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Cao Y, Almeida-Silva F, Zhang WP, Ding YM, Bai D, Bai WN, Zhang BW, Van de Peer Y, Zhang DY. Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae). Mol Biol Evol 2023; 40:msad121. [PMID: 37216901 PMCID: PMC10257982 DOI: 10.1093/molbev/msad121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes and its only congeneric species, Platycarya strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole-genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.
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Affiliation(s)
- Yu Cao
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Dan Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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52
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Wang D, Sun Y, Lei W, Zhu H, Wang J, Bi H, Feng S, Liu J, Ru D. Backcrossing to different parents produced two distinct hybrid species. Heredity (Edinb) 2023:10.1038/s41437-023-00630-9. [PMID: 37264213 PMCID: PMC10382510 DOI: 10.1038/s41437-023-00630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in the conifer Picea brachytyla. Our analyses revealed non-sister relationships for two lineages of P. brachytyla, with the southern lineage being placed within the re-circumscribed P. likiangensis species complex (PLSC) and P. brachytyla sensu stricto (s.s.) consisted solely of the northern lineage, forming a distinct clade that is paratactic to both the PLSC and P. wilsonii. Our phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from HHS between the ancestor of the PLSC before its diversification and P. wilsonii through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. Additionally, P. purpurea shares the same parents and an extinct lineage with P. brachytyla s.s. but backcrossing to the other parent, P. wilsonii at a later stage. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than previously identified.
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Affiliation(s)
- Donglei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Weixiao Lei
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ji Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Dafu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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53
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Smith CCR, Tittes S, Ralph PL, Kern AD. Dispersal inference from population genetic variation using a convolutional neural network. Genetics 2023; 224:iyad068. [PMID: 37052957 PMCID: PMC10213498 DOI: 10.1093/genetics/iyad068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
The geographic nature of biological dispersal shapes patterns of genetic variation over landscapes, making it possible to infer properties of dispersal from genetic variation data. Here, we present an inference tool that uses geographically distributed genotype data in combination with a convolutional neural network to estimate a critical population parameter: the mean per-generation dispersal distance. Using extensive simulation, we show that our deep learning approach is competitive with or outperforms state-of-the-art methods, particularly at small sample sizes. In addition, we evaluate varying nuisance parameters during training-including population density, demographic history, habitat size, and sampling area-and show that this strategy is effective for estimating dispersal distance when other model parameters are unknown. Whereas competing methods depend on information about local population density or accurate inference of identity-by-descent tracts, our method uses only single-nucleotide-polymorphism data and the spatial scale of sampling as input. Strikingly, and unlike other methods, our method does not use the geographic coordinates of the genotyped individuals. These features make our method, which we call "disperseNN," a potentially valuable new tool for estimating dispersal distance in nonmodel systems with whole genome data or reduced representation data. We apply disperseNN to 12 different species with publicly available data, yielding reasonable estimates for most species. Importantly, our method estimated consistently larger dispersal distances than mark-recapture calculations in the same species, which may be due to the limited geographic sampling area covered by some mark-recapture studies. Thus genetic tools like ours complement direct methods for improving our understanding of dispersal.
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Affiliation(s)
- Chris C R Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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54
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Jin S, Han Z, Hu Y, Si Z, Dai F, He L, Cheng Y, Li Y, Zhao T, Fang L, Zhang T. Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons. MOLECULAR PLANT 2023; 16:678-693. [PMID: 36760124 DOI: 10.1016/j.molp.2023.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/22/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication of species. However, the underlying genetic and genomic mechanisms are poorly understood. Here, we report a high-quality genome assembly of Gossypium barbadense acc. Tanguis, a landrace that is closely related to formation of extra-long-staple (ELS) cultivated cotton. An SV-based pan-genome (Pan-SV) was then constructed using a total of 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, and 82 959 deletions from 11 assembled genomes of allopolyploid cotton. The utility of this Pan-SV was then demonstrated through population structure analysis and genome-wide association studies (GWASs). Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an SV-based GWAS, certain SVs responsible for speciation, domestication, and improvement in tetraploid cottons were identified. Importantly, some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS. In particular, a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G. barbadense. Collectively, this study provides new insights into genome-wide, gene-scale SVs linked to important agronomic traits in a major crop species and highlights the importance of SVs during the speciation, domestication, and improvement of cultivated crop species.
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Affiliation(s)
- Shangkun Jin
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Zegang Han
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Zhanfeng Si
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lu He
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Cheng
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiqian Li
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Fang
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Engineering Center for Crop Precision Breeding, Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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55
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Makarenko MS, Gavrilova VA. NGS Reads Dataset of Sunflower Interspecific Hybrids. DATA 2023. [DOI: 10.3390/data8040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
The sunflower (Helianthus annuus), which belongs to the family of Asteraceae, is a crop grown worldwide for consumption by humans and livestock. Interspecific hybridization is widespread for sunflowers both in wild populations and commercial breeding. The current dataset comprises 250 bp and 76 paired-end NGS reads for six interspecific sunflower hybrids (F1). The dataset aimed to expand Helianthus species genomic information and benefit genetic research, and is useful in alloploids’ features investigations and nuclear–organelle interactions studies. Mitochondrial genomes of perennial sunflower hybrids H. annuus × H. strumosus and H. annuus × H. occidentalis were assembled and compared with parental forms.
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56
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Battlay P, Wilson J, Bieker VC, Lee C, Prapas D, Petersen B, Craig S, van Boheemen L, Scalone R, de Silva NP, Sharma A, Konstantinović B, Nurkowski KA, Rieseberg LH, Connallon T, Martin MD, Hodgins KA. Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia. Nat Commun 2023; 14:1717. [PMID: 36973251 PMCID: PMC10042993 DOI: 10.1038/s41467-023-37303-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.
