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Ikeda H. Virtual issue: phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants. JOURNAL OF PLANT RESEARCH 2023; 136:581-585. [PMID: 37462882 DOI: 10.1007/s10265-023-01478-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
Phylogeographic studies have investigated genetic variation and structure within species or closely related lineages and are fundamental for understanding factors and processes of genetic divergence as well as speciation. This virtual issue collects 35 papers on phylogeographic studies published in the Journal of Plant Research and focuses on three major topics in biodiversity: (1) biogeography, (2) systematics, and (3) evolution.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo, Meguro-ku, 153-8902, Japan.
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Novikova PY, Hohmann N, Van de Peer Y. Polyploid Arabidopsis species originated around recent glaciation maxima. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:8-15. [PMID: 29448159 DOI: 10.1016/j.pbi.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/17/2018] [Indexed: 05/20/2023]
Abstract
Polyploidy may provide adaptive advantages and is considered to be important for evolution and speciation. Polyploidy events are found throughout the evolutionary history of plants, however they do not seem to be uniformly distributed along the time axis. For example, many of the detected ancient whole-genome duplications (WGDs) seem to cluster around the K/Pg boundary (∼66Mya), which corresponds to a drastic climate change event and a mass extinction. Here, we discuss more recent polyploidy events using Arabidopsis as the most developed plant model at the level of the entire genus. We review the history of the origin of allotetraploid species A. suecica and A. kamchatica, and tetraploid lineages of A. lyrata, A. arenosa and A. thaliana, and discuss potential adaptive advantages. Also, we highlight an association between recent glacial maxima and estimated times of origins of polyploidy in Arabidopsis. Such association might further support a link between polyploidy and environmental challenge, which has been observed now for different time-scales and for both ancient and recent polyploids.
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Affiliation(s)
- Polina Yu Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nora Hohmann
- University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium; Department of Genetics, University of Pretoria, Pretoria, South Africa.
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Yew CL, Kakui H, Shimizu KK. Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica. JOURNAL OF PLANT RESEARCH 2018; 131:349-358. [PMID: 29032409 DOI: 10.1007/s10265-017-0982-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
Polyploidization has played an important role in the speciation and diversification of plant species. However, genetic analyses of polyploids are challenging because the vast majority of the model species are diploids. The allotetraploid Arabidopsis kamchatica, which originated through the hybridization of the diploid Arabidopsis halleri and Arabidopsis lyrata, is an emerging model system for studying various aspects of polyploidy. However, a transgenic method that allows the insertion of a gene of interest into A. kamchatica is still lacking. In this study, we investigated the early development of pistils in A. kamchatica and confirmed the formation of open pistils in young flower buds (stages 8-9), which is important for allowing Agrobacterium to access female reproductive tissues. We established a simple Agrobacterium-mediated floral dip transformation method to transform a gene of interest into A. kamchatica by dipping A. kamchatica inflorescences bearing many young flower buds into a 5% sucrose solution containing 0.05% Silwet L-77 and Agrobacterium harboring the gene of interest. We showed that a screenable marker comprising fluorescence-accumulating seed technology with green fluorescent protein was useful for screening the transgenic seeds of two accessions of A. kamchatica subsp. kamchatica and an accession of A. kamchatica subsp. kawasakiana.
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Affiliation(s)
- Chow-Lih Yew
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
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Ikeda H, Higashi H, Yakubov V, Barkalov V, Setoguchi H. Phylogeographical study of the alpine plantCassiope lycopodioides(Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Ikeda
- Department of Botany; National Museum of Nature and Science; 4-1-1 Amakubo Tsukuba Ibaraki 305-0005 Japan
- Institute of Plant Science and Resources; Okayama University; 2-20-1 Chuo Kurashiki Okayama 710-0046 Japan
| | - Hiroyuki Higashi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
| | - Valentin Yakubov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Vyacheslav Barkalov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
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Wolf DE, Steets JA, Houliston GJ, Takebayashi N. Genome size variation and evolution in allotetraploid Arabidopsis kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. AOB PLANTS 2014; 6:plu025. [PMID: 24887004 PMCID: PMC4076644 DOI: 10.1093/aobpla/plu025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Polyploidization and subsequent changes in genome size are fundamental processes in evolution and diversification. Little is currently known about the extent of genome size variation within taxa and the evolutionary forces acting on this variation. Arabidopsis kamchatica has been reported to contain both diploid and tetraploid individuals. The aim of this study was to determine the genome size of A. kamchatica, whether there is variation in ploidy and/or genome size in A. kamchatica and to study how genome size has evolved. We used propidium iodide flow cytometry to measure 2C DNA content of 73 plants from 25 geographically diverse populations of the putative allotetraploid A. kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. All A. kamchatica plants appear to be tetraploids. The mean 2C DNA content of A. kamchatica was 1.034 pg (1011 Mbp), which is slightly smaller than the sum of its diploid parents (A. lyrata: 0.502 pg; A. halleri: 0.571 pg). Arabidopsis kamchatica appears to have lost ∼37.594 Mbp (3.6 %) of DNA from its 2C genome. Tetraploid A. lyrata from Germany and Austria appears to have lost ∼70.366 Mbp (7.2 %) of DNA from the 2C genome, possibly due to hybridization with A. arenosa, which has a smaller genome than A. lyrata. We did find genome size differences among A. kamchatica populations, which varied up to 7 %. Arabidopsis kamchatica ssp. kawasakiana from Japan appears to have a slightly larger genome than A. kamchatica ssp. kamchatica from North America, perhaps due to multiple allopolyploid origins or hybridization with A. halleri. However, the among-population coefficient of variation in 2C DNA content is lower in A. kamchatica than in other Arabidopsis taxa. Due to its close relationship to A. thaliana, A. kamchatica has the potential to be very useful in the study of polyploidy and genome evolution.
