
| | - Pamela Paparu
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
| | - Samuel Olaboro
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
| | - Stanley Tamusange Nkalubo
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
| | - Ismail Siraj Kayondo
- International Institute of Tropical Agriculture, PMB 5320, Oyo Rd., Ibadan 20001, Nigeria;
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK; (G.S.); (S.E.S.)
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK; (G.S.); (S.E.S.)
| | - Michael Hilary Otim
- National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda; (D.K.); (P.N.); (P.P.); (S.O.); (S.T.N.)
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7
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Petrosino G, Ponte G, Volpe M, Zarrella I, Ansaloni F, Langella C, Di Cristina G, Finaurini S, Russo MT, Basu S, Musacchia F, Ristoratore F, Pavlinic D, Benes V, Ferrante MI, Albertin C, Simakov O, Gustincich S, Fiorito G, Sanges R. Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. BMC Biol 2022; 20:116. [PMID: 35581640 PMCID: PMC9115989 DOI: 10.1186/s12915-022-01303-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/21/2022] [Indexed: 01/07/2023] Open
Abstract
Background Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. Results Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. Conclusions The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01303-5.
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Affiliation(s)
- Giuseppe Petrosino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Massimiliano Volpe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ilaria Zarrella
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Federico Ansaloni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy
| | - Concetta Langella
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Giulia Di Cristina
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Institute of Zoology, University of Cologne, Cologne, Germany
| | - Sara Finaurini
- Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Monia T Russo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Swaraj Basu
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.,Strand Life Sciences, Bengaluru, India
| | - Francesco Musacchia
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Filomena Ristoratore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | - Dinko Pavlinic
- Scientific Core Facilities & Technologies, GeneCore, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Vladimir Benes
- Scientific Core Facilities & Technologies, GeneCore, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Maria I Ferrante
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy
| | | | - Oleg Simakov
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.,Department of Molecular Evolution and Development, Wien University, Althanstraße 14 (UZA I), 1090, Wien, Austria
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy.,Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy.
| | - Remo Sanges
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, SZN, 80121, Naples, Italy. .,Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Via Enrico Melen 83, 16152, Genova, Italy. .,Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy.
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8
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Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci U S A 2021; 118:e2025051118. [PMID: 34099551 PMCID: PMC8214670 DOI: 10.1073/pnas.2025051118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027;
- Department of Biological Sciences, State University of New York College at Old Westbury, Old Westbury, NY 11568
| | - Stephen E Harris
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
- Department of Biology, State University of New York Purchase College, Purchase, NY 10577
| | | | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS B2Y 4A2, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dustin R Rubenstein
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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9
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Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. Commun Biol 2021; 4:186. [PMID: 33574498 PMCID: PMC7878876 DOI: 10.1038/s42003-021-01716-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Simple sequence repeats (SSRs) are rare (approximately 1%) in most genomes and are generally considered to have no function. However, penaeid shrimp genomes have a high proportion of SSRs (>23%), raising the question of whether these SSRs play important functional and evolutionary roles in these SSR-rich species. Here, we show that SSRs drive genome plasticity and adaptive evolution in two penaeid shrimp species, Fenneropenaeus chinensis and Litopenaeus vannamei. Assembly and comparison of genomes of these two shrimp species at the chromosome-level revealed that transposable elements serve as carriers for SSR expansion, which is still occurring. The remarkable genome plasticity identified herein might have been shaped by significant SSR expansions. SSRs were also found to regulate gene expression by multi-omics analyses, and be responsible for driving adaptive evolution, such as the variable osmoregulatory capacities of these shrimp under low-salinity stress. These data provide strong evidence that SSRs are an important driver of the adaptive evolution in penaeid shrimp.
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10
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Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Sci Rep 2020; 10:18621. [PMID: 33122761 PMCID: PMC7596044 DOI: 10.1038/s41598-020-75553-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/05/2020] [Indexed: 01/06/2023] Open
Abstract
Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5'-UTR and 3'-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.
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11
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Large-scale genetic admixture suggests high dispersal in an insect pest, the apple fruit moth. PLoS One 2020; 15:e0236509. [PMID: 32785243 PMCID: PMC7423104 DOI: 10.1371/journal.pone.0236509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 11/25/2022] Open
Abstract
Knowledge about population genetic structure and dispersal capabilities is important for the development of targeted management strategies for agricultural pest species. The apple fruit moth, Argyresthia conjugella (Lepidoptera, Yponomeutidae), is a pre-dispersal seed predator. Larvae feed on rowanberries (Sorbus aucuparia), and when rowanberry seed production is low (i.e., inter-masting), the moth switches from laying eggs in rowanberries to apples (Malus domestica), resulting in devastating losses in apple crops. Using genetic methods, we investigated if this small moth expresses any local genetic structure, or alternatively if gene flow may be high within the Scandinavian Peninsula (~850.000 km2, 55o - 69o N). Genetic diversity was found to be high (n = 669, mean He = 0.71). For three out of ten tetranucleotide STRs, we detected heterozygote deficiency caused by null alleles, but tests showed little impact on the overall results. Genetic differentiation between the 28 sampling locations was very low (average FST = 0.016, P < 0.000). Surprisingly, we found that all individuals could be assigned to one of two non-geographic genetic clusters, and that a third, geographic cluster was found to be associated with 30% of the sampling locations, with weak but significant signals of isolation-by-distance. Conclusively, our findings suggest wind-aided dispersal and spatial synchrony of both sexes of the apple fruit moth over large areas and across very different climatic zones. We speculate that the species may recently have had two separate genetic origins caused by a genetic bottleneck after inter-masting, followed by rapid dispersal and homogenization of the gene pool across the landscape. We suggest further investigations of spatial genetic similarities and differences of the apple fruit moth at larger geographical scales, through life-stages, across inter-masting, and during attacks by the parasitoid wasp (Microgaster politus).
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12
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Genomewide analysis of microsatellite markers based on sequenced database in two anuran species. J Genet 2020. [DOI: 10.1007/s12041-020-01222-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019; 47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.
