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Nowling RJ, Fallas-Moya F, Sadovnik A, Emrich S, Aleck M, Leskiewicz D, Peters JG. Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 2022; 10:e12831. [PMID: 35116204 PMCID: PMC8784018 DOI: 10.7717/peerj.12831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. METHODS We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. RESULTS When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. CONCLUSION With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Fabian Fallas-Moya
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Amir Sadovnik
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Scott Emrich
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Matthew Aleck
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Daniel Leskiewicz
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - John G. Peters
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
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2
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Zivanovic G, Arenas C, Mestres F. Adaptation of Drosophila subobscura chromosomal inversions to climatic variables: the Balkan natural population of Avala. Genetica 2021; 149:155-169. [PMID: 34129131 DOI: 10.1007/s10709-021-00125-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022]
Abstract
The adaptive value of chromosomal inversions continues raising relevant questions in evolutionary biology. In many species of the Drosophila genus, different inversions have been recognized to be related to thermal adaptation, but it is necessary to determine to which specific climatic variables the inversions are adaptive. With this aim, the behavior of thermal adapted inversions of Drosophila subobscura regarding climatic variables was studied in the natural population of Avala (Serbia) during the 2014-2017 period. The results obtained were compared with those previously reported in the Font Groga (Barcelona, Spain) population, which presents different climatic and environmental conditions. In both populations, it was observed that most thermal adapted inversions were significantly associated with the first, second or both principal components, which were related with maximum, minimum and mean temperatures. Moreover, a significant increase over years (2004-2017) for the minimum temperature was detected. In parallel, a significant variation over time in Avala was only observed for the frequencies of 'warm' and 'non-thermal' adapted inversions of the U chromosome. However, stability in the chromosomal inversion polymorphism was observed for the 2014-2017 period which might result from the temporal span of the study and/or selective process acting on the population.
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Affiliation(s)
- Goran Zivanovic
- Department of Genetics, Institute for Biological Research "Sinisa Stankovic" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció de Genètica Biomèdica, Evolutiva i Desenvolupament - IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
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3
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Campos M, Rona LDP, Willis K, Christophides GK, MacCallum RM. Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae. BMC Genomics 2021; 22:422. [PMID: 34103015 PMCID: PMC8185951 DOI: 10.1186/s12864-021-07722-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07722-y.
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Affiliation(s)
- Melina Campos
- Department of Life Sciences, Imperial College London, London, UK
| | - Luisa D P Rona
- Department of Life Sciences, Imperial College London, London, UK.,Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil.,National Institute of Science and Technology in Molecular Entomology, National Council for Scientific and Technological Development (INCT-EM, CNPq), Rio de Janeiro, Brazil
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, UK
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Redmond SN, Sharma A, Sharakhov I, Tu Z, Sharakhova M, Neafsey DE. Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti. BMC Biol 2020; 18:26. [PMID: 32164699 PMCID: PMC7068900 DOI: 10.1186/s12915-020-0757-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/21/2020] [Indexed: 11/17/2022] Open
Abstract
Background Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Chromosomal inversions have been shown to play a major role in adaptation and speciation in dipteran insects and would be of great utility for studies of Ae. aegypti. However, the large and highly repetitive genome of Ae. aegypti makes it difficult to detect inversions with paired-end short-read sequencing data, and polytene chromosome analysis does not provide sufficient resolution to detect chromosome banding patterns indicative of inversions. Results To characterize chromosomal diversity in this species, we have carried out deep Illumina sequencing of linked-read (10X Genomics) libraries in order to discover inversion loci as well as SNPs. We analyzed individuals from colonies representing the geographic limits of each subspecies, one contact zone between subspecies, and a closely related sister species. Despite genome-wide SNP divergence and abundant microinversions, we do not find any inversions occurring as fixed differences between subspecies. Many microinversions are found in regions that have introgressed and have captured genes that could impact behavior, such as a cluster of odorant-binding proteins that may play a role in host feeding preference. Conclusions Our study shows that inversions are abundant and widely shared among subspecies of Aedes aegypti and that introgression has occurred in regions of secondary contact. This library of 32 novel chromosomal inversions demonstrates the capacity for linked-read sequencing to identify previously intractable genomic rearrangements and provides a foundation for future population genetics studies in this species.
