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Fan Z, Whitaker VM. Genomic signatures of strawberry domestication and diversification. THE PLANT CELL 2024; 36:1622-1636. [PMID: 38113879 PMCID: PMC11062436 DOI: 10.1093/plcell/koad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
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2
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Holt SD, Sigel EM, Sutherland BL, Schwartsburd PB, Beck JB. What is Salvinia molesta (Salviniaceae)? Determining the maternal progenitor and genetic diversity of the clonal invasive fern giant salvinia. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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3
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Xu Y, Liu Y, Yu Z, Jia X. Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia 'Xiari Qixin': Genome Features, Comparative and Phylogenetic Analysis. Genes (Basel) 2023; 14:460. [PMID: 36833387 PMCID: PMC9956581 DOI: 10.3390/genes14020460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia 'Xiari Qixin' belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. 'Xiari Qixin' was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. 'Xiari Qixin' and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. 'Xiari Qixin' and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia.
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Affiliation(s)
| | | | | | - Xiaocheng Jia
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
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4
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Cauret CMS, Mortimer SME, Roberti MC, Ashman TL, Liston A. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 (BETHESDA, MD.) 2022; 12:6603112. [PMID: 35666193 PMCID: PMC9339316 DOI: 10.1093/g3journal/jkac139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/19/2022] [Indexed: 01/07/2023]
Abstract
When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
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Affiliation(s)
- Caroline M S Cauret
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sebastian M E Mortimer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marcelina C Roberti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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5
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Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). FRONTIERS IN PLANT SCIENCE 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [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: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
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Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
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Käfer J, Méndez M, Mousset S. Labile sex expression in angiosperm species with sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210216. [PMID: 35306891 PMCID: PMC8935303 DOI: 10.1098/rstb.2021.0216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Here, we review the literature on sexual lability in dioecious angiosperm species with well-studied sex chromosomes. We distinguish three types of departures from strict dioecy, concerning either a minority of flowers in some individuals (leakiness) or the entire individual, which can constantly be bisexual or change sex. We found that for only four of the 22 species studied, reports of lability are lacking. The occurrence of lability is only weakly related to sex chromosome characteristics (number of sex-linked genes, age of the non-recombining region). These results contradict the naive idea that lability is an indication of the absence or the recent evolution of sex chromosomes, and thereby contribute to a growing consensus that sex chromosomes do not necessarily fix sex determination once and for all. We discuss some implications of these findings for the evolution of sex chromosomes, and suggest that more species with well-characterized lability should be studied with genomic data and tools. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS UMR 5558, 69622 Villeurbanne, France.,CESAB-FRB, 34000 Montpellier, France
| | - Marcos Méndez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles (Madrid), Spain
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS UMR 5558, 69622 Villeurbanne, France
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7
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Brock JR, Mandáková T, McKain M, Lysak MA, Olsen KM. Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa. HORTICULTURE RESEARCH 2022; 9:uhab050. [PMID: 35031794 PMCID: PMC8788360 DOI: 10.1093/hr/uhab050] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 05/24/2023]
Abstract
The genus Camelina (Brassicaceae) comprises 7-8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.
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Affiliation(s)
- Jordan R Brock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
| | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michael McKain
- Department of Biological Sciences, The University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, Alabama, 35487 USA
| | - Martin A Lysak
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130 USA
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8
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Evolutionary history and pan-genome dynamics of strawberry ( Fragaria spp.). Proc Natl Acad Sci U S A 2021; 118:2105431118. [PMID: 34697247 PMCID: PMC8609306 DOI: 10.1073/pnas.2105431118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.
