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Healey AL, Garsmeur O, Lovell JT, Shengquiang S, Sreedasyam A, Jenkins J, Plott CB, Piperidis N, Pompidor N, Llaca V, Metcalfe CJ, Doležel J, Cápal P, Carlson JW, Hoarau JY, Hervouet C, Zini C, Dievart A, Lipzen A, Williams M, Boston LB, Webber J, Keymanesh K, Tejomurthula S, Rajasekar S, Suchecki R, Furtado A, May G, Parakkal P, Simmons BA, Barry K, Henry RJ, Grimwood J, Aitken KS, Schmutz J, D'Hont A. The complex polyploid genome architecture of sugarcane. Nature 2024; 628:804-810. [PMID: 38538783 PMCID: PMC11041754 DOI: 10.1038/s41586-024-07231-4] [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] [Received: 02/24/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
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Affiliation(s)
- A L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - O Garsmeur
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - J T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Shengquiang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - C B Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - N Piperidis
- Sugar Research Australia, Te Kowai, Queensland, Australia
| | - N Pompidor
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - V Llaca
- Corteva Agriscience, Johnston, IA, USA
| | - C J Metcalfe
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - P Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - J W Carlson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Y Hoarau
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- ERCANE, Sainte-Clotilde, La Réunion, France
| | - C Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Zini
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Dievart
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - L B Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Tejomurthula
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Rajasekar
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - R Suchecki
- CSIRO Agriculture and Food, Urrbrae, South Australia, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - G May
- Corteva Agriscience, Johnston, IA, USA
| | | | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - K Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
| | - J Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - A D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, France.
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Wang JC, Chen HH, Hsu TW, Hung KH, Huang CC. A taxonomic revision of the genus Angelica (Apiaceae) in Taiwan with a new species A. aliensis. BOTANICAL STUDIES 2024; 65:3. [PMID: 38252347 PMCID: PMC10803708 DOI: 10.1186/s40529-023-00407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Angelica L. sensu lato is a taxonomically complex genus, and many studies have utilized morphological and molecular features to resolve its classification issues. In Taiwan, there are six taxa within Angelica, and their taxonomic treatments have been a subject of controversy. In this study, we conducted a comprehensive analysis incorporating morphological and molecular (cpDNA and nrDNA) characteristics to revise the taxonomic treatments of Angelica in Taiwan. RESULTS As a result of our research, we have revised the classification between A. dahurica var. formosana and A. pubescens and merged two varieties of A. morrisonicola into a single taxon. A new taxon, A. aliensis, has been identified and found to share a close relationship with A. tarokoensis. Based on the morphological and molecular characteristics data, it has been determined that the former three taxa should be grouped into the Eurasian Angelica clade, while the remaining four taxa should belong to the littoral Angelica clade. Furthermore, Angelica species in Taiwan distributed at higher altitudes displayed higher genetic diversity, implying that the central mountain range of Taiwan serves as a significant reservoir of plant biodiversity. Genetic drift, such as bottlenecks, has been identified as a potential factor leading to the fixation or reduction of genetic diversity of populations in most Angelica species. We provide key to taxa, synopsis, phenology, and distribution for each taxon of Taiwan. CONCLUSIONS Our comprehensive analysis of morphological and molecular features has shed light on the taxonomic complexities within Angelica in Taiwan, resolving taxonomic issues and providing valuable insights into the phylogenetic relationships of Angelica in Taiwan.
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Affiliation(s)
- Jenn-Che Wang
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Hung-Hsin Chen
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Tsai-Wen Hsu
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
- Forestry and Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Chi-Chun Huang
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan.
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Chen SY, Huang CC, Cheng YT, Wang CC, Li CY, Lai IL, Hung KH. Effect of geographic isolation on genetic variation and population structure of Euphrasia nankotaizanensis, a threatened endemic alpine herb in Taiwan. Heliyon 2023; 9:e14228. [PMID: 36938387 PMCID: PMC10018478 DOI: 10.1016/j.heliyon.2023.e14228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Euphrasia nankotaizanensis (Orobanchaceae) is a rare alpine herb that is endemic to Taiwan. Only four small populations remain in Xue, Nanhu, and Cilai Mountains of Taiwan. The distribution of alpine herbs is severely threatened by climate change, which influences genetic variation and population structure. In this study, we investigated the effects of the natural isolation of alpine habitats on the genetic diversity and geographic structure of populations of E. nankotaizanensis using chloroplast (cp) and nuclear DNA (nrDNA) markers. We found lower levels of genetic diversity in E. nankotaizanensis than in other alpine plants and little to no genetic variation within populations, which could be mainly attributed to the small population size and genetic drift. Only one nrDNA haplotype was present in each population. The lack of monophyly of the four populations in cpDNA probably resulted from lineage sorting or occasional long-distance seed dispersal. Phylogeographic analysis suggested that Nanhu Mountain was probably a refugium over the glacial maxima, agreeing with the potential refugia in central Taiwan. The STRUCTURE and AMOVA analyses revealed significant genetic differentiation in nrDNA among the mountains, which resulted from geographical isolation among these mountains. Estimates of the effective population size (Ne) and demography reflected lower Ne values and a recent population decline, probably implying a greater extinction risk for E. nankotaizanensis. We observed genetic depletion and considerable genetic differentiation among mountain populations, which should be considered in future conservation efforts for this species. In addition, this study provides important insights into the long-term potential of alpine herbs in Taiwan, which are useful for a better prediction of their responses to future climate change.