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Affiliation(s)
- Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Christopher Lee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Diana Prapas
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Sam Craig
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Lotte van Boheemen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology Center, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Nissanka P de Silva
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Amit Sharma
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bojan Konstantinović
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Kristin A Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
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57
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Liang M, Cao S, Deng T, Du L, Li K, An B, Du Y, Xu L, Zhang L, Gao X, Li J, Guo P, Gao H. MAK: a machine learning framework improved genomic prediction via multi-target ensemble regressor chains and automatic selection of assistant traits. Brief Bioinform 2023; 24:7031157. [PMID: 36752363 DOI: 10.1093/bib/bbad043] [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: 10/22/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Incorporating the genotypic and phenotypic of the correlated traits into the multi-trait model can significantly improve the prediction accuracy of the target trait in animal and plant breeding, as well as human genetics. However, in most cases, the phenotypic information of the correlated and target trait of the individual to be evaluated was null simultaneously, particularly for the newborn. Therefore, we propose a machine learning framework, MAK, to improve the prediction accuracy of the target trait by constructing the multi-target ensemble regression chains and selecting the assistant trait automatically, which predicted the genomic estimated breeding values of the target trait using genotypic information only. The prediction ability of MAK was significantly more robust than the genomic best linear unbiased prediction, BayesB, BayesRR and the multi trait Bayesian method in the four real animal and plant datasets, and the computational efficiency of MAK was roughly 100 times faster than BayesB and BayesRR.
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Affiliation(s)
- Mang Liang
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Sheng Cao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Tianyu Deng
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lili Du
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Keanning Li
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Bingxing An
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Yueying Du
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lingyang Xu
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Lupei Zhang
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Xue Gao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | - Junya Li
- Chinese Academy of Agricultural Sciences Institute of Animal Science
| | | | - Huijiang Gao
- Chinese Academy of Agricultural Sciences Institute of Animal Science
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58
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Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [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: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
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Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
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59
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Guo JF, Zhao W, Andersson B, Mao JF, Wang XR. Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. PLANT COMMUNICATIONS 2023:100574. [PMID: 36906801 PMCID: PMC10363505 DOI: 10.1016/j.xplc.2023.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/09/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.
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Affiliation(s)
- Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Bea Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden.
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60
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Cerca J, Cotoras DD, Bieker VC, De-Kayne R, Vargas P, Fernández-Mazuecos M, López-Delgado J, White O, Stervander M, Geneva AJ, Guevara Andino JE, Meier JI, Roeble L, Brée B, Patiño J, Guayasamin JM, Torres MDL, Valdebenito H, Castañeda MDR, Chaves JA, Díaz PJ, Valente L, Knope ML, Price JP, Rieseberg LH, Baldwin BG, Emerson BC, Rivas-Torres G, Gillespie R, Martin MD. Evolutionary genomics of oceanic island radiations. Trends Ecol Evol 2023:S0169-5347(23)00032-0. [PMID: 36870806 DOI: 10.1016/j.tree.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico, 28014 Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Calle Darwin 2, 28049 Madrid, Spain
| | - Julia López-Delgado
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Oliver White
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Anthony J Geneva
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Joana Isabel Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Baptiste Brée
- Université de Pau et des Pays de l'Adour (UPPA), Energy Environment Solutions (E2S), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), 64000 Pau, France
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Calle Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - Hugo Valdebenito
- Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador; Herbarium of Economic Botany of Ecuador (Herabario QUSF), Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador
| | | | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA; Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Department of Botany and Plant Physiology, University of Málaga, Málaga, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Jonathan P Price
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building 2465, University of California, Berkeley, CA 94720-2465, USA
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Spain
| | - Gonzalo Rivas-Torres
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Rosemary Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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61
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Whittemore AT, Miller RE. Dynamic properties of the pinyon pine syngameon. THE NEW PHYTOLOGIST 2023; 237:1943-1945. [PMID: 36652627 DOI: 10.1111/nph.18707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Alan T Whittemore
- Herbarium, Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
| | - Richard E Miller
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Flower Diversity Institute, Arvada, CO, 80003, USA
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62
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Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Mol Ecol 2023; 32:1441-1457. [PMID: 36433653 PMCID: PMC10946714 DOI: 10.1111/mec.16793] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a "hard" selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Sean Stankowski
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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63
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Mérot C, Stenløkk KSR, Venney C, Laporte M, Moser M, Normandeau E, Árnyasi M, Kent M, Rougeux C, Flynn JM, Lien S, Bernatchez L. Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. Mol Ecol 2023; 32:1458-1477. [PMID: 35416336 DOI: 10.1111/mec.16468] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022]
Abstract
Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Together, our results suggest that SVs may play an important role in speciation and that, by combining second- and third-generation sequencing, we now have the ability to integrate SVs into speciation genomics.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Kristina S R Stenløkk
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clare Venney
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Ministère des Forêts, de la Faune et des Parcs (MFFP) du Québec, Québec, Québec, Canada
| | - Michel Moser
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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64
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Guidini R, Jahani M, Huang K, Rieseberg L, Mathew FM. Genome-Wide Association Mapping in Sunflower ( Helianthus annuus) Reveals Common Loci and Putative Candidate Genes for Resistance to Diaporthe gulyae and D. helianthi Causing Phomopsis Stem Canker. PLANT DISEASE 2023; 107:667-674. [PMID: 35857370 DOI: 10.1094/pdis-05-22-1209-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diaporthe gulyae and D. helianthi cause Phomopsis stem canker of sunflower (Helianthus annuus L.) in the United States. Because Phomopsis stem canker did not gain importance until the disease epidemic in 2010, limited studies were conducted to understand the genetic basis of sunflower resistance to D. gulyae and D. helianthi. The objectives of this study were to evaluate the United States Department of Agriculture cultivated accessions for resistance to D. gulyae and D. helianthi as well as to utilize genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) and putative candidate genes underlying those loci common to both organisms. For each fungus, 213 accessions were screened in a complete randomized design in the greenhouse and the experiment was repeated once. Six plants per accession were inoculated with a single isolate of D. gulyae or D. helianthi at four to six true leaves using the mycelium-contact inoculation method. At 15 days (D. gulyae) and 30 days (D. helianthi) postinoculation, accessions were evaluated for disease severity and compared with the susceptible confection inbred PI 552934. GWAS identified 28 QTLs common to the two fungi, and 24 genes overlapped close to these QTLs. Additionally, it was observed that the resistance QTLs derived mainly from landraces rather than from wild species. Seventeen putative candidate genes associated with resistance to D. gulyae or D. helianthi were identified that may be related to plant-pathogen interactions. These findings advanced our understanding of the genetic basis of resistance to D. gulyae and D. helianthi and will help develop resources for genomics-assisted breeding.