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9
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Bird KA, Hardigan MA, Ragsdale AP, Knapp SJ, VanBuren R, Edger PP. Diversification, spread, and admixture of octoploid strawberry in the Western Hemisphere. AMERICAN JOURNAL OF BOTANY 2021; 108:2269-2281. [PMID: 34636416 PMCID: PMC9299191 DOI: 10.1002/ajb2.1776] [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: 04/12/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
PREMISE Polyploid species often have complex evolutionary histories that have, until recently, been intractable due to limitations of genomic resources. While recent work has further uncovered the evolutionary history of the octoploid strawberry (Fragaria L.), there are still open questions. Much is unknown about the evolutionary relationship of the wild octoploid species, Fragaria virginiana and Fragaria chiloensis, and gene flow within and among species after the formation of the octoploid genome. METHODS We leveraged a collection of wild octoploid ecotypes of strawberry representing the recognized subspecies and ranging from Alaska to southern Chile, and a high-density SNP array to investigate wild octoploid strawberry evolution. Evolutionary relationships were interrogated with phylogenetic analysis and genetic clustering algorithms. Additionally, admixture among and within species is assessed with model-based and tree-based approaches. RESULTS Phylogenetic analysis revealed that the two octoploid strawberry species are monophyletic sister lineages. The genetic clustering results show substructure between North and South American F. chiloensis populations. Additionally, model-based and tree-based methods support gene flow within and among the two octoploid species, including newly identified admixture in the Hawaiian F. chiloensis subsp. sandwicensis population. CONCLUSIONS F. virginiana and F. chiloensis are supported as monophyletic and sister lineages. All but one of the subspecies show extensive paraphyly. Furthermore, phylogenetic relationships among F. chiloensis populations supports a single population range expansion southward from North America. The inter- and intraspecific relationships of octoploid strawberry are complex and suggest substantial gene flow between sympatric populations among and within species.
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Affiliation(s)
- Kevin A. Bird
- Department of HorticultureMichigan State UniversityEast LansingMichigan48823USA
- Ecology, Evolution and Behavior ProgramMichigan State UniversityEast LansingMichigan48823USA
| | | | - Aaron P. Ragsdale
- National Laboratory of Genomics for Biodiversity (LANGEBIO)Unit of Advanced Genomics, CINVESTAVIrapuatoMexico
| | - Steven J. Knapp
- Department of Plant SciencesUniversity of CaliforniaDavisCalifornia95616USA
| | - Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMichigan48823USA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichigan48824USA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMichigan48823USA
- Ecology, Evolution and Behavior ProgramMichigan State UniversityEast LansingMichigan48823USA
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10
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Hardigan MA, Lorant A, Pincot DDA, Feldmann MJ, Famula RA, Acharya CB, Lee S, Verma S, Whitaker VM, Bassil N, Zurn J, Cole GS, Bird K, Edger PP, Knapp SJ. Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry. Mol Biol Evol 2021; 38:2285-2305. [PMID: 33507311 PMCID: PMC8136507 DOI: 10.1093/molbev/msab024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.
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Affiliation(s)
- Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Charlotte B Acharya
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Seonghee Lee
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Sujeet Verma
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Vance M Whitaker
- IFAS Gulf Coast Research and Education Center, Department of Horticulture, University of Florida, Wimauma, FL 33598, USA
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Jason Zurn
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR 92182, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Kevin Bird
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Patrick P Edger
- Department of Horticultural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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11
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Pincot DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TJ, Runcie DE, Heffelfinger C, Dellaporta SL, Cole GS, Knapp SJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3-GENES GENOMES GENETICS 2021; 11:6117203. [PMID: 33772307 PMCID: PMC8022721 DOI: 10.1093/g3journal/jkab015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/12/2020] [Indexed: 01/22/2023]
Abstract
The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.