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Affiliation(s)
- Seth N Redmond
- Institute of Vector Borne Disease, Monash University, Melbourne, Australia. .,Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Atashi Sharma
- Fralin Life Science Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Igor Sharakhov
- Fralin Life Science Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Zhijian Tu
- Fralin Life Science Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria Sharakhova
- Fralin Life Science Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Daniel E Neafsey
- Harvard TH Chan School of Public Health, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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5
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Robinson E, McKenna MJ, Bedford JS, Goodwin EH, Cornforth MN, Bailey SM, Ray FA. Directional Genomic Hybridization (dGH) for Detection of Intrachromosomal Rearrangements. Methods Mol Biol 2020; 1984:107-116. [PMID: 31267426 DOI: 10.1007/978-1-4939-9432-8_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence in situ Hybridization (FISH) techniques, including whole chromosome painting (WCP), spectral karyotyping (SKY), and multicolor FISH (mFISH), are used extensively to characterize and enumerate inter-chromosomal rearrangements (e.g., translocations). Directional genomic hybridization (dGH) is a relatively new cytogenomics-based methodology that combines the strand-specific strategy of Chromosome Orientation-FISH (CO-FISH) with bioinformatics-driven design of single-stranded DNA probe sets that are unique and of like orientation. Such a strategy produces directional probe sets that hybridize to one-and only one-chromatid of prepared (single-stranded) metaphase chromosomes, thereby facilitating high-resolution visualization of intra-chromosomal rearrangements, specifically inversions, and greatly improving our ability to detect such otherwise cryptic structural variants within the genome. In addition to its usefulness in the study of various disease states, including cancer, relevant applications of dGH include monitoring cytogenetic damage caused by exposure to clastogenic agents (e.g., ionizing radiation). dGH can be applied as a discovery tool to globally assess the integrity of the genome, but it can also be used in a more targeted fashion to interrogate fine structural changes at the kilobase level. Consequently, dGH is capable of providing significant mechanistic insight and information not easily obtainable by other approaches.
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Affiliation(s)
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Joel S Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, TX, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
| | - F Andrew Ray
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
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6
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Ruiz-Arenas C, Cáceres A, Moreno V, González JR. Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis. Hum Genomics 2019; 13:57. [PMID: 31753042 PMCID: PMC6873427 DOI: 10.1186/s40246-019-0242-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Chromosomal inversions are structural genetic variants where a chromosome segment changes its orientation. While sporadic de novo inversions are known genetic risk factors for cancer susceptibility, it is unknown if common polymorphic inversions are also associated with the prognosis of common tumors, as they have been linked to other complex diseases. We studied the association of two well-characterized human inversions at 17q21.31 and 8p23.1 with the prognosis of lung, liver, breast, colorectal, and stomach cancers. RESULTS Using data from The Cancer Genome Atlas (TCGA), we observed that inv8p23.1 was associated with overall survival in breast cancer and that inv17q21.31 was associated with overall survival in stomach cancer. In the meta-analysis of two independent studies, inv17q21.31 heterozygosity was significantly associated with colorectal disease-free survival. We found that the association was mediated by the de-methylation of cg08283464 and cg03999934, also linked to lower disease-free survival. CONCLUSIONS Our results suggest that chromosomal inversions are important genetic factors of tumor prognosis, likely affecting changes in methylation patterns.
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Affiliation(s)
- Carlos Ruiz-Arenas
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Victor Moreno
- Programa de Prevención y Control del Cáncer, Instituto Catalán de Oncología, L'Hospitalet, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
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7
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Zivanovic G, Arenas C, Mestres F. Rate of change for the thermal adapted inversions in Drosophila subobscura. Genetica 2019; 147:401-9. [PMID: 31625005 DOI: 10.1007/s10709-019-00078-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
The changes of chromosomal inversion polymorphism composition of Drosophila subobscura in samples from Apatin (Serbia) were studied in a 24-years interval (1994-2018). The variation was significant for all autosomes and directional, increasing the inversions considered as 'warm', whereas those reported as 'cold' decreased. Furthermore, the Chromosomal Thermal Index (CTI), which allows studying the thermal adaptation of the whole karyotype increased significantly in that period of time. These results were in agreement with the indicators of global warming in Apatin: a trend to increase of the mean, maximum and minimum (this latter even significant) temperatures, and an erratic pattern of rainfall (also usual in global warming). The deviations from the Wright-Fisher model of genetic drift were used to consider the possible effect of migration or selection as evolutionary factors responsible for the change in inversion frequencies. To quantify approximately the rate of change in the frequencies, for each kind of inversions ('cold', 'warm' and 'non-thermal adapted'), the difference in frequency between the Apatin samples obtained in 1994 and 2018 was computed and then it was divided by the number of years elapsed. This rate was always higher (from twice as many as thirty times more depending on the autosome) for thermal adapted inversions ('cold' or 'warm') than the 'non-thermal' adapted. From this study, it could be concluded that the chromosomal inversions of D. subobscura could change (in composition and frequencies) in a predictable direction and a rather 'rapid' rhythm to adapt to the global warming scenario.
