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Mitrenina EY, Alekseeva SS, Badaeva ED, Peruzzi L, Artemov GN, Krivenko DA, Pinzani L, Aytaç Z, Çeçen Ö, Baasanmunkh S, Choi HJ, Mesterházy A, Tashev AN, Bancheva S, Lian L, Xiang K, Wang W, Erst AS. Karyotypes and Physical Mapping of Ribosomal DNA with Oligo-Probes in Eranthis sect. Eranthis (Ranunculaceae). PLANTS (BASEL, SWITZERLAND) 2023; 13:47. [PMID: 38202355 PMCID: PMC10780877 DOI: 10.3390/plants13010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
A comparative karyotype analysis of four species of yellow-flowered Eranthis sect. Eranthis, i.e., E. bulgarica, E. cilicica, E. hyemalis, and E. longistipitata from different areas, has been carried out for the first time. All the studied specimens had somatic chromosome number 2n = 16 with basic chromosome number x = 8. Karyotypes of the investigated plants included five pairs of metacentric chromosomes and three pairs of submetacentric/subtelocentric chromosomes. The chromosome sets of the investigated species differ mainly in the ratio of submetacentric/subtelocentric chromosomes, their relative lengths, and arm ratios. A new oligonucleotide probe was developed and tested to detect 45S rDNA clusters. Using this probe and an oligonucleotide probe to 5S rDNA, 45S and 5S rDNA clusters were localized for the first time on chromosomes of E. cilicica, E. hyemalis, and E. longistipitata. Major 45S rDNA clusters were identified on satellite chromosomes in all the species; in E. cilicica, minor clusters were also identified in the terminal regions of one metacentric chromosome pair. The number and distribution of 5S rDNA clusters is more specific. In E. cilicica, two major clusters were identified in the pericentromeric region of a pair of metacentric chromosomes. Two major clusters in the pericentromeric region of a pair of submetacentric chromosomes and two major clusters in the interstitial region of a pair of metacentric chromosomes were observed in E. longistipitata. E. hyemalis has many clusters of different sizes, localized mainly in the pericentromeric regions. Summarizing new data on the karyotype structure of E. sect. Eranthis and previously obtained data on E. sect. Shibateranthis allowed conclusions to be formed about the clear interspecific karyological differences of the genus Eranthis.
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Affiliation(s)
- Elizaveta Yu. Mitrenina
- Department of Genetics and Cell Biology, Biological Institute, National Research Tomsk State University, 634050 Tomsk, Russia; (E.Y.M.); (S.S.A.); (G.N.A.)
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana S. Alekseeva
- Department of Genetics and Cell Biology, Biological Institute, National Research Tomsk State University, 634050 Tomsk, Russia; (E.Y.M.); (S.S.A.); (G.N.A.)
| | - Ekaterina D. Badaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia;
| | - Lorenzo Peruzzi
- PLANTSEED Lab, Department of Biology, University of Pisa, 56126 Pisa, Italy; (L.P.); (L.P.)
| | - Gleb N. Artemov
- Department of Genetics and Cell Biology, Biological Institute, National Research Tomsk State University, 634050 Tomsk, Russia; (E.Y.M.); (S.S.A.); (G.N.A.)
| | - Denis A. Krivenko
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Lorenzo Pinzani
- PLANTSEED Lab, Department of Biology, University of Pisa, 56126 Pisa, Italy; (L.P.); (L.P.)
| | - Zeki Aytaç
- Biology Department, Faculty of Science, Gazi University, Ankara 06500, Turkey;
| | - Ömer Çeçen
- Department of Plant and Animal Production, Technical Sciences Vocational School, Karamanoğlu Mehmetbey University, Karaman 70100, Turkey;
| | - Shukherdorj Baasanmunkh
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea; (S.B.); (H.J.C.)