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Affiliation(s)
- Christina E Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16–18, 04107 Leipzig, Germany
| | - Christian Hammann
- Ribogenetics & Biochemistry, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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14
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Trochez-Solarte JD, Ruiz-Erazo X, Almanza-Pinzon M, Zambrano-Gonzalez G. Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review. F1000Res 2019; 8:1424. [PMID: 32148760 PMCID: PMC7043130 DOI: 10.12688/f1000research.20052.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 11/23/2022] Open
Abstract
In the genome of
Bombyx mori Linnaeus (1758), the microsatellites, or simple sequence repeats (SSR), feature among their particular characteristics a high adenine and thymine (A/T) content, low number of repeats, low frequency, and a grouping in "families" with similar flanking regions. Such characteristics may be the result of a complex interaction between factors that limit the size and dispersion of SSR loci—such as their high association with transposons—and mean that microsatellites within this taxon suitable as molecular markers are relatively rare. The determination of genetic profiles in populations and cell lines has not been affected owing to the high level of polymorphism, nor has the analysis of diversity, structure and genetic relationships. However, the scarcity of suitable microsatellites has restricted their application in genetic mapping, limiting them to preliminary identification of gene location of genes or quantitative trait loci (QTLs) related to thermotolerance, resistance to viruses, pigmentation patterns, body development and the weight of the cocoon, the cortex, the pupa and the filament. The review confirms that, as markers, microsatellites are versatile and perform well. They could thus be useful both to advance research in emerging countries with few resources seeking to promote sericulture in their territories, and to advance in the genetic and molecular knowledge of characteristics of productive and biological interest, given the latest technological developments in terms of the sequencing, identification, isolation and genotyping of SSR loci.
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Affiliation(s)
- Julian David Trochez-Solarte
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Ximena Ruiz-Erazo
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Martha Almanza-Pinzon
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Giselle Zambrano-Gonzalez
- Biology Department, Geology, Ecology and Conservation Research Group (GECO), Faculty of Natural Sciences and Education, University of Cauca, Popayán, Cauca, 190002, Colombia
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15
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Gonçalves RM, Mastrangelo T, Rodrigues JCV, Paulo DF, Omoto C, Corrêa AS, de Azeredo‐Espin AML. Invasion origin, rapid population expansion, and the lack of genetic structure of cotton bollworm ( Helicoverpa armigera) in the Americas. Ecol Evol 2019; 9:7378-7401. [PMID: 31346410 PMCID: PMC6635935 DOI: 10.1002/ece3.5123] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
In 2013, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) was officially declared as present in Brazil and, after two years, the species was detected in the Caribbean and North America. Information on genetic features and accurate distribution of pests is the basis for agricultural protection policies. Furthermore, such knowledge is imperative to develop control strategies, understand the geographical range, and genetic patterns of this species in the Americas. Here, we carried out the widest sampling of H. armigera in the South American continent and Puerto Rico, after we estimated the diversity, demographic parameters, and genetic structure. The Internal Transcribed Spacer 1 (ITS1) nuclear marker was used to investigate the presence of putative hybrids between H. armigera and H. zea, and they were observed at a frequency of 1.5%. An ABC analysis, based in COI gene fragment, suggested Europe as the origin of South America specimens of H. armigeraand following a movement northward through the Caribbean. Three mtDNA genes and three nDNA markers revealed high genetic diversity distributed without the defined population structure of H. armigera in South America. Most of the genetic variation is within populations with a multidirectional expansion of H. armigera among morphoclimatic regions. High genetic diversity, rapid population expansion, and hybridization have implications for pest management since they suggest that adaptive alleles are spread through wide areas in South America that favor rapid local adaptation of H. armigera to new and disturbed environments (e.g., in agricultural areas).
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Affiliation(s)
- Rogério Martins Gonçalves
- Department of Genetics, Evolution and Bioagents, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
| | - Thiago Mastrangelo
- Centre for Nuclear Energy in AgricultureUniversity of São Paulo (USP)PiracicabaBrazil
| | | | - Daniel Fernando Paulo
- Department of Genetics, Evolution and Bioagents, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
| | - Celso Omoto
- Department of Entomology and AcarologyLuiz de Queiroz College of Agriculture, University of São Paulo (USP/ESALQ)PiracicabaBrazil
| | - Alberto Soares Corrêa
- Department of Entomology and AcarologyLuiz de Queiroz College of Agriculture, University of São Paulo (USP/ESALQ)PiracicabaBrazil
| | - Ana Maria Lima de Azeredo‐Espin
- Department of Genetics, Evolution and Bioagents, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyState University of Campinas (UNICAMP)CampinasBrazil
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16
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Walsh TK, Perera O, Anderson C, Gordon K, Czepak C, McGaughran A, Zwick A, Hackett D, Tay WT. Mitochondrial DNA genomes of five major Helicoverpa pest species from the Old and New Worlds (Lepidoptera: Noctuidae). Ecol Evol 2019; 9:2933-2944. [PMID: 30891227 PMCID: PMC6405535 DOI: 10.1002/ece3.4971] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
Five species of noctuid moths, Helicoverpa armigera, H. punctigera, H. assulta, H. zea, and H. gelotopoeon, are major agricultural pests inhabiting various and often overlapping global distributions. Visual identification of these species requires a great deal of expertise and misidentification can have repercussions for pest management and agricultural biosecurity. Here, we report on the complete mitochondrial genomes of H. assulta assulta and H. assulta afra, H. gelotopoeon, H. punctigera, H. zea, and H. armigera armigera and H. armigera conferta' assembled from high-throughput sequencing data. This study significantly increases the mitogenome resources for these five agricultural pests with sequences assembled from across different continents, including an H. armigera individual collected from an invasive population in Brazil. We infer the phylogenetic relationships of these five Helicoverpa species based on the 13 mitochondrial DNA protein-coding genes (PCG's) and show that two publicly available mitogenomes of H. assulta (KP015198 and KR149448) have been misidentified or incorrectly assembled. We further consolidate existing PCR-RFLP methods to cover all five Helicoverpa pest species, providing an updated method that will contribute to species differentiation and to future monitoring efforts of Helicoverpa pest species across different continents. We discuss the value of Helicoverpa mitogenomes to assist with species identification in view of the context of the rapid spread of H. armigera in the New World. With this work, we provide the molecular resources necessary for future studies of the evolutionary history and ecology of these species.