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Affiliation(s)
- Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mirko Ledda
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas J Poorten
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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12
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Bowers JE, Paterson AH. Chromosome number is key to longevity of polyploid lineages. THE NEW PHYTOLOGIST 2021; 231:19-28. [PMID: 33772797 DOI: 10.1111/nph.17361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy is ubiquitous and often recursive in plant lineages, most frequently resulting in extinction but occasionally associated with great evolutionary success. However, instead of chromosome numbers exponentially increasing due to recurrent polyploidy, most angiosperm species have fewer than 14 chromosome pairs. Following genome duplication, diploidisation can render one copy of essential genes nonfunctional without fitness cost. In isolated subpopulations, alternate (homoeologous) gene copies can be lost, creating incompatibilities that reduce fitness of hybrids between subpopulations, constraining exchange of favourable genetic changes and reducing species fitness. When multiple sets of incompatible genes are genetically linked, their deleterious effects are not independent. The effective number of independently acting sets of incompatible loci in hybrids is limited by chromosome number and recombination. Therefore, species with many chromosomes are subject to a higher fitness penalty during diploidisation. Karyotypic changes, especially fusions, that reduce gene flow are normally fitness disadvantages, but during the diploidisation process, can increase fitness by reducing mixing of differentially diploidised alleles. Fitness penalties caused by diploidisation favour accelerated karyotypic change, with each change increasing barriers to gene flow, contributing to speciation. Lower chromosome numbers and increased chromosome fusions confer advantages to surviving the diploidisation process following polyploid formation, by independent mechanisms.
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Affiliation(s)
- John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
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13
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Sun J, Sun R, Liu H, Chang L, Li S, Zhao M, Shennan C, Lei J, Dong J, Zhong C, Xue L, Gao Y, Wang G, Zhang Y. Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria. Genomics 2021; 113:1170-1179. [PMID: 33705887 DOI: 10.1016/j.ygeno.2021.01.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/02/2021] [Accepted: 01/23/2021] [Indexed: 02/04/2023]
Abstract
Complete chloroplast genomes of ten wild Fragaria species native to China were sequenced. Phylogenetic analysis clustered Fragaria species into two clades: The south clade (F. iinumae, F. chinensis, F. pentaphylla, F. nilgerrensis, F. daltoniana, F. corymbosa, F. moupinensis, F. tibetica, F. nipponica, F. gracilis, and F. nubicola and north clade (F. viridis, F. orientalis, F. moschata, F. mandshurica, F. vesca, F. chiloensis, F. virginiana, and F. × ananassa), while F. iinumae is the oldest extant species. Molecular clock analysis suggested present Fragaria species share a common ancestor 3.57 million years ago (Ma), F. moschata and octoploid species evolve 0.89 and 0.97 Ma, respectively, but F. moschata be not directly involved in current octoploid species formation. Drastic global temperature change since the Palaeocene-Eocene, approx. 55 Ma, especially during uplifting of the Qinghai-Tibet plateau and quaternary glaciation may have driven the formation of Fragaria, separation of two groups and polyploidization.
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Affiliation(s)
- Jian Sun
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Rui Sun
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Huabo Liu
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Linlin Chang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Shuangtao Li
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Mizhen Zhao
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, 210014 Nanjing, China
| | - Carol Shennan
- Environmental Studies, University of California Santa Cruz, 95064 Santa Cruz, CA, USA.
| | - Jiajun Lei
- Department of Horticulture, Shenyang Agricultural University, 110866 Shenyang, China
| | - Jing Dong
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Chuanfei Zhong
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Li Xue
- Department of Horticulture, Shenyang Agricultural University, 110866 Shenyang, China
| | - Yongshun Gao
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China
| | - Guixia Wang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China.
| | - Yuntao Zhang
- Beijing Academy of Forestry and Pomology Sciences; Beijing Engineering Research Center for Strawberry; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100093 Beijing, China.