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Affiliation(s)
- Syuan-Yu Chen
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chi-Chun Huang
- Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - Yu-Tzu Cheng
- Department of Forestry, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Chiang Wang
- Department of Forestry, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - I-Ling Lai
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
- Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
- Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Corresponding author. Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan.
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Hirota SK, Yasumoto AA, Nitta K, Tagane M, Miki N, Suyama Y, Yahara T. Evolutionary history of Hemerocallis in Japan inferred from chloroplast and nuclear phylogenies and levels of interspecific gene flow. Mol Phylogenet Evol 2021; 164:107264. [PMID: 34273506 DOI: 10.1016/j.ympev.2021.107264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
The perennial herb genus Hemerocallis (Asphodelaceae) shows four flowering types: diurnal half-day, diurnal one-day, nocturnal half-day, and nocturnal one-day flowering. These flowering types are corresponding to their main pollinators, and probably act as a primary mechanism of reproductive isolation. To examine how the four flowering types diverged, we reconstructed the phylogeny of the Japanese species of Hemerocallis using 1615 loci of nuclear genome-wide SNPs and 2078 bp sequences of four cpDNA regions. We also examined interspecific gene flows among taxa by an Isolation-with-Migration model and a population structure analysis. Our study revealed an inconsistency between chloroplast and nuclear genome phylogenies, which may have resulted from chloroplast capture. Each of the following five clusters is monophyletic and clearly separated on the nuclear genome-wide phylogenetic tree: (I) two nocturnal flowering species with lemon-yellow flowers, H. citrina (half-day flowering) and H. lilioasphodelus (one-day flowering); (II) a diurnal one-day flowering species with yellow-orange flowers, H. middendorffii; (III) a variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. disticha; (IV) another variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. aurantiaca, and a diurnal one-day flowering species with yellow-orange flowers, H. major; (V) a diurnal half-day flowering species with yellow-orange flowers, H. hakuunensis. The five clusters are consistent with traditional phenotype-based taxonomy (cluster I, cluster II, and clusters III-V correspond to Hemerocallis sect. Hemerocallis, Capitatae, and Fulvae, respectively). These findings could indicate that three flowering types (nocturnal flowering, diurnal one-day flowering, and diurnal half-day flowering) diverged in early evolutionary stages of Hemerocallis and subsequently a change from diurnal half-day flowering to diurnal one-day flowering occurred in a lineage of H. major. While genetic differentiation among the five clusters was well maintained, significant gene flow was detected between most pairs of taxa, suggesting that repeated hybridization played a role in the evolution of those taxa.
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Affiliation(s)
- Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan.