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Affiliation(s)
- Tom K. Walsh
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Omaththage Perera
- USDA‐ARS Southern Insect Management Research UnitStonevilleMississippi
| | - Craig Anderson
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General HospitalUniversity of EdinburghEdinburghUK
| | - Karl Gordon
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Cecilia Czepak
- Escola de AgronomiaUniversidade Federal de GoiásGoiâniaBrazil
| | - Angela McGaughran
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACTAustralia
| | - Andreas Zwick
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | | | - Wee Tek Tay
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
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17
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Jones CM, Parry H, Tay WT, Reynolds DR, Chapman JW. Movement Ecology of Pest Helicoverpa: Implications for Ongoing Spread. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:277-295. [PMID: 30296859 DOI: 10.1146/annurev-ento-011118-111959] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The recent introduction and spread of Helicoverpa armigera throughout South America highlight the invasiveness and adaptability of moths in the Helicoverpa genus. Long-range movement in three key members, H. armigera, H. zea, and H. punctigera, occurs by migration and international trade. These movements facilitate high population admixture and genetic diversity, with important economic, biosecurity, and control implications in today's agricultural landscape. This is particularly true for the spread of resistance alleles to transgenic crops expressing Bacillus thuringiensis (Bt) toxins that are planted over vast areas to suppress Helicoverpa spp. The ability to track long-distance movement through radar technology, population genetic markers, and/or long-distance dispersal modeling has advanced in recent years, yet we still know relatively little about the population trajectories or migratory routes in Helicoverpa spp. Here, we consider how experimental and theoretical approaches can be integrated to fill key knowledge gaps and assist management practices.
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Affiliation(s)
- Christopher M Jones
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom;
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Hazel Parry
- Ecosciences Precinct, CSIRO, Brisbane, Queensland 4102, Australia;
| | - Wee Tek Tay
- Black Mountain Laboratories, CSIRO, Canberra, Australian Capital Territory 2601, Australia;
| | - Don R Reynolds
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham ME4 4TB, United Kingdom;
| | - Jason W Chapman
- Centre for Ecology and Conservation, and Environment and Sustainability Institute, University of Exeter, Penryn TR10 9FE, United Kingdom;
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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18
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Song SV, Anderson C, Good RT, Leslie S, Wu Y, Oakeshott JG, Robin C. Population differentiation between Australian and Chinese Helicoverpa armigera occurs in distinct blocks on the Z-chromosome. BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:817-830. [PMID: 29397798 DOI: 10.1017/s0007485318000081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Over the last 40 years, many types of population genetic markers have been used to assess the population structure of the pest moth species Helicoverpa armigera. While this species is highly vagile, there is evidence of inter-continental population structure. Here, we examine Z-chromosome molecular markers within and between Chinese and Australian populations. Using 1352 polymorphic sites from 40 Z-linked loci, we compared two Chinese populations of moths separated by 700 km and found virtually no population structure (n = 41 and n = 54, with <1% of variation discriminating between populations). The levels of nucleotide diversity within these populations were consistent with previous estimates from introns in Z-linked genes of Australian samples (π = 0.028 vs. 0.03). Furthermore, all loci surveyed in these Chinese populations showed a skew toward rare variants, with ten loci having a significant Tajima's D statistic, suggesting that this species could have undergone a population expansion. Eight of the 40 loci had been examined in a previous study of Australian moths, of which six revealed very little inter-continental population structure. However, the two markers associated with the Cyp303a1 locus that has previously been proposed to be a target of a selective sweep, exhibited allele structuring between countries. Using a separate dataset of 19 Australian and four Chinese moths, we scanned the molecular variation distributed across the entire Z-chromosome and found distinct blocks of differentiation that include the region containing Cyp303a1. We recommend some of these loci join those associated with insecticide resistance to form a set of genes best suited to analyzing population structure in this global pest.
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Affiliation(s)
- S V Song
- School of Biosciences, University of Melbourne,Victoria,Australia
| | - C Anderson
- MRC Human Genetics Unit,MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital,Edinburgh,UK
| | - R T Good
- School of Biosciences, University of Melbourne,Victoria,Australia
| | - S Leslie
- School of Biosciences, University of Melbourne,Victoria,Australia
| | - Y Wu
- College of Plant Protection, Nanjing Agricultural University,Nanjing,China
| | - J G Oakeshott
- Land and Water Flagship,Commonwealth Scientific and Industrial Research Organisation,Australian Capital Territory,Australia
| | - C Robin
- School of Biosciences, University of Melbourne,Victoria,Australia
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19
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Nishiyama E, Ohshima K. Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons. Genome Biol Evol 2018; 10:1471-1483. [PMID: 29850801 PMCID: PMC6007223 DOI: 10.1093/gbe/evy098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/15/2022] Open
Abstract
In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.
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Affiliation(s)
- Eri Nishiyama
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
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20
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Zhu WC, Sun JT, Dai J, Huang JR, Chen L, Hong XY. New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler). BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:636-644. [PMID: 29173200 DOI: 10.1017/s000748531700116x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.
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Affiliation(s)
- W-C Zhu
- Department of Entomology,Nanjing Agricultural University,Nanjing, Jiangsu 210095,China
| | - J-T Sun
- Department of Entomology,Nanjing Agricultural University,Nanjing, Jiangsu 210095,China
| | - J Dai
- Department of Entomology,Nanjing Agricultural University,Nanjing, Jiangsu 210095,China
| | - J-R Huang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences,Zhengzhou, Henan 450002,China
| | - L Chen
- Department of Entomology,Nanjing Agricultural University,Nanjing, Jiangsu 210095,China
| | - X-Y Hong
- Department of Entomology,Nanjing Agricultural University,Nanjing, Jiangsu 210095,China
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21
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Serrato-Capuchina A, Matute DR. The Role of Transposable Elements in Speciation. Genes (Basel) 2018; 9:E254. [PMID: 29762547 PMCID: PMC5977194 DOI: 10.3390/genes9050254] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/20/2023] Open
Abstract
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Biology Department, Genome Sciences Building, University of North Carolina, Chapel Hill, NC 27514, USA.