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14
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Schneider JV, Paule J, Jungcurt T, Cardoso D, Amorim AM, Berberich T, Zizka G. Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:638650. [PMID: 33613613 PMCID: PMC7890083 DOI: 10.3389/fpls.2021.638650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family's backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family's species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
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Affiliation(s)
- Julio V. Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Entomology III, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Tanja Jungcurt
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - André Márcio Amorim
- Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- Herbário André Maurício Vieira de Carvalho, CEPEC, CEPLAC, Itabuna, Brazil
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Lab-Center, Frankfurt am Main, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- *Correspondence: Georg Zizka, ;
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15
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Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming. Mol Phylogenet Evol 2020; 147:106784. [DOI: 10.1016/j.ympev.2020.106784] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/07/2020] [Accepted: 02/26/2020] [Indexed: 12/15/2022]
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16
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Whitaker VM, Knapp SJ, Hardigan MA, Edger PP, Slovin JP, Bassil NV, Hytönen T, Mackenzie KK, Lee S, Jung S, Main D, Barbey CR, Verma S. A roadmap for research in octoploid strawberry. HORTICULTURE RESEARCH 2020; 7:33. [PMID: 32194969 PMCID: PMC7072068 DOI: 10.1038/s41438-020-0252-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/26/2020] [Indexed: 05/02/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
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Affiliation(s)
- Vance M Whitaker
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Steven J Knapp
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Michael A Hardigan
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Patrick P Edger
- 3Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Janet P Slovin
- USDA-ARS Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MA 20705 USA
| | - Nahla V Bassil
- 5USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333 USA
| | - Timo Hytönen
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- 7Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- NIAB EMR, Kent, ME19 6BJ UK
| | - Kathryn K Mackenzie
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
| | - Seonghee Lee
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sook Jung
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Dorrie Main
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Christopher R Barbey
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sujeet Verma
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
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17
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Morales-Briones DF, Romoleroux K, Tank DC. Three new species of Lachemilla (Rosaceae) from South America. PHYTOKEYS 2019; 127:93-119. [PMID: 31379452 PMCID: PMC6661262 DOI: 10.3897/phytokeys.127.36324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/22/2019] [Indexed: 06/10/2023]
Abstract
Three new species of Lachemilla (Rosaceae), two from Colombia and one from Peru, are described and illustrated. Lachemillarothmaleriana is characterized by its stout stems, sericeous-villous indumentum, and wide ascending sheaths with trilobate lateral lobes. Lachemillaargentea presents a unique combination of tripartite basal leaves with an adaxial silvery villous indumentum, and decumbent branches with verticillate lobed sheaths. Finally, Lachemillacyanea has distinctly basal reniform leaves with a blue-green color and hirsute pubescence. Phylogenetic analyses of the nuclear ribosomal cistron and multiple regions of the plastid genome revealed the allopolyploid origin of the three new taxa.
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Affiliation(s)
- Diego F. Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, Minnesota, 55108, USAUniversity of IdahoMoscowUnited States of America
- Department of Biological Sciences and Stillinger Herbarium, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, Idaho 83844-3051, USAUniversity of MinnesotaSaint PaulUnited States of America
| | - Katya Romoleroux
- Herbario QCA, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, EcuadorPontificia Universidad Católica del EcuadorRoca QuitoEcuador
| | - David C. Tank
- Department of Biological Sciences and Stillinger Herbarium, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, Idaho 83844-3051, USAUniversity of MinnesotaSaint PaulUnited States of America
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18
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Wei N, Cronn R, Liston A, Ashman T. Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments. THE NEW PHYTOLOGIST 2019; 221:2286-2297. [PMID: 30281801 PMCID: PMC6587808 DOI: 10.1111/nph.15508] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/24/2018] [Indexed: 05/09/2023]
Abstract
Polyploidy, or whole-genome duplication often with hybridization, is common in eukaryotes and is thought to drive ecological and evolutionary success, especially in plants. The mechanisms of polyploid success in ecologically relevant contexts, however, remain largely unknown. We conducted an extensive test of functional trait divergence and plasticity in conferring polyploid fitness advantage in heterogeneous environments, by growing clonal replicates of a worldwide genotype collection of six allopolyploid and five diploid wild strawberry (Fragaria) taxa in three climatically different common gardens. Among leaf functional traits, we detected divergence in trait means but not plasticities between polyploids and diploids, suggesting that increased genomic redundancy in polyploids does not necessarily translate into greater trait plasticity in response to environmental change. Across the heterogeneous garden environments, however, polyploids exhibited fitness advantage, which was conferred by both trait means and adaptive trait plasticities, supporting a 'jack-and-master' hypothesis for polyploids. Our findings elucidate essential ecological mechanisms underlying polyploid adaptation to heterogeneous environments, and provide an important insight into the prevalence and persistence of polyploid plants.