| | - Akiko A Yasumoto
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kozue Nitta
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, 1-17-71 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5201, Japan
| | - Misa Tagane
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Nozomu Miki
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan
| | - Tetsukazu Yahara
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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Kikuchi S, Osone Y. Subspecies divergence and pronounced phylogenetic incongruence in the East-Asia-endemic shrub Magnolia sieboldii. ANNALS OF BOTANY 2021; 127:75-90. [PMID: 32966556 PMCID: PMC7750721 DOI: 10.1093/aob/mcaa174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS The biogeographic patterns of the East-Asia-endemic shrub Magnolia sieboldii, in which the range of the subsp. sieboldii is interposed with the disjunct distribution of subsp. japonica, implies a complex evolutionary history, involving rapid speciation and hybridization. Here, we aim to reveal the evolutionary and phylogeographic histories of the species with a particular focus on the time of subspecies divergence, the hypothesis of secondary hybridization and the Pleistocene survival of each subspecies, using a combination of genetic analyses and ecological niche modelling. METHODS Genetic variation, genetic structures and phylogenetic relationships were elucidated based on nuclear low-copy genes, chloroplast DNA, and nuclear simple sequence repeats (SSRs). A scenario selection analysis and divergence time estimation were performed using coalescent simulation in DIYABC and *BEAST. Ecological niche modelling and a test of niche differentiation were performed using Maxent and ENMTools. KEY RESULTS All marker types showed deep, but pronouncedly incongruent, west-east genetic divergences, with the subspecies being delineated only by the nuclear low-copy genes. Phylogenetic tree topologies suggested that ancient hybridization and introgression were likely to have occurred; however, this scenario did not receive significant support in the DIYABC analysis. The subspecies differentiated their niches, but both showed a dependence on high humidity and were predicted to have persisted during the last glacial cycle by maintaining a stable latitudinal distribution via migration to lower altitudes. CONCLUSIONS We found a deep genetic divergence and a pronounced phylogenetic incongruence among the two subspecies of M. sieboldii, which may have been driven by major paleogeographic and paleoclimatic events that have occurred since the Neogene in East Asia, including global cooling, climate oscillations and the formation of land bridges. Both subspecies were, however, considered to persist in situ in stable climatic conditions during the late Pleistocene.
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Affiliation(s)
- Satoshi Kikuchi
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
- Hokkaido Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitsujigaoka, Toyohira, Sapporo City, Hokkaido, Japan
| | - Yoko Osone
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Matsunosato, Tsukuba City, Ibaraki Prefecture, Japan
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Franzke A, Koch MA, Mummenhoff K. Turnip Time Travels: Age Estimates in Brassicaceae. TRENDS IN PLANT SCIENCE 2016; 21:554-561. [PMID: 26917156 DOI: 10.1016/j.tplants.2016.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/31/2016] [Indexed: 05/07/2023]
Abstract
Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Marcus A Koch
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany; Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, German
| | - Klaus Mummenhoff
- Biology Department, Botany, Osnabrück University, D-49069 Osnabrück, Germany
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7
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Santiso X, Lopez L, Retuerto R, Barreiro R. Phylogeography of a widespread species: pre-glacial vicariance, refugia, occasional blocking straits and long-distance migrations. AOB PLANTS 2016; 8:plw003. [PMID: 26768603 DOI: 10.1093/aobpla/plwoo3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/28/2015] [Indexed: 05/26/2023]
Abstract
Phylogeographic studies give us the opportunity to reconstruct the historical migrations of species and link them with climatic and geographic variation. They are, therefore, a key tool to understanding the relationships among biology, geology and history. One of the most interesting biogeographical areas of the world is the Mediterranean region. However, in this area, the description of concordant phylogeographic patterns is quite scarce, which limits the understanding of evolutionary patterns related to climate. Species with one-dimensional distribution ranges, such as the strawberry tree (Arbutus unedo), are particularly useful to unravel these patterns. Here, we describe its phylogeographic structure and check for concordance with patterns seen in other Mediterranean plants: longitudinal/latitudinal clines of diversity, evidence for glacial refugia and the role of sea straits in dispersal. We also identify the most likely source for the disjunct Irish population. With this aim, we sequenced four chloroplast non-coding fragments of A. unedo from 23 populations covering its whole distribution. We determined the genetic diversity, population structure, haplotype genealogy and time to the most recent common ancestor. The genealogy revealed two clades that separated during the last 700 ky but before the last glacial maximum. One clade occupies Atlantic Iberia and North Africa, while the other occurs in the Western Mediterranean. The Eastern Mediterranean is inhabited by newer haplotypes derived from both clades, while the Irish population is closely related to Iberian demes. The straits of Sicily and Gibraltar partially restricted the gene flow. We concluded that a vicariance event during the Late Quaternary in the western end of the species' range followed by eastward migration seems a likely explanation for the observed phylogeographic pattern. The role of straits indicates an occasional communication between Europe and North Africa, suggesting that the latter was a novel refugia. The East-West genetic split in Iberia is consistent with the refugia-within-refugia model. Finally, the strawberry tree possibly reached Ireland from Iberia instead of throughout the maritime fringe of France as previously thought.