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22
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Ma X, Sun B, Zhu F. Molecular cloning of Kuruma shrimp Marsupenaeus japonicus endonuclease-reverse transcriptase and its positive role in white spot syndrome virus and Vibrio alginolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2018; 73:297-308. [PMID: 29275132 DOI: 10.1016/j.fsi.2017.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/08/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
This study investigated the function of endonuclease-reverse transcriptase (mjERT) in Marsupenaeus japonicus. The 1129 bp cDNA sequence of mjERT was cloned from M. japonicus using rapid amplification of cDNA ends (RACE) PCR, and RT-qPCR analysis indicated that mjERT was highly expressed in the gills and hepatopancreas of M. japonicus. We also found that white spot syndrome virus (WSSV) or Vibrio alginolyticus challenge could enhance the expression of mjERT. When mjERT was inhibited, immune genes such as toll, p53, hemocyanin and tumor necrosis factor-α (TNF-α) were significantly down-regulated (P < .01) in the hemocytes of shrimp, while myosin was significantly up-regulated (P < .01). We demonstrated that mjERT is very important for the progression of WSSV infection and that the cumulative mortality of WSSV-infected and V. alginolyticus-infected shrimps was significantly increased following mjERT RNA interfere (RNAi). Apoptosis data provided information to suggest that mjERT-dsRNA challenge caused less apoptosis in hemocytes in both the disease-free and viral group. We also revealed that mjERT-dsRNA treatment resulted in a lower phagocytosis rate in the hemocytes of V. alginolyticus-challenged shrimp. Finally, we found that the absence of mjERT had an significantly negative impact upon shrimp phenoloxidase (PO) activity, superoxide dismutase (SOD) activity and total hemocyte count (THC) following WSSV or V. alginolyticus infection, indicating a regulative role for mjERT in the innate immunity of shrimp in response to pathogenic infection. In summary, we concluded that mjERT might promote the anti-WSSV immune response of shrimp by regulating apoptosis, PO activity, THC and SOD activity, and also exert a positive role in the immune response against V. alginolyticus by regulating phagocytosis, SOD activity, PO activity and THC.
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Affiliation(s)
- Xiongchao Ma
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Baozhen Sun
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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Ding S, Wang S, He K, Jiang M, Li F. Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects. BMC Genomics 2017; 18:848. [PMID: 29110701 PMCID: PMC5674736 DOI: 10.1186/s12864-017-4234-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown. RESULTS We identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2-93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22-73 bp) were longer than perfect SSRs (16-30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level. CONCLUSION Millions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.
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Affiliation(s)
- Simin Ding
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Entry-exit Inspection and Quarantine Bureau, Shanghai, 200135 China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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Ahmed MM, Shen C, Khan AQ, Wahid MA, Shaban M, Lin Z. A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium. Hereditas 2017; 154:12. [PMID: 28529469 PMCID: PMC5437633 DOI: 10.1186/s41065-017-0034-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
Background Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. Results Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites. Moreover, comparative genomics approach aided in exploration of microsatellites conservation footprints in Gossypium evolution. Based on our results, motif imperfection in repeat length was found intricately related to genomic abundance of imperfect microsatellites among 13 genomes. Microsatellite decay estimation depicted slower decay of long motif repeats which led to predominant abundance of 5-nt repeat motif in Gossypium species. Short motif repeats exhibited rapid decay through the evolution of Gossypium lineage ensuing drastic decrease of 2-nt repeats, of which, “AT” motif type dilapidated in cultivated tetraploids of cotton. Conclusion The outcome could be a directive to explore comparative evolutionary footprints of simple non-coding genetic elements i.e., repeat elements, through the evolution of genus-specific characteristics in cotton genomes. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0034-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Atif Wahid
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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25
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Guérin F, Arnaiz O, Boggetto N, Denby Wilkes C, Meyer E, Sperling L, Duharcourt S. Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements. BMC Genomics 2017; 18:327. [PMID: 28446146 PMCID: PMC5405496 DOI: 10.1186/s12864-017-3713-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/20/2017] [Indexed: 12/02/2022] Open
Abstract
Background DNA elimination is developmentally programmed in a wide variety of eukaryotes, including unicellular ciliates, and leads to the generation of distinct germline and somatic genomes. The ciliate Paramecium tetraurelia harbors two types of nuclei with different functions and genome structures. The transcriptionally inactive micronucleus contains the complete germline genome, while the somatic macronucleus contains a reduced genome streamlined for gene expression. During development of the somatic macronucleus, the germline genome undergoes massive and reproducible DNA elimination events. Availability of both the somatic and germline genomes is essential to examine the genome changes that occur during programmed DNA elimination and ultimately decipher the mechanisms underlying the specific removal of germline-limited sequences. Results We developed a novel experimental approach that uses flow cell imaging and flow cytometry to sort subpopulations of nuclei to high purity. We sorted vegetative micronuclei and macronuclei during development of P. tetraurelia. We validated the method by flow cell imaging and by high throughput DNA sequencing. Our work establishes the proof of principle that developing somatic macronuclei can be sorted from a complex biological sample to high purity based on their size, shape and DNA content. This method enabled us to sequence, for the first time, the germline DNA from pure micronuclei and to identify novel transposable elements. Sequencing the germline DNA confirms that the Pgm domesticated transposase is required for the excision of all ~45,000 Internal Eliminated Sequences. Comparison of the germline DNA and unrearranged DNA obtained from PGM-silenced cells reveals that the latter does not provide a faithful representation of the germline genome. Conclusions We developed a flow cytometry-based method to purify P. tetraurelia nuclei to high purity and provided quality control with flow cell imaging and high throughput DNA sequencing. We identified 61 germline transposable elements including the first Paramecium retrotransposons. This approach paves the way to sequence the germline genomes of P. aurelia sibling species for future comparative genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3713-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frédéric Guérin
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France
| | - Olivier Arnaiz
- Institute of Integrative Biology of the Cell, UMR9198 CNRS CEA Univ, Paris-Sud Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Nicole Boggetto
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France
| | - Cyril Denby Wilkes
- Institute of Integrative Biology of the Cell, UMR9198 CNRS CEA Univ, Paris-Sud Université Paris-Saclay, 91198, Gif-sur-Yvette, France.,Current address: Institut de Biologie et de Technologies de Saclay (IBITECS), CEA, F-91191, Gif-sur-Yvette Cedex, France
| | - Eric Meyer
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Linda Sperling
- Institute of Integrative Biology of the Cell, UMR9198 CNRS CEA Univ, Paris-Sud Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Sandra Duharcourt
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, F-75205, France.
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Anderson CJ, Tay WT, McGaughran A, Gordon K, Walsh TK. Population structure and gene flow in the global pest, Helicoverpa armigera. Mol Ecol 2016; 25:5296-5311. [PMID: 27661785 DOI: 10.1111/mec.13841] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/27/2016] [Accepted: 09/14/2016] [Indexed: 01/03/2023]
Abstract
Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages. Here, we integrate several end points derived from high-throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping-by-sequencing and whole-genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from diverse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field-caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.