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Affiliation(s)
- Diana E Wolf
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
| | - Janette A Steets
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078-3013, USA
| | - Gary J Houliston
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Landcare Research, Gerald St, Lincoln 7608, New Zealand
| | - Naoki Takebayashi
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
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Lee S, Maki M. Comparative phylogeographic study of Hosta sieboldiana and Hosta albomarginata (Asparagaceae) in Japan. Ecol Evol 2013; 3:4767-85. [PMID: 24363903 PMCID: PMC3867910 DOI: 10.1002/ece3.838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 11/28/2022] Open
Abstract
We analyzed variations in chloroplast DNA (cpDNA) in the widespread herbaceous species Hosta sieboldiana and Hosta albomarginata across large portions of their geographic ranges in the Japanese archipelago. Our objective was to compare the phylogeographic histories and phylogeographic structures of the two congeneric species in the Japanese archipelago. The location of the study is Japanese archipelago. We sequenced 1380 bp of noncoding cpDNA from 45 populations of H. sieboldiana (n = 362) and 55 populations of H. albomarginata (n = 436) to assess genetic variations within and among populations across almost the entire distributions of the species in Japan. Extant patterns of geographic structure were analyzed using statistical parsimony networks and spatial analysis of molecular variance (SAMOVA). We also used Monmonier's algorithm to detect genetic barriers between regions. Relationships between the populations were examined using a neighbor-joining (NJ) method. Four haplotypes were found for H. sieboldiana, whereas eight haplotypes were identified for H. albomarginata. Total genetic haplotype diversity (hT) and within-population haplotype diversity (hS) for H. sieboldiana were 0.352 and 0.040, respectively, while the values for H. albomarginata were 0.529 and 0.085, respectively. The population differentiations (GST) for H. sieboldiana and H. albomarginata were 0.839 and 0.886, respectively. The SAMOVA analysis revealed two clusters in H. sieboldiana and four clusters in H. albomarginata. Differentiations between and among the clusters were supported by the BARRIER analysis and the NJ tree. We detected differences in the population genetic structure between the two species. We found that H. sieboldiana had lower haplotype diversity than H. albomarginata. These results may be partially explained by the difference in ecological habitats and geographic distributions between the species. Hosta albomarginata is more widely distributed than H. sieboldiana in East Asia including Russia, and this large distribution range would enable more chances to intraspecific gene flow.
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Affiliation(s)
- Sangryong Lee
- Botanical Gardens, Tohoku University Kawauchi 12-2, Aoba-ku, Sendai, 980-0862, Japan
| | - Masayuki Maki
- Botanical Gardens, Tohoku University Kawauchi 12-2, Aoba-ku, Sendai, 980-0862, Japan
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Tsuchimatsu T, Kaiser P, Yew CL, Bachelier JB, Shimizu KK. Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica. PLoS Genet 2012; 8:e1002838. [PMID: 22844253 PMCID: PMC3405996 DOI: 10.1371/journal.pgen.1002838] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/04/2012] [Indexed: 01/01/2023] Open
Abstract
The evolutionary transition from outcrossing to self-fertilization (selfing) through the loss of self-incompatibility (SI) is one of the most prevalent events in flowering plants, and its genetic basis has been a major focus in evolutionary biology. In the Brassicaceae, the SI system consists of male and female specificity genes at the S-locus and of genes involved in the female downstream signaling pathway. During recent decades, much attention has been paid in particular to clarifying the genes responsible for the loss of SI. Here, we investigated the pattern of polymorphism and functionality of the female specificity gene, the S-locus receptor kinase (SRK), in allotetraploid Arabidopsis kamchatica. While its parental species, A. lyrata and A. halleri, are reported to be diploid and mainly self-incompatible, A. kamchatica is self-compatible. We identified five highly diverged SRK haplogroups, found their disomic inheritance and, for the first time in a wild allotetraploid species, surveyed the geographic distribution of SRK at the two homeologous S-loci across the species range. We found intact full-length SRK sequences in many accessions. Through interspecific crosses with the self-incompatible and diploid congener A. halleri, we found that the female components of the SI system, including SRK and the female downstream signaling pathway, are still functional in these accessions. Given the tight linkage and very rare recombination of the male and female components on the S-locus, this result suggests that the degradation of male components was responsible for the loss of SI in A. kamchatica. Recent extensive studies in multiple Brassicaceae species demonstrate that the loss of SI is often derived from mutations in the male component in wild populations, in contrast to cultivated populations. This is consistent with theoretical predictions that mutations disabling male specificity are expected to be more strongly selected than mutations disabling female specificity, or the female downstream signaling pathway.
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Affiliation(s)
| | | | | | | | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, Institute of Plant Biology, and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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