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea; (S.B.); (H.J.C.)
| | | | | | - Svetlana Bancheva
- Botanical Garden, Bulgarian Academy of Sciences, 1616 Sofia, Bulgaria;
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, G. Bonchev, Bl.23, 1113 Sofia, Bulgaria
| | - Lian Lian
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (L.L.); (K.X.); (W.W.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunli Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (L.L.); (K.X.); (W.W.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (L.L.); (K.X.); (W.W.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andrey S. Erst
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
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Wang Y, Li X, Feng Y, Wang J, Zhang J, Liu Z, Wang H, Chen T, He W, Wu Z, Lin Y, Zhang Y, Li M, Chen Q, Zhang Y, Luo Y, Tang H, Wang X. Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3116. [PMID: 37687365 PMCID: PMC10490022 DOI: 10.3390/plants12173116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Xueou Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Rural Revitalization Service Center, Agricultural and Rural Bureau of Cuiping District Yibin City, Yibin 644000, China
| | - Juan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Tao Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China;
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Zhiwei Wu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
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Yu RM, Zhang N, Zhang BW, Liang Y, Pang XX, Cao L, Chen YD, Zhang WP, Yang Y, Zhang DY, Pang EL, Bai WN. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol 2023; 21:168. [PMID: 37553642 PMCID: PMC10408227 DOI: 10.1186/s12915-023-01668-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. RESULTS Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. CONCLUSIONS Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
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Affiliation(s)
- Rui-Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ning Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Dan Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Variation in Ribosomal DNA in the Genus Trifolium (Fabaceae). PLANTS 2021; 10:plants10091771. [PMID: 34579303 PMCID: PMC8465422 DOI: 10.3390/plants10091771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023]
Abstract
The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state.
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Xiong Z, Gaeta RT, Edger PP, Cao Y, Zhao K, Zhang S, Pires JC. Chromosome inheritance and meiotic stability in allopolyploid Brassica napus. G3-GENES GENOMES GENETICS 2021; 11:6044140. [PMID: 33704431 PMCID: PMC8022990 DOI: 10.1093/g3journal/jkaa011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022]
Abstract
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A–C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors were non-uniformly distributed across the genome in resynthesized B. napus, and in particular homoeologs sharing synteny along their entire length exhibited multivalents at diakinesis and polysomic inheritance at telophase I. Natural B. napus appeared to resolve meiotic errors mainly by suppressing homoeologous pairing, resolving nonhomologous centromere associations and 45S rDNA associations before diakinesis, and reducing homoeologous cross-overs.
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Affiliation(s)
- Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China.,Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Robert T Gaeta
- Bayer's Crop Science Division, Chesterfield, MO 63017, USA
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Siqi Zhang
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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Evolutionary history of the Pasque-flowers (Pulsatilla, Ranunculaceae): Molecular phylogenetics, systematics and rDNA evolution. Mol Phylogenet Evol 2019; 135:45-61. [PMID: 30831271 DOI: 10.1016/j.ympev.2019.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/25/2019] [Accepted: 02/17/2019] [Indexed: 11/23/2022]
Abstract
Pulsatilla (Anemoneae, Ranunculaceae) is sister to Anemone s.s. and contains ca 40 perennial species of considerable horticultural and medical importance. We sequenced 31 of those species, plus nine subspecies, two cultivars and six outgroups, for two nuclear regions (high-copy nrITS and low-copy MLH1) and three plastid regions (rbcL, accD-psaI, trnL intron) in order to generate the first comprehensive species-level phylogeny of the genus. Phylogenetic trees were constructed using both concatenation-based (maximum likelihood and Bayesian inference) and coalescence methods. The better supported among the internal nodes were subjected to molecular clock dating and ancestral area reconstruction, and karyotypic characters identified by us using Fluorescence In Situ Hybridization were mapped across the tree. The preferred species tree from the coalescence analysis formed the basis of a new infrageneric classification based on monophyly plus degree of divergence. The earliest divergent of the three subgenera, Kostyczewianae, is represented by only a single species that is morphologically intermediate between Anemone s.s. and 'core' Pulsatilla. Subgenus Pulsatilla is considerably richer in species than its sister subgenus Preonanthus and contains three monophyletic sections. Species possessing nodding flowers and pectinately dissected leaves are phylogenetically derived compared with groups possessing erect flowers and palmately lobed leaves. Pulsatilla separated from Anemone s.s. at ca 25 Ma. Our results indicate a central Asian mountain origin of the genus and an initial diversification correlated with late Tertiary global cooling plus regional mountain uplift, aridification and consequent expansion of grasslands. The more rapid and extensive diversification within subgenus Pulsatilla began at ca 3 Ma and continued throughout the Quaternary, driven not only by major perturbations in global climate but also by well-documented polyploidy.