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Affiliation(s)
- C J Anderson
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK. .,Black Mountain Laboratories, CSIRO, Acton, ACT, 2601, Australia.
| | - W T Tay
- Black Mountain Laboratories, CSIRO, Acton, ACT, 2601, Australia
| | - A McGaughran
- Black Mountain Laboratories, CSIRO, Acton, ACT, 2601, Australia.,School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - K Gordon
- Black Mountain Laboratories, CSIRO, Acton, ACT, 2601, Australia
| | - T K Walsh
- Black Mountain Laboratories, CSIRO, Acton, ACT, 2601, Australia
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27
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Schmid M, Csencsics D, Gugerli F. Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea. Mol Ecol Resour 2016; 16:1499-1507. [PMID: 27273885 DOI: 10.1111/1755-0998.12547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/15/2016] [Accepted: 05/06/2016] [Indexed: 11/28/2022]
Abstract
Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages repark and repeatmasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.
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Affiliation(s)
- Max Schmid
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, CH-8903, Switzerland.,University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Daniela Csencsics
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, CH-8903, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, CH-8903, Switzerland.
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28
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Tay WT, Kerr PJ, Jermiin LS. Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia. PLoS One 2016; 11:e0146699. [PMID: 26771743 PMCID: PMC4714883 DOI: 10.1371/journal.pone.0146699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 12/20/2015] [Indexed: 11/18/2022] Open
Abstract
Culicoides brevitarsis is a vector of the bluetongue virus (BTV), which infects sheep and cattle. It is an invasive species in Australia with an assumed Asian/South East Asian origin. Using one mitochondrial marker (i.e., part of the cytochrome oxidase subunit I gene) and six nuclear markers, we inferred population genetic structure and possible incursion pathways for Australian C. brevitarsis. Nine mitochondrial haplotypes, with low nucleotide sequence diversity (0.0-0.7%) among these, were identified in a sample of 70 individuals from seven sites. Both sets of markers revealed a homogeneous population structure, albeit with evidence of isolation by distance and two genetically distinct clusters distributed along a north-to-south cline. No evidence of a cryptic species complex was found. The geographical distribution of the mitochondrial haplotypes is consistent with at least two incursion pathways into Australia since the arrival of suitable livestock hosts. By contrast, 15 mitochondrial haplotypes, with up to four times greater nucleotide sequence diversity (0.0-2.9%) among these, were identified in a sample of 16 individuals of the endemic C. marksi (sampled from a site in South Australia and another in New South Wales). A phylogenetic tree inferred using the mitochondrial marker revealed that the Australian and Japanese samples of C. brevitarsis are as evolutionarily different from one another as some of the other Australian species (e.g., C. marksi, C. henryi, C. pallidothorax) are. The phylogenetic tree placed four of the species endemic to Australia (C. pallidothorax, C. bundyensis, C. marksi, C. henryi) in a clade, with a fifth such species (C. bunrooensis) sharing a common ancestor with that clade and a clade comprising two Japanese species (C. verbosus, C. kibunensis).
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Affiliation(s)
- W. T. Tay
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
| | - P. J. Kerr
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
- School of Biological Sciences, The University of Sydney, Sydney, 2006, Australia
| | - L. S. Jermiin
- CSIRO, Black Mountain Laboratories, Canberra, ACT, 2601, Australia
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29
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Genetic diversity of Parides ascanius (Lepidoptera: Papilionidae: Troidini): implications for the conservation of Brazil’s most iconic endangered invertebrate species. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0802-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Characterization of microsatellites and repetitive flanking sequences (ReFS) from the topmouth culter (Culter alburnus Basilewsky). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Tay WT, Mahon RJ, Heckel DG, Walsh TK, Downes S, James WJ, Lee SF, Reineke A, Williams AK, Gordon KHJ. Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein. PLoS Genet 2015; 11:e1005534. [PMID: 26583651 PMCID: PMC4652872 DOI: 10.1371/journal.pgen.1005534] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton) expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests) to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC) marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC) transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the detailed mode-of-action of the two Bt Cry toxins. Transgenic crops expressing the insecticidal protein Cry2Ab from Bacillus thuringiensis (Bt) are used worldwide to suppress damage by lepidopteran pests, often used in combination with Cry1Ac toxin to delay resistance evolution. Until now, the Cry2Ab mode of action and the mechanism of resistance were unknown, with field-isolated Cry2Ab resistant Helicoverpa armigera showing no cross-resistance to Cry1Ac. In this study, biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by EPIC marker mapping and candidate gene sequencing identified three independent INDEL mutations in an ATP-Binding Cassette transporter subfamily A gene (ABCA2). A deletion mutation was identified in the same gene of resistant H. punctigera. All four mutations are predicted to truncate the ABCA2 protein. This is the first molecular genetic characterization of insect resistance to the Cry2Ab toxin, and detection of diverse Cry2Ab resistance alleles will contribute to understanding the micro-evolutionary processes that underpinned lepidopteran Bt-resistance.
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Affiliation(s)
- Wee Tek Tay
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Rod J. Mahon
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - David G. Heckel
- Department of Entomology, Max-Planck Institute for Chemical Ecology, Beutenberg Campus, Jena, Germany
| | - Thomas K. Walsh
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Sharon Downes
- CSIRO, Australian Cotton Research Institute, Narrabri, New South Wales, Australia
| | - William J. James
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Sui-Fai Lee
- Department of Genetics, University of Melbourne, Parkville, Victoria, Australia
| | - Annette Reineke
- Institute for Phytomedicine, Center of Applied Biology, Geisenheim University, Geiesenheim, Germany
| | - Adam K. Williams
- Department of Genetics, University of Melbourne, Parkville, Victoria, Australia
| | - Karl H. J. Gordon
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
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32
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Biswas MK, Liu Y, Li C, Sheng O, Mayer C, Yi G. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential. PLoS One 2015; 10:e0131312. [PMID: 26121637 PMCID: PMC4488140 DOI: 10.1371/journal.pone.0131312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/01/2015] [Indexed: 01/14/2023] Open
Abstract
The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.
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Affiliation(s)
- Manosh Kumar Biswas
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- The College of Life Science, South China Agricultural University, Guangzhou, China
| | - Yuxuan Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Ou Sheng
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Ganjun Yi
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
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Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages. Sci Rep 2015; 5:11042. [PMID: 26047353 PMCID: PMC4457133 DOI: 10.1038/srep11042] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 05/08/2015] [Indexed: 12/29/2022] Open
Abstract
Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.
