1
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Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, Sharakhova MV. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes. BMC Biol 2024; 22:16. [PMID: 38273363 PMCID: PMC10809549 DOI: 10.1186/s12915-024-01825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. METHODS In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. RESULTS We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. CONCLUSION The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
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Affiliation(s)
- Sergei S Ryazansky
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Molecular Genetics of Cell, NRC "Kurchatov Institute", Moscow, Russia
| | - Chujia Chen
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Group of Genomic Mechanisms of Development, Institute of Cytology and Genetics, Novosibirsk, Russia
- Laboratory of Structural and Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Vitor L Dos Anjos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Rong Guo
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Theresa Menna
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily Ferrill
- County of San Diego Vector Control Program, San Diego, CA, USA
| | - Karen E Schultz
- Mosquito and Vector Management District of Santa Barbara County, Santa Barbara, CA, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | | | | | - Chunhong Mao
- Biocomplexity Institute & Initiative University of Virginia, Charlottesville, VA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, the University of Tennessee, Knoxville, TN, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Zhijian Tu
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia.
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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2
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Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Bayarmaa GA, Erst A, Park I, Choi HJ. Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe. Sci Rep 2023; 13:22014. [PMID: 38086985 PMCID: PMC10716127 DOI: 10.1038/s41598-023-49381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Adonis mongolica is a threatened species that is endemic to Mongolia. It is a medicinal plant from the Adonis genus and has been used to treat heart diseases. However, the genomics and evolution of this species have not been thoroughly studied. We sequenced the first complete plastome of A. mongolica and compared it with ten Adonideae species to describe the plastome structure and infer phylogenetic relationships. The complete plastome of A. mongolica was 157,521 bp long and had a typical quadripartite structure with numerous divergent regions. The plastomes of Adonideae had relatively constant genome structures and sizes, except for those of Adonis. The plastome structure was consistent across Adonis. We identified a 44.8 kb large-scale inversion within the large single-copy region and rpl32 gene loss in the Adonis plastomes compared to other members of the Adonideae tribe. Additionally, Adonis had a smaller plastome size (156,917-157,603 bp) than the other genera within the tribe (159,666-160,940 bp), which was attributed to deletions of intergenic regions and partial and complete gene losses. These results suggested that an intramolecular mutation occurred in the ancestor of the Adonis genus. Based on the phylogenetic results, Adonis separated earlier than the other genera within the Adonideae tribe. The genome structures and divergences of specific regions in the Adonis genus were unique to the Adonideae tribe. This study provides fundamental knowledge for further genomic research in Mongolia and a better understanding of the evolutionary history of endemic plants.
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Affiliation(s)
- Nudkhuu Nyamgerel
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Shukherdorj Baasanmunkh
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Gun-Aajav Bayarmaa
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Andrey Erst
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Science, Novosibirsk, 630090, Russia
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea.
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3
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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4
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Hanlon VCT, Lansdorp PM, Guryev V. A survey of current methods to detect and genotype inversions. Hum Mutat 2022; 43:1576-1589. [PMID: 36047337 DOI: 10.1002/humu.24458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/11/2022]
Abstract
Polymorphic inversions are ubiquitous in humans, and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short- and long-read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
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5
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Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Ffrench-Constant R, Martin SH. Stepwise evolution of a butterfly supergene via duplication and inversion. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210207. [PMID: 35694743 PMCID: PMC9189502 DOI: 10.1098/rstb.2021.0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Kang-Wook Kim
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ian J Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye Campus, Huye, Rwanda
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA.,Mpala Research Centre, Nanyuki, Kenya
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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6
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Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun 2022; 13:1960. [PMID: 35413948 PMCID: PMC9005712 DOI: 10.1038/s41467-022-29599-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin. Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
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7
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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] [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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8
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Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
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Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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9
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Schultz DT, Francis WR, McBroome JD, Christianson LM, Haddock SHD, Green RE. A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 (BETHESDA, MD.) 2021; 11:jkab302. [PMID: 34545398 PMCID: PMC8527503 DOI: 10.1093/g3journal/jkab302] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/18/2021] [Indexed: 11/12/2022]
Abstract
Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.
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Affiliation(s)
- Darrin T Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Jakob D McBroome
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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10
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McBroome J, Liang D, Corbett-Detig R. Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster. Genome Biol Evol 2021; 12:1378-1391. [PMID: 32437518 PMCID: PMC7487137 DOI: 10.1093/gbe/evaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Chromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. Although there is an impressive array of theory and empirical analyses that have identified conditions under which inversions can be positively selected, comparatively little data are available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can disrupt functional elements and alter chromatin domains, the precise positioning of an inversion’s breakpoints can strongly affect its fitness. Here, we compared the fine-scale distribution of low-frequency inversion breakpoints with those of high-frequency inversions and inversions that have gone to fixation between Drosophila species. We identified a number of differences among frequency classes that may influence inversion fitness. In particular, breakpoints that are proximal to insulator elements, generate large tandem duplications, and minimize impacts on gene coding spans which are more prevalent in high-frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high-fitness arrangements when suppressed recombination is favorable.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - David Liang
- Department of Biomolecular Engineering, University of California Santa Cruz
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11
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Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol 2021; 13:evab098. [PMID: 33964136 PMCID: PMC8214408 DOI: 10.1093/gbe/evab098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.