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Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, Lysak MA, Hodges SA, Nordborg M. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. eLife 2018; 7:e36426. [PMID: 30325307 PMCID: PMC6255393 DOI: 10.7554/elife.36426] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
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Affiliation(s)
- Danièle L Filiault
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Evangeline S Ballerini
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Terezie Mandáková
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Gökçe Aköz
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Nathan J Derieg
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Jeremy Schmutz
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jerry Jenkins
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jane Grimwood
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Shengqiang Shu
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Richard D Hayes
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Uffe Hellsten
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Kerrie Barry
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Juying Yan
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | | | - Miroslava Karafiátová
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Elena M Kramer
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
| | - Martin A Lysak
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
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8
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Joachimiak AJ, Hasterok R, Sliwinska E, Musiał K, Grabowska-Joachimiak A. FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa. PROTOPLASMA 2018; 255. [PMID: 29541843 PMCID: PMC6133112 DOI: 10.1007/s00709-018-1238-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The location of 5S and 35S rDNA sequences in chromosomes of four Aconitum subsp. Aconitum species was analyzed after fluorescence in situ hybridization (FISH). Both in diploids (2n = 2x = 16; Aconitum variegatum, A. degenii) and tetraploids (2n = 4× = 32; A. firmum, A. plicatum), rDNA repeats were localized exclusively on the shorter arms of chromosomes, in subterminal or pericentromeric sites. All analyzed species showed similar basal genome size (Cx = 5.31-5.71 pg). The most striking features of tetraploid karyotypes were the conservation of diploid rDNA loci and emergence of many additional 5S rDNA clusters. Chromosomal distribution of excessive ribosomal sites suggests their role in the secondary diploidization of tetraploid karyotypes.
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Affiliation(s)
- Andrzej J Joachimiak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387, Kraków, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics and Biotechnology, University of Technology and Life Sciences in Bydgoszcz, Kaliskiego 7, 85-789, Bydgoszcz, Poland
| | - Krystyna Musiał
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387, Kraków, Poland
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9
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Ortiz AM, Robledo G, Seijo G, Valls JFM, Lavia GI. Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section Rhizomatosae and related diploid species (Arachis, Leguminosae). JOURNAL OF PLANT RESEARCH 2017; 130:791-807. [PMID: 28536982 DOI: 10.1007/s10265-017-0949-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 05/17/2023]
Abstract
Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n = 4x = 40) and only one diploid (A. burkartii, 2n = 2x = 20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18-26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species-A. burkartii-has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.
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Affiliation(s)
- Alejandra Marcela Ortiz
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina.
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina.
| | - Germán Robledo
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
| | | | - Graciela Inés Lavia
- Instituto de Botánica del Nordeste (CONICET-UNNE), CC 209, Sargento Juan Bautista Cabral 2131, 3402BKG, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Av. Libertad 5000, 3402BKG, Corrientes, Argentina
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10
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Autopolyploidy leads to rapid genomic changes in Arabidopsis thaliana. Theory Biosci 2017; 136:199-206. [PMID: 28612184 DOI: 10.1007/s12064-017-0252-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
Abstract
Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism. The results showed that in contrast with diploids, the rapid genomic changes (including gain and loss of DNA sequences) in autopolyploids were definitely found within the first generations after autopolyploidization, but slow down and probably stabilized in the higher generations as a source of genetic diversity in the long term. The sequencing of these DNA fragments indicated that these changes occurred both on genic and inter-genic (or intronic) regions, and quantitative PCR showed that the expression of some corresponding genes in the genic regions was obviously affected (including upregulation, downregulation and silencing) in autopolyploids. Therefore, this study demonstrated that autopolyploidy could lead to rapid genomic changes and probably influence expression and function of certain genes within the first generations, giving rising to genetic diversification after polyploidization.