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8
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Galludo M, Canals J, Pineda-Cirera L, Esteve C, Rosselló M, Balanyà J, Arenas C, Mestres F. Climatic adaptation of chromosomal inversions in Drosophila subobscura. Genetica 2018; 146:433-441. [PMID: 30151609 DOI: 10.1007/s10709-018-0035-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023]
Abstract
Drosophila subobscura is a species with a rich chromosomal polymorphism which is adaptive to different climatic conditions. Five samples of the Font Groga population (Barcelona, Spain) were sampled in autumn during 5 consecutive years (2011-2015) to obtain their inversion chromosomal polymorphism, and climatic data of several meteorological variables were also collected. The aim was to analyze the adaptive potential of inversions with regard to climatic variables, being the most relevant: mean temperature (Tmean), maximum temperature (Tmax), minimum temperature (Tmin), humidity (Hm) and rainfall (Rf). As expected, no significant variation in inversion frequencies were detected over this short period of time. However, from a climatic point of view it was possible to differentiate 'warm' and 'dry' from 'cold' and 'humid' samples. The joint study of maximum (Tmax) and minimum (Tmin) temperatures was a key element to understand the effect on adaptation of many inversions. It was also observed that temperature had to be considered in conjunction with humidity and rainfall. All these factors would condition the biota of D. subobscura habitat, and chromosomal inversions could provide an adaptive response to it.
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Affiliation(s)
- Maria Galludo
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Jordi Canals
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Laura Pineda-Cirera
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Carla Esteve
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Maria Rosselló
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Joan Balanyà
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
- IRBio-Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Conxita Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
- IRBio-Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain.
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Mestres F, Balañá J, Segarra C, Prevosti A, Serra L. COLONIZATION OF AMERICA BY DROSOPHILA SUBOBSCURA: ANALYSIS OF THE O 5 INVERSIONS FROM EUROPE AND AMERICA AND THEIR IMPLICATIONS FOR THE COLONIZING PROCESS. Evolution 2017; 46:1564-1568. [PMID: 28568991 DOI: 10.1111/j.1558-5646.1992.tb01147.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/1991] [Accepted: 01/24/1992] [Indexed: 11/28/2022]
Affiliation(s)
- F Mestres
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - J Balañá
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - C Segarra
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - A Prevosti
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - L Serra
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
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10
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Liang J, Cheng B, Zhu G, Wei Y, Tang J, Cao J, Ma Y, Sharakhova MV, Xia A, Sharakhov IV. Structural divergence of chromosomes between malaria vectors Anopheles lesteri and Anopheles sinensis. Parasit Vectors 2016; 9:608. [PMID: 27887641 PMCID: PMC5124334 DOI: 10.1186/s13071-016-1855-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anopheles lesteri and Anopheles sinensis are two major malaria vectors in China and Southeast Asia. They are dramatically different in terms of geographical distribution, host preference, resting habitats, and other traits associated with ecological adaptation and malaria transmission. Both species belong to the Anopheles hyrcanus group, but the extent of genetic differences between them is not well understood. To provide an effective way to differentiate between species and to find useful markers for population genetics studies, we performed a comparative cytogenetic analysis of these two malaria vectors. RESULTS Presented here is a standard cytogenetic map for An. lesteri, and a comparative analysis of chromosome structure and gene order between An. lesteri and An. sinensis. Our results demonstrate that much of the gene order on chromosomes X and 2 was reshuffled between the two species. However, the banding pattern and the gene order on chromosome 3 appeared to be conserved. We also found two new polymorphic inversions, 2Lc and 3Rb, in An. lesteri, and we mapped the breakpoints of these two inversions on polytene chromosomes. CONCLUSIONS Our results demonstrate the extent of structural divergence of chromosomes between An. lesteri and An. sinensis, and provide a new taxonomic cytogenetic tool to distinguish between these two species. Polymorphic inversions of An. lesteri could serve as markers for studies of the population structure and ecological adaptations of this major malaria vector.