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Affiliation(s)
- Anna Tigano
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Arne Jacobs
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Aryn P Wilder
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
- Conservation Genetics, San Diego Zoo Global, Escondido, California, USA
| | - Ankita Nand
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ye Zhan
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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12
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Villoutreix R, Ayala D, Joron M, Gompert Z, Feder JL, Nosil P. Inversion breakpoints and the evolution of supergenes. Mol Ecol 2021; 30:2738-2755. [PMID: 33786937 PMCID: PMC7614923 DOI: 10.1111/mec.15907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
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Affiliation(s)
- Romain Villoutreix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | - Diego Ayala
- UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, 34934 Montpellier, France
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | | | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame,
Indiana 46556, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
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13
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Lezcano ÓM, Sánchez-Polo M, Ruiz JL, Gómez-Díaz E. Chromatin Structure and Function in Mosquitoes. Front Genet 2020; 11:602949. [PMID: 33365050 PMCID: PMC7750206 DOI: 10.3389/fgene.2020.602949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.
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Affiliation(s)
| | | | - José L. Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
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14
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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15
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Compton A, Sharakhov IV, Tu Z. Recent advances and future perspectives in vector-omics. CURRENT OPINION IN INSECT SCIENCE 2020; 40:94-103. [PMID: 32650287 PMCID: PMC8041138 DOI: 10.1016/j.cois.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
We have reviewed recent progress and the remaining challenges in vector-omics. We have highlighted several technologies and applications that facilitate novel biological insights beyond achieving a reference-quality genome assembly. Among other topics, we have discussed the applications of chromatin conformation capture, chromatin accessibility assays, optical mapping, full-length RNA sequencing, single cell RNA analysis, proteomics, and population genomics. We anticipate that we will witness a great expansion in vector-omics research not only in its application in a broad range of species, but also its ability to uncover novel genetic elements and tackle previously inaccessible regions of the genome. It is our hope that the continued innovation in device portability, cost reduction, and informatics support will in the foreseeable future bring vector-omics to every vector laboratory and field station in the world, which will have an unparalleled impact on basic research and the control of vector-borne infectious diseases.
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Affiliation(s)
- Austin Compton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States; Department of Entomology, Virginia Tech, Blacksburg, VA 24061, United States; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States; Department of Genetics and Cell Biology, Tomsk State University, Tomsk 634050, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Department of Entomology, Virginia Tech, Blacksburg, VA 24061, United States; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States.
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16
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Adams M, McBroome J, Maurer N, Pepper-Tunick E, Saremi N, Green RE, Vollmers C, Corbett-Detig R. One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Nucleic Acids Res 2020; 48:e75. [PMID: 32491177 PMCID: PMC7367183 DOI: 10.1093/nar/gkaa450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 02/02/2023] Open
Abstract
A high quality genome assembly is a vital first step for the study of an organism. Recent advances in technology have made the creation of high quality chromosome scale assemblies feasible and low cost. However, the amount of input DNA needed for an assembly project can be a limiting factor for small organisms or precious samples. Here we demonstrate the feasibility of creating a chromosome scale assembly using a hybrid method for a low input sample, a single outbred Drosophila melanogaster. Our approach combines an Illumina shotgun library, Oxford nanopore long reads, and chromosome conformation capture for long range scaffolding. This single fly genome assembly has a N50 of 26 Mb, a length that encompasses entire chromosome arms, contains 95% of expected single copy orthologs, and a nearly complete assembly of this individual's Wolbachia endosymbiont. The methods described here enable the accurate and complete assembly of genomes from small, field collected organisms as well as precious clinical samples.
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Affiliation(s)
- Matthew Adams
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Evan Pepper-Tunick
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nedda F Saremi
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Dovetail Genomics, Scotts Valley, CA 95066, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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17
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Ostevik KL, Samuk K, Rieseberg LH. Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower. Genetics 2020; 214:1031-1045. [PMID: 32033968 PMCID: PMC7153943 DOI: 10.1534/genetics.120.303026] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
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Affiliation(s)
- Kate L Ostevik
- Department of Biology, Duke University, Durham, North Carolina 27701
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kieran Samuk
- Department of Biology, Duke University, Durham, North Carolina 27701
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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