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Affiliation(s)
- Xabier Santiso
- Área de Ecoloxía, Facultade de Bioloxía, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lúa Lopez
- Área de Ecología, Facultad de Ciencias, Campus A Zapateira, Universidad de A Coruña, 15071 A Coruña, Spain
| | - Rubén Retuerto
- Área de Ecoloxía, Facultade de Bioloxía, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rodolfo Barreiro
- Área de Ecología, Facultad de Ciencias, Campus A Zapateira, Universidad de A Coruña, 15071 A Coruña, Spain
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8
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Santiso X, Lopez L, Retuerto R, Barreiro R. Phylogeography of a widespread species: pre-glacial vicariance, refugia, occasional blocking straits and long-distance migrations. AOB PLANTS 2016; 8:plw003. [PMID: 26768603 PMCID: PMC4768523 DOI: 10.1093/aobpla/plw003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/28/2015] [Indexed: 05/26/2023]
Abstract
Phylogeographic studies give us the opportunity to reconstruct the historical migrations of species and link them with climatic and geographic variation. They are, therefore, a key tool to understanding the relationships among biology, geology and history. One of the most interesting biogeographical areas of the world is the Mediterranean region. However, in this area, the description of concordant phylogeographic patterns is quite scarce, which limits the understanding of evolutionary patterns related to climate. Species with one-dimensional distribution ranges, such as the strawberry tree (Arbutus unedo), are particularly useful to unravel these patterns. Here, we describe its phylogeographic structure and check for concordance with patterns seen in other Mediterranean plants: longitudinal/latitudinal clines of diversity, evidence for glacial refugia and the role of sea straits in dispersal. We also identify the most likely source for the disjunct Irish population. With this aim, we sequenced four chloroplast non-coding fragments of A. unedo from 23 populations covering its whole distribution. We determined the genetic diversity, population structure, haplotype genealogy and time to the most recent common ancestor. The genealogy revealed two clades that separated during the last 700 ky but before the last glacial maximum. One clade occupies Atlantic Iberia and North Africa, while the other occurs in the Western Mediterranean. The Eastern Mediterranean is inhabited by newer haplotypes derived from both clades, while the Irish population is closely related to Iberian demes. The straits of Sicily and Gibraltar partially restricted the gene flow. We concluded that a vicariance event during the Late Quaternary in the western end of the species' range followed by eastward migration seems a likely explanation for the observed phylogeographic pattern. The role of straits indicates an occasional communication between Europe and North Africa, suggesting that the latter was a novel refugia. The East-West genetic split in Iberia is consistent with the refugia-within-refugia model. Finally, the strawberry tree possibly reached Ireland from Iberia instead of throughout the maritime fringe of France as previously thought.
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Affiliation(s)
- Xabier Santiso
- Área de Ecoloxía, Facultade de Bioloxía, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lúa Lopez
- Área de Ecología, Facultad de Ciencias, Campus A Zapateira, Universidad de A Coruña, 15071 A Coruña, Spain
| | - Rubén Retuerto
- Área de Ecoloxía, Facultade de Bioloxía, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rodolfo Barreiro
- Área de Ecología, Facultad de Ciencias, Campus A Zapateira, Universidad de A Coruña, 15071 A Coruña, Spain
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Herden T, Hanelt P, Friesen N. Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen (Amaryllidaceae). Mol Phylogenet Evol 2015; 95:79-93. [PMID: 26639102 DOI: 10.1016/j.ympev.2015.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/26/2023]
Abstract
The disjunct distribution of the subgenus Anguinum of the genus Allium makes it a good candidate to test models of Northern hemisphere biogeography. Here we conduct phylogenetic analysis with the nuclear marker ITS and three different chloroplast markers (rps16 intron, rbcL-atpB spacer, rpl32-trnL spacer). Divergence time estimations (Beast) relying on published ITS substitution rates and ancestral range reconstructions were calculated to elucidate the biogeographical history of the subgenus. Additionally we compiled distribution maps for all species with data taken from the literature, herbariums and data from field observations. The main radiation of the subgenus took place in the last one million years and is still going on. They have their origins in the mid Miocene in East Asia and were highly influenced by the climate fluctuations in the Pliocene/Pleistocene period. Conflicting tree topologies between nuclear and cpDNA markers of Allium tricoccum Solander indicate that the species is of hybridogenous origin. Cloning the ITS sequence revealed the parental copies and confirmed our conclusion. One originated from the Eurasian and the other from the East Asian clade. We were able to show that it reached North America most likely via the Beringia around 2.5mya (95% HPD of 0.35-5.26mya). Our data suggest that Allium victorialis L. is only distributed in mountain pastures in Europe as it forms a well-supported clade in the ITS tree. In the analysis of the molecular markers we found two distinct types of Allium ochotense Prokh. and we suggest splitting the species based on Prokhanov's (1930) proposal. Taxonomical remarks and an identification key to all species of the subgenus Anguinum is provided.