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Affiliation(s)
- Renan Guidini
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
| | - Mojtaba Jahani
- Department of Botany and Beaty Biodiversity Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Kaichi Huang
- Department of Botany and Beaty Biodiversity Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Loren Rieseberg
- Department of Botany and Beaty Biodiversity Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Febina M Mathew
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
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65
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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66
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Coughlan JM. The role of hybrid seed inviability in angiosperm speciation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-14. [PMID: 36801827 DOI: 10.1002/ajb2.16135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
Understanding which reproductive barriers contribute to speciation is essential to understanding the diversity of life on earth. Several contemporary examples of strong hybrid seed inviability (HSI) between recently diverged species suggest that HSI may play a fundamental role in plant speciation. Yet, a broader synthesis of HSI is needed to clarify its role in diversification. Here, I review the incidence and evolution of HSI. Hybrid seed inviability is common and evolves rapidly, suggesting that it may play an important role early in speciation. The developmental mechanisms that underlie HSI involve similar developmental trajectories in endosperm, even between evolutionarily deeply diverged incidents of HSI. In hybrid endosperm, HSI is often accompanied by whole-scale gene misexpression, including misexpression of imprinted genes which have a key role in endosperm development. I explore how an evolutionary perspective can clarify the repeated and rapid evolution of HSI. In particular, I evaluate the evidence for conflict between maternal and paternal interests in resource allocation to offspring (i.e., parental conflict). I highlight that parental conflict theory generates explicit predictions regarding the expected hybrid phenotypes and genes responsible for HSI. While much phenotypic evidence supports a role of parental conflict in the evolution of HSI, an understanding of the underlying molecular mechanisms of this barrier is essential to test parental conflict theory. Lastly, I explore what factors may influence the strength of parental conflict in natural plant populations as an explanation for why rates of HSI may differ between plant groups and the consequences of strong HSI in secondary contact.
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Affiliation(s)
- Jenn M Coughlan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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67
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Wersebe MJ, Sherman RE, Jeyasingh PD, Weider LJ. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Mol Ecol 2023; 32:1478-1496. [PMID: 35119153 DOI: 10.1111/mec.16383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.
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Affiliation(s)
- Matthew J Wersebe
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ryan E Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
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68
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Trible W, Chandra V, Lacy KD, Limón G, McKenzie SK, Olivos-Cisneros L, Arsenault SV, Kronauer DJC. A caste differentiation mutant elucidates the evolution of socially parasitic ants. Curr Biol 2023; 33:1047-1058.e4. [PMID: 36858043 PMCID: PMC10050096 DOI: 10.1016/j.cub.2023.01.067] [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: 05/31/2022] [Revised: 08/31/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023]
Abstract
Most ant species have two distinct female castes-queens and workers-yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with a clonal ant, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. The prevailing theory for the evolution of these workerless social parasites is that they evolve from reproductively isolated populations of facultative intermediates that acquire parasitic phenotypes in a stepwise fashion. However, empirical evidence for such facultative ancestors remains weak, and it is unclear how reproductive isolation could gradually arise in sympatry. In contrast, we isolated these variants just a few generations after they arose within their WT parent colony, implying that the complex phenotype reported here was induced in a single genetic step. This suggests that a single genetic module can decouple the coordinated mechanisms of caste development, allowing an obligately parasitic variant to arise directly from a free-living ancestor. Consistent with this hypothesis, the variants have lost one of the two alleles of a putative supergene that is heterozygous in WTs. These findings provide a plausible explanation for the evolution of ant social parasites and implicate new candidate molecular mechanisms for ant caste differentiation.
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Affiliation(s)
- Waring Trible
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Vikram Chandra
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gina Limón
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Oxford Nanopore Technologies, Oxford OX4 4DQ, UK
| | - Leonora Olivos-Cisneros
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Samuel V Arsenault
- John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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69
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Liu B, Chen J, Yang Y, Shen W, Guo J, Dou Q. Single-gene FISH maps and major chromosomal rearrangements in Elymus sibiricus and E. nutans. BMC PLANT BIOLOGY 2023; 23:98. [PMID: 36800944 PMCID: PMC9936730 DOI: 10.1186/s12870-023-04110-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Chromosomal variations have been revealed in both E. sibiricus and E. nutans, but chromosomal structural variations, such as intra-genome translocations and inversions, are still not recognized due to the cytological limitations of previous studies. Furthermore, the syntenic relationship between both species and wheat chromosomes remains unknown. RESULTS Fifty-nine single-gene fluorescence in situ hybridization (FISH) probes, including 22 single-gene probes previously mapped on wheat chromosomes and other newly developed probes from the cDNA of Elymus species, were used to characterize the chromosome homoeologous relationship and collinearity of both E. sibiricus and E. nutans with those of wheat. Eight species-specific chromosomal rearrangements (CRs) were exclusively identified in E. sibiricus, including five pericentric inversions in 1H, 2H, 3H, 6H and 2St; one possible pericentric inversion in 5St; one paracentric inversion in 4St; and one reciprocal 4H/6H translocation. Five species-specific CRs were identified in E. nutans, including one possible pericentric inversion in 2Y, three possible pericentric multiple-inversions in 1H, 2H and 4Y, and one reciprocal 4Y/5Y translocation. Polymorphic CRs were detected in three of the six materials in E. sibiricus, which were mainly represented by inter-genomic translocations. More polymorphic CRs were identified in E. nutans, including duplication and insertion, deletion, pericentric inversion, paracentric inversion, and intra- or inter-genomic translocation in different chromosomes. CONCLUSIONS The study first identified the cross-species homoeology and the syntenic relationship between E. sibiricus, E. nutans and wheat chromosomes. There are distinct different species-specific CRs between E. sibiricus and E. nutans, which may be due to their different polyploidy processes. The frequencies of intra-species polymorphic CRs in E. nutans were higher than that in E. sibiricus. To conclude, the results provide new insights into genome structure and evolution and will facilitate the utilization of germplasm diversity in both E. sibiricus and E. nutans.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Ying Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wenjie Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jialei Guo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
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70
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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71