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11
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Kameoka S, Sakio H, Abe H, Ikeda H, Setoguchi H. Genetic structure of Hepatica nobilis var. japonica, focusing on within population flower color polymorphism. JOURNAL OF PLANT RESEARCH 2017; 130:263-271. [PMID: 28004280 DOI: 10.1007/s10265-016-0893-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
How phenotypic or genetic diversity is maintained in a natural habitat is a fundamental question in evolutionary biology. Flower color polymorphism in plants is a common polymorphism. Hepatica nobilis var. japonica on the Sea of Japan (SJ) side of the Japanese mainland exhibits within population flower color polymorphism (e.g., white, pink, and purple), while only white flowers are observed on the Pacific Ocean (PO) side. To determine the relationships between flower color polymorphism, within and among populations, and the genetic structure of H. nobilis var. japonica, we estimated the genetic variation using simple sequence repeat (SSR) markers. First, we examined whether cryptic lineages corresponding to distinct flower colors contribute to the flower color polymorphisms in H. nobilis var. japonica. In our field observations, no bias in color frequency was observed among populations on Sado Island, a region with high variation in flower color. Simple sequence repeat (SSR) analyses revealed that 18% of the genetic variance was explained by differences among populations, whereas no genetic variation was explained by flower color hue or intensity (0% for both components). These results indicate that the flower color polymorphism is likely not explained by cryptic lineages that have different flower colors. In contrast, populations in the SJ and PO regions were genetically distinguishable. As with the other plant species in these regions, refugial isolation and subsequent migration history may have caused the genetic structure as well as the spatially heterogeneous patterns of flower color polymorphisms in H. nobilis var. japonica.
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Affiliation(s)
- Shinichiro Kameoka
- Dept of Biology, Graduate School of Human and Environmental Studies, Kyoto University, Yoshida, Nihonmatsu-cho, Sakyoku, Kyoto, 606-8501, Japan.
| | - Hitoshi Sakio
- Sado Station, Field center for sustainable agriculture and forestry, Faculty of agriculture, Niigata University, 94-2 Koda, Sado, Niigata, 952-2206, Japan
| | - Harue Abe
- Sado Station, Field center for sustainable agriculture and forestry, Faculty of agriculture, Niigata University, 94-2 Koda, Sado, Niigata, 952-2206, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroaki Setoguchi
- Dept of Biology, Graduate School of Human and Environmental Studies, Kyoto University, Yoshida, Nihonmatsu-cho, Sakyoku, Kyoto, 606-8501, Japan
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12
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Chung GY, Nam BM, Choi MJ, Jang HD, Choi HJ, Oh BU. Chromosome numbers of 50 vascular plants in South Korea. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2016. [DOI: 10.1016/j.japb.2016.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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13
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Jang TS, McCann J, Parker JS, Takayama K, Hong SP, Schneeweiss GM, Weiss-Schneeweiss H. rDNA Loci Evolution in the Genus Glechoma (Lamiaceae). PLoS One 2016; 11:e0167177. [PMID: 27870903 PMCID: PMC5117774 DOI: 10.1371/journal.pone.0167177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
Glechoma L. (Lamiaceae) is distributed in eastern Asia and Europe. Understanding chromosome evolution in Glechoma has been strongly hampered by its small chromosomes, constant karyotype and polyploidy. Here phylogenetic patterns and chromosomal variation in Glechoma species are considered, using genome sizes, chromosome mapping of 5S and 35S rDNAs by fluorescence in situ hybridisation (FISH), and phylogenetic analyses of internal transcribed spacers (nrITS) of 35S rDNA and 5S rDNA NTS sequences. Species and populations of Glechoma are tetraploid (2n = 36) with base chromosome number of x = 9. Four chromosomes carry pericentric 5S rDNA sites in their short arms in all the species. Two to four of these chromosomes also carry 35S rDNA in subterminal regions of the same arms. Two to four other chromosomes have 35S rDNA sites, all located subterminally within short arms; one individual possessed additional weak pericentric 35S rDNA signals on three other chromosomes. Five types of rDNA locus distribution have been defined on the basis of 35S rDNA variation, but none is species-specific, and most species have more than one type. Glechoma hederacea has four types. Genome size in Glechoma ranges from 0.80 to 0.94 pg (1C), with low levels of intrapopulational variation in all species. Phylogenetic analyses of ITS and NTS sequences distinguish three main clades coinciding with geographical distribution: European (G. hederacea–G. hirsuta), Chinese and Korean (G. longituba), and Japanese (G. grandis). The paper presents the first comparative cytogenetic analyses of Glechoma species including karyotype structure, rDNA location and number, and genome size interpreted in a phylogenetic context. The observed variation suggests that the genus is still in genomic flux. Genome size, but not rDNA loci number and distribution, provides a character for species delimitation which allows better inferences of interspecific relationships to be made, in the absence of well-defined morphological differentiation.