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34
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Cao LJ, Wen JB, Wei SJ, Liu J, Yang F, Chen M. Characterization of novel microsatellite markers for Hyphantria cunea and implications for other Lepidoptera. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:273-284. [PMID: 25772405 DOI: 10.1017/s0007485315000061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers for H. cunea from SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified as Grouped should not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy-Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, and F ST performed better than did R ST for the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies of H. cunea.
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Affiliation(s)
- L J Cao
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - J B Wen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - S J Wei
- Institute of Plant and Environmental Protection,Beijing Academy of Agriculture and Forestry Sciences,Beijing 100097,China
| | - J Liu
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - F Yang
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
| | - M Chen
- Beijing Key Laboratory for Forest Pest Control,College of Forestry,Beijing Forestry University,Beijing 100083,China
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Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d'Alençon E. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species? Genetica 2015; 143:305-16. [PMID: 25694156 PMCID: PMC4419160 DOI: 10.1007/s10709-015-9829-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022]
Abstract
The moth Spodoptera frugiperda is a well-known pest of crops throughout the Americas, which consists of two strains adapted to different host-plants: the first feeds preferentially on corn, cotton and sorghum whereas the second is more associated with rice and several pasture grasses. Though morphologically indistinguishable, they exhibit differences in their mating behavior, pheromone compositions, and show development variability according to the host-plant. Though the latter suggest that both strains are different species, this issue is still highly controversial because hybrids naturally occur in the wild, not to mention the discrepancies among published results concerning mating success between the two strains. In order to clarify the status of the two host-plant strains of S. frugiperda, we analyze features that possibly reflect the level of post-zygotic isolation: (1) first generation (F1) hybrid lethality and sterility; (2) patterns of meiotic segregation of hybrids in reciprocal second generation (F2), as compared to the meiosis of the two parental strains. We found a significant reduction of mating success in F1 in one direction of the cross and a high level of microsatellite markers showing transmission ratio distortion in the F2 progeny. Our results support the existence of post-zygotic reproductive isolation between the two laboratory strains and are in accordance with the marked level of genetic differentiation that was recovered between individuals of the two strains collected from the field. Altogether these results provide additional evidence in favor of a sibling species status for the two strains.
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Affiliation(s)
- Pascaline Dumas
- UM - UMR 1333 DGIMI, Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, France,
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36
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Montiel EE, Ruiz-Ruano FJ, Cabrero J, Marchal JA, Sánchez A, Perfectti F, López-León MD, Camacho JPM. Intragenomic distribution of RTE retroelements suggests intrachromosomal movement. Chromosome Res 2015; 23:211-23. [PMID: 25605325 DOI: 10.1007/s10577-014-9461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/25/2014] [Accepted: 12/18/2014] [Indexed: 11/25/2022]
Abstract
Much is known about the abundance of transposable elements (TEs) in eukaryotic genomes, but much is still unknown on their behaviour within cells. We employ here a combination of cytological, molecular and genomic approaches providing information on the intragenomic distribution and behaviour of non-long terminal repeat (LTR) retrotransposon-like elements (RTE). We microdissected every chromosome in a single first meiotic metaphase cell of the grasshopper Eyprepocnemis plorans and polymerase chain reaction (PCR) amplified a fragment of the RTE reverse transcriptase gene with specific primers. PCR products were cloned and 139 clones were sequenced. Analysis of molecular variance (AMOVA) showed significant intragenomic structure for these elements, with 4.6 % of molecular variance being found between chromosomes. A maximum likelihood tree built with the RTE sequences revealed the frequent presence of two or more elements showing very high similarity and being located on the same chromosome, thus suggesting intrachromosome movement. The 454 pyrosequencing of genomic DNA gave strong support to the microdissection results and provided evidence for the existence of 5' truncated elements. Our results thus indicate a tendency of RTE elements to reinsert into the same chromosome from where they were transcribed, which could be achieved if retrotranscription and insertion takes place immediately after transcription.
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Affiliation(s)
- Eugenia E Montiel
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain,
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Lance SL, Love CN, Nunziata SO, O’Bryhim JR, Scott DE, Flynn RW, Jones KL. 32 species validation of a new Illumina paired-end approach for the development of microsatellites. PLoS One 2013; 8:e81853. [PMID: 24312368 PMCID: PMC3842982 DOI: 10.1371/journal.pone.0081853] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 10/17/2013] [Indexed: 11/30/2022] Open
Abstract
Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs) remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485), with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.
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Affiliation(s)
- Stacey L. Lance
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- * E-mail:
| | - Cara N. Love
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - Schyler O. Nunziata
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - Jason R. O’Bryhim
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - David E. Scott
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - R. Wesley Flynn
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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High-throughput sequencing of a single chromosome: a moth W chromosome. Chromosome Res 2013; 21:491-505. [PMID: 23949445 DOI: 10.1007/s10577-013-9376-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
Y and W chromosomes have mostly been excluded from whole genome sequencing projects. Due to the high amount of repetitive sequences they are 'difficult' to assemble and therefore need special treatment in the form of, e.g. adapted assembly programs, a range of different libraries, and accurate maps, if possible. A minimum requirement for these approaches is pure template DNA. We therefore microdissected the W chromatin of highly polyploid cells from the flour moth, Ephestia kuehniella, and used Roche/454 and Sanger sequencing to generate 72.6 Mbp of DNA sequence. Nominal coverage was 4.3× of the 16.7 Mbp of W chromosomal DNA. We used these data to assess the genetic content of the W chromosome. This approach allowed us to determine constituent families of transposable elements, microsatellites, and recent insertion sites of mitochondrial DNA. However, no conventional protein-coding gene has yet been found. The sequence collection is a rich source for the definition of W-specific PCR markers and the reconstruction of W chromosome loci, as a step towards full reconstruction of the chromosome.
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Gao C, Ren X, Mason AS, Li J, Wang W, Xiao M, Fu D. Revisiting an important component of plant genomes: microsatellites. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:645-661. [PMID: 32481138 DOI: 10.1071/fp12325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/16/2013] [Indexed: 06/11/2023]
Abstract
Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.