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Feder JL, Nosil P. Beyond dichotomies in species and speciation. Natl Sci Rev 2023; 9:nwad018. [PMID: 36778105 PMCID: PMC9905644 DOI: 10.1093/nsr/nwad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
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72
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Martin CH. Is sympatric speciation in nature only possible with micro-parapatry? A new case study of glacial lake cyprinid fishes. Natl Sci Rev 2023; 9:nwad006. [PMID: 36751304 PMCID: PMC9894001 DOI: 10.1093/nsr/nwad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
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73
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Owens GL, Huang K, Todesco M, Rieseberg LH. Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers. Mol Biol Evol 2023; 40:6989481. [PMID: 36648104 PMCID: PMC9907532 DOI: 10.1093/molbev/msad013] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best-studied examples of homoploid hybrid speciation. To understand a broader picture of hybridization within the annual sunflowers, we used whole-genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with increasing recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. This means our results are consistent with, but not definitive proof of, two ancient independent homoploid hybrid speciation events in the genus. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
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Affiliation(s)
| | - Kaichi Huang
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Marco Todesco
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Beaty Biodiversity Center, University of British Columbia, Vancouver, BC, Canada
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74
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Shan B, Yu G, Wang L, Liu Y, Yang C, Liu M, Sun D. Genetic Signature of Pinctada fucata Inferred from Population Genomics: Source Tracking of the Invasion in Mischief Reef of Nansha Islands. BIOLOGY 2023; 12:biology12010097. [PMID: 36671789 PMCID: PMC9855575 DOI: 10.3390/biology12010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Among the anthropogenic stresses that marine ecosystems face, biological invasions are one of the major threats. Recently, as a result of increasingly intense anthropogenic disturbance, numerous marine species have been introduced to their non-native ranges. However, many introduced species have uncertain original sources. This prevents the design and establishment of methods for controlling or preventing these introduced species. In the present study, genomic sequencing and population genetic analysis were performed to detect the geographic origin of the introduced Pinctada fucata population in the Mischief Reef of the South China Sea. The results of population genetic structure analysis showed a close relationship between the Mischief Reef introduced population and the Lingshui population, indicating that Lingshui may be the potential geographical origin. Furthermore, lower heterozygosity and nucleotide diversity were observed in the introduced population in Mischief Reef, indicating lower genetic diversity than in other native populations. We also identified some selected genomic regions and genes of the introduced population, including genes related to temperature and salinity tolerance. These genes may play important roles in the adaptation of the introduced population. Our study will improve our understanding of the invasion history of the P. fucata population. Furthermore, the results of the present study will also facilitate further control and prevention of invasion in Mischief Reef, South China Sea.
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Affiliation(s)
- Binbin Shan
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
- Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Liangming Wang
- Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Yan Liu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572000, China
- Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Changping Yang
- Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Manting Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Dianrong Sun
- Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
- Correspondence: ; Tel.: +86-020-8910-0850
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75
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Lasky JR, Josephs EB, Morris GP. Genotype-environment associations to reveal the molecular basis of environmental adaptation. THE PLANT CELL 2023; 35:125-138. [PMID: 36005926 PMCID: PMC9806588 DOI: 10.1093/plcell/koac267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/23/2022] [Indexed: 06/14/2023]
Abstract
A fundamental goal in plant biology is to identify and understand the variation underlying plants' adaptation to their environment. Climate change has given new urgency to this goal, as society aims to accelerate adaptation of ecologically important plant species, endangered plant species, and crops to hotter, less predictable climates. In the pre-genomic era, identifying adaptive alleles was painstaking work, leveraging genetics, molecular biology, physiology, and ecology. Now, the rise of genomics and new computational approaches may facilitate this research. Genotype-environment associations (GEAs) use statistical associations between allele frequency and environment of origin to test the hypothesis that allelic variation at a given gene is adapted to local environments. Researchers may scan the genome for GEAs to generate hypotheses on adaptive genetic variants (environmental genome-wide association studies). Despite the rapid adoption of these methods, many important questions remain about the interpretation of GEA findings, which arise from fundamental unanswered questions on the genetic architecture of adaptation and limitations inherent to association-based analyses. We outline strategies to ground GEAs in the underlying hypotheses of genetic architecture and better test GEA-generated hypotheses using genetics and ecophysiology. We provide recommendations for new users who seek to learn about the molecular basis of adaptation. When combined with a rigorous hypothesis testing framework, GEAs may facilitate our understanding of the molecular basis of climate adaptation for plant improvement.
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Affiliation(s)
- Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily B Josephs
- Department of Plant Biology; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Sciences; Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80526, USA
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76
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John M, Grimm D, Korte A. Predicting Gene Regulatory Interactions Using Natural Genetic Variation. Methods Mol Biol 2023; 2698:301-322. [PMID: 37682482 DOI: 10.1007/978-1-0716-3354-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.
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Affiliation(s)
- Maura John
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Dominik Grimm
- Technical University of Munich & Weihenstephan-Triesdorf University of Applied Sciences, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany.
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77
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Wang N, Li Y, Shen C, Yang Y, Wang H, Yao T, Zhang X, Lindsey K, Lin Z. High-resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:145-159. [PMID: 36453190 DOI: 10.1111/tpj.16041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s-2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88-1.47 × 104 SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high-throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton.
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Affiliation(s)
- Nian Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanxue Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Shen
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, Guangdong, China
| | - Yang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongya Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tian Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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78
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Zhang W, Tan C, Hu H, Pan R, Xiao Y, Ouyang K, Zhou G, Jia Y, Zhang X, Hill CB, Wang P, Chapman B, Han Y, Xu L, Xu Y, Angessa T, Luo H, Westcott S, Sharma D, Nevo E, Barrero RA, Bellgard MI, He T, Tian X, Li C. Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:46-62. [PMID: 36054248 PMCID: PMC9829399 DOI: 10.1111/pbi.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.