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Affiliation(s)
- Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- * E-mail: (TJS); (HWS)
| | - Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - John S. Parker
- Cambridge University Botanic Garden, Cambridge, United Kingdom
| | - Koji Takayama
- Museum of Natural and Environmental History, Shizuoka, Oya 5762, Suruga-ku, Shizuoka-shi, Sizuoka, Japan
| | - Suk-Pyo Hong
- Laboratory of Plant Systematics, Department of Biology, Kyung Hee University, 1 Hoegi-Dong, Dongdaemun-Gu, Seoul, Korea
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- * E-mail: (TJS); (HWS)
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14
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Totta C, Rosato M, Ferrer-Gallego P, Lucchese F, Rosselló JA. Temporal frames of 45S rDNA site-number variation in diploid plant lineages: lessons from the rock rose genusCistus(Cistaceae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chiara Totta
- Università degli Studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Marcela Rosato
- Jardín Botánico-ICBiBE-Unidad Asociada CSIC; Universidad de Valencia; c/Quart 80 E46008 Valencia Spain
| | - Pablo Ferrer-Gallego
- CIEF, Servicio de Vida Silvestre; Generalitat Valenciana; Avda. Comarques del País Valencià 114 E46930 Valencia Spain
| | - Fernando Lucchese
- Università degli Studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Josep A. Rosselló
- Jardín Botánico-ICBiBE-Unidad Asociada CSIC; Universidad de Valencia; c/Quart 80 E46008 Valencia Spain
- Carl Faust Fdn.; PO Box 112 E17300 Blanes Spain
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15
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Abdel Samad N, Bou Dagher-Kharrat M, Hidalgo O, El Zein R, Douaihy B, Siljak-Yakovlev S. Unlocking the Karyological and Cytogenetic Diversity of Iris from Lebanon: Oncocyclus Section Shows a Distinctive Profile and Relative Stasis during Its Continental Radiation. PLoS One 2016; 11:e0160816. [PMID: 27525415 PMCID: PMC4985135 DOI: 10.1371/journal.pone.0160816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/26/2016] [Indexed: 12/02/2022] Open
Abstract
Despite being an important target of conservation concern and horticultural interest, Lebanese irises yet have a confusing taxonomic history and species’ delimitation is often considered problematic, more especially among royal irises (Iris section Oncocyclus). Indeed, these irises of exceptionally large and spectacular flowers have radiated across Caucasus and eastern Mediterranean giving rise to a number of strict endemic taxa, many of them being considered under threat. Whilst efforts have mostly focused on clarifying the evolutionary relationships in the group based on morphological and molecular data, karyological and cytogenetic characters have been comparatively overlooked. In this study, we established for the first time the physical mapping of 35S rDNA loci and heterochromatin, and obtained karyo-morphological data for ten Lebanese Iris species belonging to four sections (Iris, Limniris, Oncocyclus and Scorpiris). Our results evidenced distinctive genomic profiles for each one of the sections, where Oncocyclus irises, while having the lowest chromosome numbers, exhibit both the highest number of 35S loci and CMA3+ sites. The continental radiation of royal irises has been accompanied by a relative karyological and cytogenetic stasis, even though some changes were observed regarding karyotype formula and asymmetry indexes. In addition to that, our results enabled taxonomic differentiation between I. germanica and I. mesopotamica–two taxa currently considered as synonyms–and highlighted the need for further studies on populations of I. persica and I. wallasiae in the Eastern Mediterranean Region.