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Affiliation(s)
- Na Wei
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260USA
| | - Richard Cronn
- Pacific Northwest Research StationUnited States Department of Agriculture Forest ServiceCorvallisOR97331USA
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260USA
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19
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Liu BB, Liu GN, Hong DY, Wen J. Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data. FRONTIERS IN PLANT SCIENCE 2019; 10:1731. [PMID: 32117331 PMCID: PMC7019104 DOI: 10.3389/fpls.2019.01731] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/09/2019] [Indexed: 05/03/2023]
Abstract
The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya and Rhaphiolepis have been supported to form a clade, the monophyly of Eriobotrya and Rhaphiolepis at the genus level has never been well tested and their phylogenetic positions in Maleae still remain uncertain. This study aims to reconstruct a robust phylogeny of the ER clade in the framework of Maleae with a broad taxon sampling and clarify the phylogenetic relationship between Eriobotrya and Rhaphiolepis. This study employed sequences of the whole plastome (WP) and entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach and included 83 samples representing 76 species in 32 genera of Rosaceae, especially Maleae. The Maximum Likelihood (ML) and Bayesian Analysis (BI) based on three datasets, i.e., WP, coding sequences of plastome (CDS), and nrDNA, strongly supported the paraphyly of Eriobotrya, within which Rhaphiolepis was nested. Our plastid tree supported the sister relationship between the ER clade and Heteromeles, and the nrDNA tree, however, did not resolve the phylogenetic placement of the ER clade in Maleae. Strong incongruence between the plastid and the nuclear trees is most likely explained by hybridization events, which may have played an important role in the evolutionary history of the ER clade. Molecular, morphological, and geographic evidence all supports the merge of Eriobotrya with Rhaphiolepis, which has the nomenclatural priority. We herein transferred 36 taxa of Eriobotrya to Rhaphiolepis. We also proposed a new name, Rhaphiolepis loquata B.B.Liu & J.Wen, for the economically important loquat, as the specific epithet "japonica" was pre-occupied in Rhaphiolepis.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Guang-Ning Liu
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- *Correspondence: Jun Wen,
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20
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Tennessen JA, Wei N, Straub SCK, Govindarajulu R, Liston A, Ashman TL. Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries. PLoS Biol 2018; 16:e2006062. [PMID: 30148831 PMCID: PMC6128632 DOI: 10.1371/journal.pbio.2006062] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/07/2018] [Accepted: 08/09/2018] [Indexed: 11/30/2022] Open
Abstract
Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes—but conservation of the master sex-determining genes—characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxonomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to three different chromosomes in different taxa. To characterize these turnovers, we identified sequences unique to females and assembled their reads into contigs. For most octoploid Fragaria taxa, a short (13 kb) sequence was observed in all females and never in males, implicating it as the sex-determining region (SDR). This female-specific “SDR cassette” contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Phylogenetic comparison of SDR cassettes revealed three clades and a history of repeated translocation. Remarkably, the translocations can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of the “souvenir” sequence—and the resultant expansion of the hemizygous SDR over time—could have been adaptive by locking genes into linkage with sex. Terminal inverted repeats at the insertion borders suggest a means of movement. To our knowledge, this is the first plant SDR shown to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes. Sex chromosomes frequently restructure themselves during organismal evolution, often becoming highly differentiated. This dynamic process is poorly understood for most taxa, especially during the early stages typical of many dioecious flowering plants. We show that in wild strawberries, a female-specific region of DNA is associated with sex and has repeatedly changed its genomic location, each time increasing the size of the hemizygous female-specific sequence on the W sex chromosome. This observation shows, for the first time to our knowledge, that plant sex regions can “jump” and suggests that this phenomenon may be adaptive by gathering and locking new genes into linkage with sex. This conserved and presumed causal sex-determining sequence, which varies in both genomic location and degree of differentiation, will facilitate future studies to understand how sex chromosomes first begin to differentiate.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shannon C. K. Straub
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rajanikanth Govindarajulu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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