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Affiliation(s)
- Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Cong Tan
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Haifei Hu
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rui Pan
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yuhui Xiao
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Kai Ouyang
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiao‐Qi Zhang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Penghao Wang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Brett Chapman
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Han
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Tefera Angessa
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Hao Luo
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Sharon Westcott
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Darshan Sharma
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Roberto A. Barrero
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Matthew I. Bellgard
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Tianhua He
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
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79
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Lüthi MN, Berardi AE, Mandel T, Freitas LB, Kuhlemeier C. Single gene mutation in a plant MYB transcription factor causes a major shift in pollinator preference. Curr Biol 2022; 32:5295-5308.e5. [PMID: 36473466 DOI: 10.1016/j.cub.2022.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/16/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
Understanding the molecular basis of reproductive isolation and speciation is a key goal of evolutionary genetics. In the South American genus Petunia, the R2R3-MYB transcription factor MYB-FL regulates the biosynthesis of UV-absorbing flavonol pigments, a major determinant of pollinator preference. MYB-FL is highly expressed in the hawkmoth-pollinated P. axillaris, but independent losses of its activity in sister taxa P. secreta and P. exserta led to UV-reflective flowers and associated pollinator shifts in each lineage (bees and hummingbirds, respectively). We created a myb-fl CRISPR mutant in P. axillaris and studied the effect of this single gene on innate pollinator preference. The mutation strongly reduced the expression of the two key flavonol-related biosynthetic genes but only affected the expression of few other genes. The mutant flowers were UV reflective as expected but additionally contained low levels of visible anthocyanin pigments. Hawkmoths strongly preferred the wild-type P. axillaris over the myb-fl mutant, whereas both social and solitary bee preference depended on the level of visible color of the mutants. MYB-FL, with its specific expression pattern, small number of target genes, and key position at the nexus of flavonol and anthocyanin biosynthetic pathways, provides a striking example of evolution by single mutations of large phenotypic effect.
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Affiliation(s)
- Martina N Lüthi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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80
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Barstow AC, Prasifka JR, Attia Z, Kane NC, Hulke BS. Genetic mapping of a pollinator preference trait: Nectar volume in sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1056278. [PMID: 36600919 PMCID: PMC9806390 DOI: 10.3389/fpls.2022.1056278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Although high pollinator visitation is crucial to ensure the yields of pollinator-dependent crops, the quantitative trait loci (QTL) controlling nectar volume in sunflower (Helianthus annuus L.), a pollinator preference trait, have yet to be identified. To address this, a recombinant inbred line mapping population, derived from lines with contrasting nectar volume, was used to identify loci responsible for the phenotype. As a result, linkage mapping and QTL analysis discovered major loci on chromosomes 2 and 16 that are associated with variation in nectar volume in sunflower. Increased nectar volume is also associated with increased sugars and total energy available per floret. The regions on chromosomes 2 and 16 associated with the nectar phenotype exhibit indications of chromosome structural variation, such that the phenotype is associated with rearrangements affecting regions containing hundreds of genes. Candidate genes underlying QTL on chromosomes 9 and 16 are homologous to genes with nectary function in Arabidopsis. These results have implications for sunflower breeding, to enhance pollination efficiency in sunflower, as well as current and future studies on sunflower evolution.
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Affiliation(s)
- Ashley C. Barstow
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jarrad R. Prasifka
- Sunflower and Plant Biology Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, United States
| | - Ziv Attia
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, United States
| | - Nolan C. Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, United States
| | - Brent S. Hulke
- Sunflower and Plant Biology Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, United States
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81
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [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: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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82
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Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol 2022; 6:1965-1979. [PMID: 36253543 PMCID: PMC9715431 DOI: 10.1038/s41559-022-01890-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because inversions can be challenging to detect, the prevalence and hence the significance of inversions segregating within species remains largely unknown, especially in natural populations of mammals. Here, by combining population-genomic and long-read sequencing analyses in a single, widespread species of deer mouse (Peromyscus maniculatus), we identified 21 polymorphic inversions that are large (1.5-43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0-0.03 cM Mb-1). We found that inversion breakpoints frequently occur in centromeric and telomeric regions and are often flanked by long inverted repeats (0.5-50 kb), suggesting that they probably arose via ectopic recombination. By genotyping inversions in populations across the species' range, we found that the inversions are often widespread and do not harbour deleterious mutational loads, and many are likely to be maintained as polymorphisms by divergent selection. Comparisons of forest and prairie ecotypes of deer mice revealed 13 inversions that contribute to differentiation between populations, of which five exhibit significant associations with traits implicated in local adaptation. Taken together, these results show that inversion polymorphisms have a significant impact on recombination, genome structure and genetic diversity in deer mice and likely facilitate local adaptation across the widespread range of this species.
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Affiliation(s)
- Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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83
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Imaizumi T, Kawahara Y, Auge G. Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy. Mol Ecol 2022; 31:6556-6569. [PMID: 36178060 DOI: 10.1111/mec.16709] [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: 03/17/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | | | - Gabriela Auge
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Instituto de Biociencias, Biotecnología y Biología Traslacional, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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84
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Bercovich N, Genze N, Todesco M, Owens GL, Légaré JS, Huang K, Rieseberg LH, Grimm DG. HeliantHOME, a public and centralized database of phenotypic sunflower data. Sci Data 2022; 9:735. [PMID: 36450875 PMCID: PMC9712528 DOI: 10.1038/s41597-022-01842-0] [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: 04/01/2022] [Accepted: 11/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.