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Affiliation(s)
- Tobias Herden
- Botanical Garden of the University of Osnabrueck, Albrechtstrasse 29, 49076 Osnabrueck, Germany
| | - Peter Hanelt
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), OT Gartersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Nikolai Friesen
- Botanical Garden of the University of Osnabrueck, Albrechtstrasse 29, 49076 Osnabrueck, Germany.
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10
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An M, Zeng L, Zhang T, Zhong Y. Phylogeography of Thlaspi arvense (Brassicaceae) in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling. Int J Mol Sci 2015; 16:13339-55. [PMID: 26110380 PMCID: PMC4490498 DOI: 10.3390/ijms160613339] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 11/17/2022] Open
Abstract
Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima's D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model.
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Affiliation(s)
- Miao An
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences/ Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Ticao Zhang
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China.
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa 850000, China.
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11
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Stockenhuber R, Zoller S, Shimizu-Inatsugi R, Gugerli F, Shimizu KK, Widmer A, Fischer MC. Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing. PLoS One 2015; 10:e0128181. [PMID: 26061739 PMCID: PMC4465667 DOI: 10.1371/journal.pone.0128181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies.
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Affiliation(s)
- Reinhold Stockenhuber
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre, ETH Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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12
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Filloux D, Murrell S, Koohapitagtam M, Golden M, Julian C, Galzi S, Uzest M, Rodier-Goud M, D’Hont A, Vernerey MS, Wilkin P, Peterschmitt M, Winter S, Murrell B, Martin DP, Roumagnac P. The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed. Virus Evol 2015; 1:vev002. [PMID: 27774276 PMCID: PMC5014472 DOI: 10.1093/ve/vev002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Endogenous viral sequences are essentially 'fossil records' that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21-24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species.
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Affiliation(s)
- Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Sasha Murrell
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maneerat Koohapitagtam
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
- Department of Pest Management, Faculty of Natural Resources, Prince of Songkla University, Hat Yai campus, Thailand 90120
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
| | - Charlotte Julian
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Serge Galzi
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Marilyne Uzest
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | | | - Angélique D’Hont
- CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Marie Stephanie Vernerey
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Michel Peterschmitt
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Stephan Winter
- DSMZ Plant Virus Department, Messeweg 11/12, 38102, Braunschweig, Germany
| | - Ben Murrell
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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13
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One or three species in Megadenia (Brassicaceae): insight from molecular studies. Genetica 2014; 142:337-50. [PMID: 25027851 DOI: 10.1007/s10709-014-9778-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.
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14
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Zhu A, Guo W, Jain K, Mower JP. Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome. Mol Biol Evol 2014; 31:1228-36. [DOI: 10.1093/molbev/msu079] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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15
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Christensen AC. Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol Evol 2013; 5:1079-86. [PMID: 23645599 PMCID: PMC3698917 DOI: 10.1093/gbe/evt069] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Plant mitochondrial genomes are notorious for their large and variable size, nonconserved open reading frames of unknown function, and high rates of rearrangement. Paradoxically, the mutation rates are very low. However, mutation rates can only be measured in sequences that can be aligned—a very small part of plant mitochondrial genomes. Comparison of the complete mitochondrial genome sequences of two ecotypes of Arabidopsis thaliana allows the alignment of noncoding as well as coding DNA and estimation of the mutation rates in both. A recent chimeric duplication is also analyzed. A hypothesis is proposed that the mechanisms of plant mitochondrial DNA repair account for these features and includes different mechanisms in transcribed and nontranscribed regions. Within genes, a bias toward gene conversion would keep measured mutation rates low, whereas in noncoding regions, break-induced replication (BIR) explains the expansion and rearrangements. Both processes are types of double-strand break repair, but enhanced second-strand capture in transcribed regions versus BIR in nontranscribed regions can explain the two seemingly contradictory features of plant mitochondrial genome evolution—the low mutation rates in genes and the striking expansions of noncoding sequences.
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Affiliation(s)
- Alan C Christensen
- School of Biological Sciences, E249 Beadle Center, University of Nebraska-Lincoln, USA.
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16
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Abstract
It is now well established that plants have an important place in studies of sex chromosome evolution because of the repeated independent evolution of separate sexes and sex chromosomes. There has been considerable recent progress in studying plant sex chromosomes. In this review, I focus on how these recent studies have helped clarify or answer several important questions about sex chromosome evolution, and I shall also try to clarify some common misconceptions. I also outline future work that will be needed to make further progress, including testing some important ideas by genetic, molecular, and developmental approaches. Systems with different ages can clearly help show the time course of events during changes from an ancestral co-sexual state (hermaphroditism or monoecy), and I will also explain how different questions can be studied in lineages whose dioecy or sex chromosomes evolved at different times in the past.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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