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Affiliation(s)
- Jiangtao Liang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Biao Cheng
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Guoding Zhu
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Yun Wei
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jianxia Tang
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Jun Cao
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Yajun Ma
- Department of Tropical Infectious Diseases, Faculty of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, 200433, China
| | - Maria V Sharakhova
- Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Laboratory for Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Ai Xia
- Department of Entomology, Nanjing Agricultural University, Nanjing, China.
| | - Igor V Sharakhov
- Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA. .,Laboratory for Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia.
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11
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Abstract
This article describes how empirical discoveries in the 1930s-1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species. Their different trajectories illustrate how scientists' commitments affect how they interpret new evidence and adjust to it. Dobzhansky was moved to revised views about selection, while Goldschmidt moved his attention to different genetic phenomena. However different, there are significant connections between the two that enrich our understanding of their views. I focus on two: the role of developmental considerations in Dobzhansky's thought and the role of neutrality and drift in Goldschmidt's evolutionary account. Dobzhansky's struggle with chromosomal variation is not solely about competing schools of thought within the selectionist camp, as insightfully articulated by John Beatty, but also a story of competition between selectionist thinking and developmental perspectives. In contraposition, Goldschmidt emphasized the role of low penetrance mutations that spread neutrally and pointed out that drift could result from developmental canalization. This account adds to the dominant story about Goldschmidt's resistance to the splitting of development from genetics, as told by Garland Allen and Michael Dietrich. The story I tell illustrates how developmental thinking and genetic thinking conflicted and influenced researchers with different convictions about the significance of chromosomal organization.
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Affiliation(s)
- Ehud Lamm
- The Cohn Institute for the History and Philosophy of Sciences and Ideas, Tel Aviv University, 69978, Tel Aviv, Israel.
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12
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Rousset F, Kirkpatrick M, Guerrero RF. Matrix inversions for chromosomal inversions: a method to construct summary statistics in complex coalescent models. Theor Popul Biol 2014; 97:1-10. [PMID: 25091264 DOI: 10.1016/j.tpb.2014.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 07/09/2014] [Accepted: 07/22/2014] [Indexed: 12/27/2022]
Abstract
Chromosomal inversions allow genetic divergence of locally adapted populations by reducing recombination between chromosomes with different arrangements. While patterns of genetic variation within inverted regions are increasingly documented, inferential methods are largely missing to analyze such data. Previous work has provided expectations for coalescence patterns of neutral sites linked to an inversion polymorphism in two locally adapted populations. Here, we define a method to construct summary statistics in such complex population structure models. Under a scenario of selection on the inversion breakpoints, we first construct estimators of the migration rate between the two habitats, and of the recombination rate of a nucleotide site between the two inversion backgrounds. Next, we analyze the disequilibrium between two sites within an inversion and provide an estimator of the distinct recombination rate between these two sites in homokaryotypes and heterokaryotypes. These estimators should be suitable summary statistics for simulation-based methods that can handle the complex dependences in the data.
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Alves JM, Lopes AM, Chikhi L, Amorim A. On the structural plasticity of the human genome: chromosomal inversions revisited. Curr Genomics 2013; 13:623-32. [PMID: 23730202 PMCID: PMC3492802 DOI: 10.2174/138920212803759703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 01/02/2023] Open
Abstract
With the aid of novel and powerful molecular biology techniques, recent years have witnessed a dramatic increase in the number of studies reporting the involvement of complex structural variants in several genomic disorders. In fact, with the discovery of Copy Number Variants (CNVs) and other forms of unbalanced structural variation, much attention has been directed to the detection and characterization of such rearrangements, as well as the identification of the mechanisms involved in their formation. However, it has long been appreciated that chromosomes can undergo other forms of structural changes - balanced rearrangements - that do not involve quantitative variation of genetic material. Indeed, a particular subtype of balanced rearrangement – inversions – was recently found to be far more common than had been predicted from traditional cytogenetics. Chromosomal inversions alter the orientation of a specific genomic sequence and, unless involving breaks in coding or regulatory regions (and, disregarding complex trans effects, in their close vicinity), appear to be phenotypically silent. Such a surprising finding, which is difficult to reconcile with the classical interpretation of inversions as a mechanism causing subfertility (and ultimately reproductive isolation), motivated a new series of theoretical and empirical studies dedicated to understand their role in human genome evolution and to explore their possible association to complex genetic disorders. With this review, we attempt to describe the latest methodological improvements to inversions detection at a genome wide level, while exploring some of the possible implications of inversion rearrangements on the evolution of the human genome.
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Affiliation(s)
- Joao M Alves
- Doctoral Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Portugal ; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal ; Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
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