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Affiliation(s)
- Natalia Bercovich
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Nikita Genze
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany
| | - Marco Todesco
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Gregory L. Owens
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.143640.40000 0004 1936 9465Department of Biology, University of Victoria, Victoria, BC Canada
| | - Jean-Sébastien Légaré
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada ,grid.17091.3e0000 0001 2288 9830Department of Computer Science, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Data Science Institute, University of British Columbia, Vancouver, British Columbia Canada
| | - Kaichi Huang
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H. Rieseberg
- grid.17091.3e0000 0001 2288 9830Department of Botany, University of British Columbia, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Dominik G. Grimm
- grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Straubing, Germany ,grid.4819.40000 0001 0704 7467Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Department of Informatics, Garching, Germany
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85
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Liu B, Tao XY, Dou QW. Molecular cytogenetic study on the plants of Elymus nutans with varying fertility on the Qinghai-Tibet Plateau. PLANT DIVERSITY 2022; 44:617-624. [PMID: 36540708 PMCID: PMC9751082 DOI: 10.1016/j.pld.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 06/15/2023]
Abstract
A molecular cytogenetic investigation was conducted on plants of the allohexaploid species Elymus nutans with varying fertility on the Qinghai-Tibet Plateau. Molecular karyotyping revealed that chromosome variants were distributed unevenly among genomes and among different homologue chromosomes in each genome. The plants with varying fertility exhibited significantly higher numbers of chromosome variants than did the normal fertility samples, although both kinds of plants showed the same pattern of high-to-low polymorphism from the Y to St and H genomes. Heterozygosis and karyotype heterozygosity in the plants with varying fertility were 3- and 13-fold higher than those in normal samples, respectively. Significant negative correlations were found not only between seed setting rates and total genome heterozygosity but also between seed setting rates and heterozygosity of each genome in the plants of varying fertility. Chromosome pairing analysis was performed using genomic in situ hybridization in selected plants of different fertility levels. The pairing of chromosomes at meiotic metaphase I was mostly bivalent, although univalent, trivalent, quadrivalent, and other polyvalents also occurred; in addition, chromosome configuration forms and frequencies varied among the studied samples. ANOVA results showed that the average number of ring bivalents in the Y genome was significantly higher than those in the St and H genomes. Significant positive correlations between pollen grain fertility and ring bivalent number were found in the St and H genomes but not in the Y genome. Furthermore, chromosome configuration parameters (total bivalents, numbers of ring and rod bivalents) were found to be significantly correlated with heterozygosity and seed setting rates in the St and H genomes, respectively, but not in the Y genome. It was inferred that the seed setting rate and pollen grain fertility in E. nutans are strongly influenced by the heterozygosity of each genome, but the Y genome differs from the St and H genomes due to chromosome pair alterations. The St and H genomes may contain more chromosome structural variations than the Y genome in E. nutans.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yan Tao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quan-Wen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, China
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86
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Christie K, Fraser LS, Lowry DB. The strength of reproductive isolating barriers in seed plants: Insights from studies quantifying premating and postmating reproductive barriers over the past 15 years. Evolution 2022; 76:2228-2243. [PMID: 35838076 PMCID: PMC9796645 DOI: 10.1111/evo.14565] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Speciation is driven by the evolution of reproductive isolating barriers that reduce, and ultimately prevent, substantial gene flow between lineages. Despite its central role in evolutionary biology, the process can be difficult to study because it proceeds differently among groups and may occur over long timescales. Due to this complexity, we typically rely on generalizations of empirical data to describe and understand the process. Previous reviews of reproductive isolation (RI) in flowering plants have suggested that prezygotic or extrinsic barriers generally have a stronger effect on reducing gene flow compared to postzygotic or intrinsic barriers. Past conclusions have rested on relatively few empirical estimates of RI; however, RI data have become increasingly abundant over the past 15 years. We analyzed data from recent studies quantifying multiple pre- and postmating barriers in plants and compared the strengths of isolating barriers across 89 taxa pairs using standardized RI metrics. Individual prezygotic barriers were on average stronger than individual postzygotic barriers, and the total strength of prezygotic RI was approximately twice that of postzygotic RI. These findings corroborate that ecological divergence and extrinsic factors, as opposed to solely the accumulation of genetic incompatibilities, are important to speciation and the maintenance of species boundaries in plants. Despite an emphasis in the literature on asymmetric postmating and postzygotic RI, we found that prezygotic barriers acted equally asymmetrically. Overall, substantial variability in the strengths of 12 isolating barriers highlights the great diversity of mechanisms that contribute to plant diversification.
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Affiliation(s)
- Kyle Christie
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824,Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizona86011
| | - Linnea S. Fraser
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
| | - David B. Lowry
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
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87
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John M, Ankenbrand MJ, Artmann C, Freudenthal JA, Korte A, Grimm DG. Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions. Bioinformatics 2022; 38:ii5-ii12. [PMID: 36124808 PMCID: PMC9486594 DOI: 10.1093/bioinformatics/btac455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWAS) are an integral tool for studying the architecture of complex genotype and phenotype relationships. Linear mixed models (LMMs) are commonly used to detect associations between genetic markers and a trait of interest, while at the same time allowing to account for population structure and cryptic relatedness. Assumptions of LMMs include a normal distribution of the residuals and that the genetic markers are independent and identically distributed-both assumptions are often violated in real data. Permutation-based methods can help to overcome some of these limitations and provide more realistic thresholds for the discovery of true associations. Still, in practice, they are rarely implemented due to the high computational complexity. RESULTS We propose permGWAS, an efficient LMM reformulation based on 4D tensors that can provide permutation-based significance thresholds. We show that our method outperforms current state-of-the-art LMMs with respect to runtime and that permutation-based thresholds have lower false discovery rates for skewed phenotypes compared to the commonly used Bonferroni threshold. Furthermore, using permGWAS we re-analyzed more than 500 Arabidopsis thaliana phenotypes with 100 permutations each in less than 8 days on a single GPU. Our re-analyses suggest that applying a permutation-based threshold can improve and refine the interpretation of GWAS results. AVAILABILITY AND IMPLEMENTATION permGWAS is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maura John
- To whom correspondence should be addressed. or
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Carolin Artmann
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Jan A Freudenthal
- Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
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88
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He M, He Y, Zhang K, Lu X, Zhang X, Gao B, Fan Y, Zhao H, Jha R, Huda MN, Tang Y, Wang J, Yang W, Yan M, Cheng J, Ruan J, Dulloo E, Zhang Z, Georgiev MI, Chapman MA, Zhou M. Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation. THE NEW PHYTOLOGIST 2022; 235:1927-1943. [PMID: 35701896 DOI: 10.1111/nph.18306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/22/2022] [Indexed: 05/09/2023]
Abstract
Golden buckwheat (Fagopyrum dibotrys or Fagopyrum cymosum) and Tartary buckwheat (Fagopyrum tataricum) belong to the Polygonaceae and the Fagopyrum genus is rich in flavonoids. Golden buckwheat is a wild relative of Tartary buckwheat, yet golden buckwheat is a traditional Chinese herbal medicine and Tartary buckwheat is a food crop. The genetic basis of adaptive divergence between these two buckwheats is poorly understood. Here, we assembled a high-quality chromosome-level genome of golden buckwheat and found a one-to-one syntenic relationship with the chromosomes of Tartary buckwheat. Two large inversions were identified that differentiate golden buckwheat and Tartary buckwheat. Metabolomic and genetic comparisons of golden buckwheat and Tartary buckwheat indicate an amplified copy number of FdCHI, FdF3H, FdDFR, and FdLAR gene families in golden buckwheat, and a parallel increase in medicinal flavonoid content. Resequencing of 34 wild golden buckwheat accessions across the two morphologically distinct ecotypes identified candidate genes, including FdMYB44 and FdCRF4, putatively involved in flavonoid accumulation and differentiation of plant architecture, respectively. Our comparative genomic study provides abundant genomic resources of genomic divergent variation to improve buckwheat with excellent nutritional and medicinal value.