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Affiliation(s)
- Caihua Gao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaodong Ren
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Annaliese S Mason
- Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Qld, Australia
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Meili Xiao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
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Kirk H, Dorn S, Mazzi D. Worldwide population genetic structure of the oriental fruit moth (Grapholita molesta), a globally invasive pest. BMC Ecol 2013; 13:12. [PMID: 23531126 PMCID: PMC3637152 DOI: 10.1186/1472-6785-13-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/11/2013] [Indexed: 11/17/2022] Open
Abstract
Background Invasive pest species have large impacts on agricultural crop yields, and understanding their population dynamics is important for ensuring food security. The oriental fruit moth Grapholita molesta is a cosmopolitan pest of stone and pome fruit species including peach and apple, and historical records indicate that it has invaded North and South America, Europe, Australia and Africa from its putative native range in Asia over the past century. Results We used 13 microsatellite loci, including nine newly developed markers, to characterize global population structure of G. molesta. Approximately 15 individuals from each of 26 globally distributed populations were genotyped. A weak but significant global pattern of isolation-by-distance was found, and G. molesta populations were geographically structured on a continental scale. Evidence does not support that G. molesta was introduced to North America from Japan as previously proposed. However, G. molesta was probably introduced from North America to The Azores, South Africa, and Brazil, and from East Asia to Australia. Shared ancestry was inferred between populations from Western Europe and from Brazil, although it remains unresolved whether an introduction occurred from Europe to Brazil, or vice versa. Both genetic diversity and levels of inbreeding were surprisingly high across the range of G. molesta and were not higher or lower overall in introduced areas compared to native areas. There is little evidence for multiple introductions to each continent (except in the case of South America), or for admixture between populations from different origins. Conclusions Cross-continental introductions of G. molesta appear to be infrequent, which is surprising given its rapid worldwide expansion over the past century. We suggest that area-wide spread via transport of fruits and other plant materials is a major mechanism of ongoing invasion, and management efforts should therefore target local and regional farming communities and distribution networks.
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Affiliation(s)
- Heather Kirk
- ETH Zurich, Institute of Agricultural Sciences, Applied Entomology, Schmelzbergstrasse 9/LFO, Zurich 8092, Switzerland
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41
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Behere GT, Tay WT, Russell DA, Kranthi KR, Batterham P. Population genetic structure of the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in India as inferred from EPIC-PCR DNA markers. PLoS One 2013; 8:e53448. [PMID: 23326431 PMCID: PMC3543461 DOI: 10.1371/journal.pone.0053448] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/28/2012] [Indexed: 11/18/2022] Open
Abstract
Helicoverpa armigera is an important pest of cotton and other agricultural crops in the Old World. Its wide host range, high mobility and fecundity, and the ability to adapt and develop resistance against all common groups of insecticides used for its management have exacerbated its pest status. An understanding of the population genetic structure in H. armigera under Indian agricultural conditions will help ascertain gene flow patterns across different agricultural zones. This study inferred the population genetic structure of Indian H. armigera using five Exon-Primed Intron-Crossing (EPIC)-PCR markers. Nested alternative EPIC markers detected moderate null allele frequencies (4.3% to 9.4%) in loci used to infer population genetic structure but the apparently genome-wide heterozygote deficit suggests in-breeding or a Wahlund effect rather than a null allele effect. Population genetic analysis of the 26 populations suggested significant genetic differentiation within India but especially in cotton-feeding populations in the 2006–07 cropping season. In contrast, overall pair-wise FST estimates from populations feeding on food crops indicated no significant population substructure irrespective of cropping seasons. A Baysian cluster analysis was used to assign the genetic make-up of individuals to likely membership of population clusters. Some evidence was found for four major clusters with individuals in two populations from cotton in one year (from two populations in northern India) showing especially high homogeneity. Taken as a whole, this study found evidence of population substructure at host crop, temporal and spatial levels in Indian H. armigera, without, however, a clear biological rationale for these structures being evident.
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Affiliation(s)
- Gajanan Tryambak Behere
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
- Division of Entomology, Indian Council of Agricultural Research, Research Complex for North Eastern Hill Region, Shilong, Meghalaya, India
| | - Wee Tek Tay
- CSIRO Ecosystem Sciences, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Derek Alan Russell
- Department of Agriculture and Food Systems, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | | | - Philip Batterham
- Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
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Stolle E, Kidner JH, Moritz RFA. Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera. Genome Biol Evol 2013; 5:151-62. [PMID: 23292136 PMCID: PMC3595035 DOI: 10.1093/gbe/evs133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution.
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Affiliation(s)
- Eckart Stolle
- Department of Zoology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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43
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Agunbiade TA, Coates BS, Kim KS, Forgacs D, Margam VM, Murdock LL, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Tamò M, Pittendrigh BR. The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Crambidae) populations in West Africa. BULLETIN OF ENTOMOLOGICAL RESEARCH 2012; 102:589-599. [PMID: 22717014 DOI: 10.1017/s0007485312000156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa. The application of population genetic tools is important in the management of insect pests but such data on M. vitrata is lacking. We applied a set of six microsatellite markers to assess the population structure of M. vitrata collected at five sites from Burkina Faso, Niger and Nigeria. Observed polymorphisms ranged from one (marker 3393) to eight (marker 32008) alleles per locus. Observed and expected heterozygosities ranged from 0.0 to 0.8 and 0.0 to 0.6, respectively. Three of the loci in samples from Nigeria and Burkina Faso deviated significantly from Hardy-Weinberg Equilibrium (HWE), whereas no loci deviated significantly in samples from Niger. Analysis of molecular variance (AMOVA) indicated that 67.3% level of the genetic variation was within individuals compared to 17.3% among populations. A global estimate of F ST=0.1 (ENA corrected F ST=0.1) was significant (P⩽0.05) and corroborated by pairwise F ST values that were significant among all possible comparisons. A significant correlation was predicted between genetic divergence and geographic distance between subpopulations (R2=0.6, P=0.04), and cluster analysis by the program STRUCTURE predicted that co-ancestry of genotypes were indicative of three distinct populations. The spatial genetic variance among M. vitrata in West Africa may be due to limited gene flow, south-north seasonal movement pattern or other reproductive barriers. This information is important for the cultural, chemical and biological control strategies for managing M. vitrata.