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Affiliation(s)
- Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Md Nurul Huda
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Junzhen Wang
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150, Sichuan, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Ehsan Dulloo
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Zongwen Zhang
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4002, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, 4002, Plovdiv, Bulgaria
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
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89
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Earley AM, Temme AA, Cotter CR, Burke JM. Genomic regions associate with major axes of variation driven by gas exchange and leaf construction traits in cultivated sunflower (Helianthus annuus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1425-1438. [PMID: 35815412 PMCID: PMC9545426 DOI: 10.1111/tpj.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Stomata and leaf veins play an essential role in transpiration and the movement of water throughout leaves. These traits are thus thought to play a key role in the adaptation of plants to drought and a better understanding of the genetic basis of their variation and coordination could inform efforts to improve drought tolerance. Here, we explore patterns of variation and covariation in leaf anatomical traits and analyze their genetic architecture via genome-wide association (GWA) analyses in cultivated sunflower (Helianthus annuus L.). Traits related to stomatal density and morphology as well as lower-order veins were manually measured from digital images while the density of minor veins was estimated using a novel deep learning approach. Leaf, stomatal, and vein traits exhibited numerous significant correlations that generally followed expectations based on functional relationships. Correlated suites of traits could further be separated along three major principal component (PC) axes that were heavily influenced by variation in traits related to gas exchange, leaf hydraulics, and leaf construction. While there was limited evidence of colocalization when individual traits were subjected to GWA analyses, major multivariate PC axes that were most strongly influenced by several traits related to gas exchange or leaf construction did exhibit significant genomic associations. These results provide insight into the genetic basis of leaf trait covariation and showcase potential targets for future efforts aimed at modifying leaf anatomical traits in sunflower.
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Affiliation(s)
- Ashley M. Earley
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Andries A. Temme
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Division of Intensive Plant Food SystemsHumboldt‐Universität zu Berlin10117BerlinGermany
| | | | - John M. Burke
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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90
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Woods P, Price N, Matthews P, McKay JK. Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa. G3 (BETHESDA, MD.) 2022; 13:jkac209. [PMID: 36018239 PMCID: PMC9911069 DOI: 10.1093/g3journal/jkac209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022]
Abstract
A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as Cannabis sativa (C. sativa), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of C. sativa. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high F̄ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene SMALLER TRICHOMES WITH VARIABLE BRANCHES 2 to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall, the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in C. sativa.
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Affiliation(s)
- Patrick Woods
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Nicholas Price
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Paul Matthews
- Present address for Paul Matthews: Hopsteiner, Yakima, WA 98903, USA
| | - John K McKay
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
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91
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Repeated genetic adaptation to altitude in two tropical butterflies. Nat Commun 2022; 13:4676. [PMID: 35945236 PMCID: PMC9363431 DOI: 10.1038/s41467-022-32316-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 07/26/2022] [Indexed: 01/02/2023] Open
Abstract
Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene, which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes from altitudinal transects and found many regions differentiated between highland (~ 1200 m) and lowland (~ 200 m) populations. We show repeated genetic differentiation across replicate populations within species, including allopatric comparisons. In contrast, there is little molecular parallelism between the two species. By sampling five close relatives, we find that a large proportion of divergent regions identified within species have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a role for both standing genetic variation and gene flow from independently adapted species in promoting parallel local adaptation to the environment. Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
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92
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Cortés AJ, López-Hernández F, Blair MW. Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives. Front Genet 2022; 13:910386. [PMID: 35991553 PMCID: PMC9389289 DOI: 10.3389/fgene.2022.910386] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. “I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.
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Affiliation(s)
- Andrés J. Cortés
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
| | - Felipe López-Hernández
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Matthew W. Blair
- Department of Agricultural & Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
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93
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Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
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Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden,Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia,Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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94
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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish. Nat Commun 2022; 13:4479. [PMID: 35918341 PMCID: PMC9345977 DOI: 10.1038/s41467-022-32181-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar. Additionally, we highlight the possible role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique trait combinations and ecology. These results highlight the importance of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation. In this genomic study on Alpine whitefish radiations, the authors reveal details on the genetic architecture underlying the repeated eco-morphological diversification and the role of hybridization in the evolution of endemic whitefish species.