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Affiliation(s)
- T A Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Illinois, USA
| | - B S Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - K S Kim
- College of Veterinary Medicine, Seoul National University, Seoul, South Korea and USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - D Forgacs
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Illinois, USA
| | - V M Margam
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - L L Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - M N Ba
- Institut de L'Environnement et de Recherches Agricole Station de Kamboinse, Ouagadougou, Burkina Faso, France
| | - C L Binso-Dabire
- Institut de L'Environnement et de Recherches Agricole Station de Kamboinse, Ouagadougou, Burkina Faso, France
| | - I Baoua
- Institut National de la Recherche Agronomique du Niger, Maradi, Niger
| | - M F Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | - M Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - B R Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Illinois, USA
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Mattila ALK, Duplouy A, Kirjokangas M, Lehtonen R, Rastas P, Hanski I. High genetic load in an old isolated butterfly population. Proc Natl Acad Sci U S A 2012; 109:E2496-505. [PMID: 22908265 PMCID: PMC3443129 DOI: 10.1073/pnas.1205789109] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated inbreeding depression and genetic load in a small (N(e) ∼ 100) population of the Glanville fritillary butterfly (Melitaea cinxia), which has been completely isolated on a small island [Pikku Tytärsaari (PT)] in the Baltic Sea for at least 75 y. As a reference, we studied conspecific populations from the well-studied metapopulation in the Åland Islands (ÅL), 400 km away. A large population in Saaremaa, Estonia, was used as a reference for estimating genetic diversity and N(e). We investigated 58 traits related to behavior, development, morphology, reproductive performance, and metabolism. The PT population exhibited high genetic load (L = 1 - W(PT)/W(ÅL)) in a range of fitness-related traits including adult weight (L = 0.12), flight metabolic rate (L = 0.53), egg viability (L = 0.37), and lifetime production of eggs in an outdoor population cage (L = 0.70). These results imply extensive fixation of deleterious recessive mutations, supported by greatly reduced diversity in microsatellite markers and immediate recovery (heterosis) of egg viability and flight metabolic rate in crosses with other populations. There was no significant inbreeding depression in most traits due to one generation of full-sib mating. Resting metabolic rate was significantly elevated in PT males, which may be related to their short lifespan (L = 0.25). The demographic history and the effective size of the PT population place it in the part of the parameter space in which models predict mutation accumulation. This population exemplifies the increasingly common situation in fragmented landscapes, in which small and completely isolated populations are vulnerable to extinction due to high genetic load.
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Affiliation(s)
- Anniina L. K. Mattila
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Anne Duplouy
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Malla Kirjokangas
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Rainer Lehtonen
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pasi Rastas
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilkka Hanski
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
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Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor. PLoS One 2012; 7:e40197. [PMID: 22870194 PMCID: PMC3411680 DOI: 10.1371/journal.pone.0040197] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 06/04/2012] [Indexed: 01/07/2023] Open
Abstract
Background The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.
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Meglécz E, Nève G, Biffin E, Gardner MG. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 2012; 7:e40861. [PMID: 22815847 PMCID: PMC3397955 DOI: 10.1371/journal.pone.0040861] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/14/2012] [Indexed: 11/19/2022] Open
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
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Affiliation(s)
- Emese Meglécz
- IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France.
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Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PLoS One 2012; 7:e40532. [PMID: 22792363 PMCID: PMC3391268 DOI: 10.1371/journal.pone.0040532] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 06/10/2012] [Indexed: 11/23/2022] Open
Abstract
Background Retroelements can successfully colonize eukaryotic genome through RNA-mediated transposition, and are considered to be some of the major mediators of genome size. The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements. Results We performed a de novo assembly from deep sequencing RNA-seq data and identified 105 retroelements in the locust transcriptome. Phylogenetic analysis of reverse transcriptase sequences revealed 1 copia, 1 BEL, 8 gypsy and 23 non-long terminal repeat (LTR) retroelements in the locust transcriptome. A novel approach was developed to identify full-length LTR retroelements. A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified. Structural analysis indicated that all these retroelements may have been activated or deprived of retrotransposition activities very recently. Expression profiling analysis revealed that the retroelements exhibited a unique expression pattern at the egg stage and showed differential expression profiles between the solitarious and gregarious phases at the fifth instar and adult stage. Conclusion We hereby present the first de novo transcriptome analysis of retroelements in a species whose genome is not available. This work contributes to a comprehensive understanding of the landscape of retroelements in the locust transcriptome. More importantly, the results reveal that non-LTR retroelements are abundant and diverse in the locust transcriptome.
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Wang J, Wang A, Han Z, Zhang Z, Li F, Li X. Characterization of three novel SINE families with unusual features in Helicoverpa armigera. PLoS One 2012; 7:e31355. [PMID: 22319625 PMCID: PMC3272025 DOI: 10.1371/journal.pone.0031355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 01/06/2012] [Indexed: 01/03/2023] Open
Abstract
Although more than 120 families of short interspersed nuclear elements (SINEs) have been isolated from the eukaryotic genomes, little is known about SINEs in insects. Here, we characterize three novel SINEs from the cotton bollworm, Helicoverpa armigera. Two of them, HaSE1 and HaSE2, share similar 5′ -structure including a tRNA-related region immediately followed by conserved central domain. The 3′ -tail of HaSE1 is significantly similar to that of one LINE retrotransposon element, HaRTE1.1, in H. armigera genome. The 3′ -region of HaSE2 showed high identity with one mariner-like element in H. armigera. The third family, termed HaSE3, is a 5S rRNA-derived SINE and shares both body part and 3′-tail with HaSE1, thus may represent the first example of a chimera generated by recombination between 5S rRNA and tRNA-derived SINE in insect species. Further database searches revealed the presence of these SINEs in several other related insect species, but not in the silkworm, Bombyx mori, indicating a relatively narrow distribution of these SINEs in Lepidopterans. Apart from above, we found a copy of HaSE2 in the GenBank EST entry for the cotton aphid, Aphis gossypii, suggesting the occurrence of horizontal transfer.
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Affiliation(s)
- Jianjun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- * E-mail: (JW); (XL)
| | - Aina Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Zhaojun Han
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zan Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Fei Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (JW); (XL)
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Li F, Niu B, Huang Y, Meng Z. Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae). PLoS One 2012; 7:e29664. [PMID: 22253755 PMCID: PMC3256165 DOI: 10.1371/journal.pone.0029664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 12/02/2011] [Indexed: 11/19/2022] Open
Abstract
Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs) discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM) curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae). Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest.
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Affiliation(s)
- FengBo Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - BaoLong Niu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - YongPing Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (YPH); (ZQM)
| | - ZhiQi Meng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Laboratory of Entomo-molecular Biology, Sericulture Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (YPH); (ZQM)
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Meglécz E, Nève G, Biffin E, Gardner MG. Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 2012. [PMID: 22815847 DOI: 10.1371/journal.pone.004086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
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Affiliation(s)
- Emese Meglécz
- IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France.
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