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95
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Jay P, Leroy M, Le Poul Y, Whibley A, Arias M, Chouteau M, Joron M. Association mapping of colour variation in a butterfly provides evidence that a supergene locks together a cluster of adaptive loci. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210193. [PMID: 35694756 PMCID: PMC9189503 DOI: 10.1098/rstb.2021.0193] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between sets of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining a landmark-free phenotyping algorithm with multivariate genome-wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We show that the supergene controlling the striking wing pattern polymorphism displayed by this species contains several independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are, however, associated with colour variations only in a subset of morphs where the phenotype is controlled by derived inversion forms, indicating that they were recruited after the formation of the inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Paul Jay
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Manon Leroy
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Yann Le Poul
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Mónica Arias
- CIRAD, UMR PHIM, F-34398 Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, CEDEX 5, 34398 Montpellier, France
| | - Mathieu Chouteau
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France.,LEEISA, USR 63456, Université de Guyane, CNRS, IFREMER, 275 route de Montabo, 797334 Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
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96
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Abstract
Speciation is the process by which barriers to gene flow evolve between populations. Although we now know that speciation is largely driven by natural selection, knowledge of the agents of selection and the genetic and genomic mechanisms that facilitate divergence is required for a satisfactory theory of speciation. In this essay, we highlight three advances/problems in our understanding of speciation that have arisen from studies of the genes and genomic regions that underlie the evolution of reproductive isolation. First, we describe how the identification of “speciation” genes makes it possible to identify the agents of selection causing the evolution of reproductive isolation, while also noting that the link between the genetics of phenotypic divergence and intrinsic postzygotic reproductive barriers remains tenuous. Second, we discuss the important role of recombination suppressors in facilitating speciation with gene flow, but point out that the means and timing by which reproductive barriers become associated with recombination cold spots remains uncertain. Third, we establish the importance of ancient genetic variation in speciation, although we argue that the focus of speciation studies on evolutionarily young groups may bias conclusions in favor of ancient variation relative to new mutations.
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97
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Cai X, Li X, Qi L. A Quantitative Genetic Study of Sclerotinia Head Rot Resistance Introgressed from the Wild Perennial Helianthus maximiliani into Cultivated Sunflower ( Helianthus annuus L.). Int J Mol Sci 2022; 23:ijms23147727. [PMID: 35887074 PMCID: PMC9321925 DOI: 10.3390/ijms23147727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Sclerotinia head rot (HR), caused by Sclerotinia sclerotiorum, is an economically important disease of sunflower with known detrimental effects on yield and quality in humid climates worldwide. The objective of this study was to gain insight into the genetic architecture of HR resistance from a sunflower line HR21 harboring HR resistance introgressed from the wild perennial Helianthus maximiliani. An F2 population derived from the cross of HA 234 (susceptible-line)/HR21 (resistant-line) was evaluated for HR resistance at two locations during 2019−2020. Highly significant genetic variations (p < 0.001) were observed for HR disease incidence (DI) and disease severity (DS) in both individual and combined analyses. Broad sense heritability (H2) estimates across environments for DI and DS were 0.51 and 0.62, respectively. A high-density genetic map of 1420.287 cM was constructed with 6315 SNP/InDel markers developed using genotype-by-sequencing technology. A total of 16 genomic regions on eight sunflower chromosomes, 1, 2, 10, 12, 13, 14, 16 and 17 were associated with HR resistance, each explaining between 3.97 to 16.67% of the phenotypic variance for HR resistance. Eleven of these QTL had resistance alleles from the HR21 parent. Molecular markers flanking the QTL will facilitate marker-assisted selection breeding for HR resistance in sunflower.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (Z.I.T.); (X.L.)
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Christopher G. Misar
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Gerald J. Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
| | - Xiwen Cai
- USDA-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, 251 Filley Hall, 1625 Arbor Drive, Lincoln, NE 68583, USA;
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (Z.I.T.); (X.L.)
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND 58102, USA; (W.U.); (C.G.M.); (G.J.S.)
- Correspondence: ; Tel.: +1-701-239-1351
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98
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Rubin CJ, Enbody ED, Dobreva MP, Abzhanov A, Davis BW, Lamichhaney S, Pettersson M, Sendell-Price AT, Sprehn CG, Valle CA, Vasco K, Wallerman O, Grant BR, Grant PR, Andersson L. Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules. SCIENCE ADVANCES 2022; 8:eabm5982. [PMID: 35857449 PMCID: PMC9269886 DOI: 10.1126/sciadv.abm5982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/25/2022] [Indexed: 05/21/2023]
Abstract
Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.
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Affiliation(s)
- Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Erik D. Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mariya P. Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ashley T. Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - C. Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlos A. Valle
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Karla Vasco
- Colegio de Ciencias Biológicas y Ambientales, Galápagos Science Center GSC, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Corresponding author.
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99
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Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat Commun 2022; 13:3891. [PMID: 35794156 PMCID: PMC9259585 DOI: 10.1038/s41467-022-31581-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization. The contribution of ancient haplotypes to domestication is largely unknown. Here, the authors develop an ancestral genomic haploblock dissection method to generate a mosaic pan-ancestry genomic map and reveal that the domesticated polyploidy wheat emerged from the admixture of six founder wild emmer linages.
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100
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Feng C, Wang X, Wu S, Ning W, Song B, Yan J, Cheng S. HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables. FRONTIERS IN PLANT SCIENCE 2022; 13:927407. [PMID: 35845648 PMCID: PMC9284118 DOI: 10.3389/fpls.2022.927407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Haplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the context of a large amount of genomic data. Here, we describe the tool HAPPE, which uses the agglomerative hierarchical clustering algorithm to characterize and visualize the genotypes and haplotypes in a phylogenetic context. The tool displays the plots by coloring the cells and/or their borders in Excel tables for any given gene and genomic region of interest. HAPPE facilitates informative displays wherein data in plots are easy to read and access. It allows parallel display of several lines of values, such as phylogenetic trees, P values of GWAS, the entry of genes or SNPs, and the sequencing depth at each position. These features are informative for the detection of insertion/deletions or copy number variations. Overall, HAPPE provides editable plots consisting of cells in Excel tables, which are user-friendly to non-programmers. This pipeline is coded in Python and is available at https://github.com/fengcong3/HAPPE.
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Affiliation(s)
- Cong Feng
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Xingwei Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Shenzhen Research Institute of Henan University, Shenzhen, China
| | - Shishi Wu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Shenzhen Research Institute of Henan University, Shenzhen, China
| | - Weidong Ning
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Bo Song
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Jianbin Yan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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