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Affiliation(s)
- Nour Abdel Samad
- Faculté des Sciences, Département Sciences de la Vie et de la Terre, Laboratoire Caractérisation Génomique des Plantes, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos Mkalles, Lebanon
- Ecologie, Systématique, Evolution, UMR 8079 Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, Bat. 360, 91405 Orsay, France
| | - Magda Bou Dagher-Kharrat
- Faculté des Sciences, Département Sciences de la Vie et de la Terre, Laboratoire Caractérisation Génomique des Plantes, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos Mkalles, Lebanon
- * E-mail:
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom
| | - Rana El Zein
- Faculté des Sciences, Département Sciences de la Vie et de la Terre, Laboratoire Caractérisation Génomique des Plantes, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos Mkalles, Lebanon
| | - Bouchra Douaihy
- Faculté des Sciences, Département Sciences de la Vie et de la Terre, Laboratoire Caractérisation Génomique des Plantes, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos Mkalles, Lebanon
| | - Sonja Siljak-Yakovlev
- Ecologie, Systématique, Evolution, UMR 8079 Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, Bat. 360, 91405 Orsay, France
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16
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Mlinarec J, Franjević D, Harapin J, Besendorfer V. The impact of the Tekay chromoviral elements on genome organisation and evolution of Anemone s.l. (Ranunculaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:332-347. [PMID: 26370195 DOI: 10.1111/plb.12393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
We studied the highly abundant chromoviral Tekay clade in species from three sister genera - Anemone, Pulsatilla and Hepatica (Ranunculaceae). With this clade, we performed a concomitant survey of its phylogenetic diversity, chromosomal organisation and transcriptional activity in Anemone s.l. in order to investigate dynamics of the Tekay elements at a finer scale than previously achieved in this or any other flowering clade. The phylogenetic tree built from Tekay sequences conformed to expected evolutionary relationships of the species; exceptions being A. nemorosa and A. sylvestris, which appeared more closely related that expected, and we invoke hybridisation events to explain the observed topology. The separation of elements into six clusters could be explained by episodic bursts of activity since divergence from a common ancestor at different points in their respective evolutionary histories. In Anemone s.l. the Tekay elements do not have a preferential position on chromosomes, i.e. they can have a: (i) centromeric/pericentromeric position; (ii) interstitial position in DAPI-positive AT-rich heterochromatic regions; can be (iii) dispersed throughout chromosomes; or even (iv) be absent from large heterochromatic blocks. Widespread transcriptional activity of the Tekay elements in Anemone s.l. taxa indicate that some copies of Tekay elements could still be active in this plant group, contributing to genome evolution and speciation within Anemone s.l. Identification of Tekay elements in Anemone s.l. provides valuable information for understanding how different localisation patterns might help to facilitate plant genome organisation in a structural and functional manner.
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Affiliation(s)
- J Mlinarec
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - D Franjević
- Division of Biology, Zoology Department, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - J Harapin
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - V Besendorfer
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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17
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Frajman B, Rešetnik I, Weiss-Schneeweiss H, Ehrendorfer F, Schönswetter P. Cytotype diversity and genome size variation in Knautia (Caprifoliaceae, Dipsacoideae). BMC Evol Biol 2015; 15:140. [PMID: 26182989 PMCID: PMC4504173 DOI: 10.1186/s12862-015-0425-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/26/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Polyploidisation is one of the most important mechanisms in the evolution of angiosperms. As in many other genera, formation of polyploids has significantly contributed to diversification and radiation of Knautia (Caprifoliaceae, Dipsacoideae). Comprehensive studies of fine- and broad-scale patterns of ploidy and genome size (GS) variation are, however, still limited to relatively few genera and little is known about the geographic distribution of ploidy levels within these genera. Here, we explore ploidy and GS variation in Knautia based on a near-complete taxonomic and comprehensive geographic sampling. RESULTS Genome size is a reliable indicator of ploidy level in Knautia, even if monoploid genome downsizing is observed in the polyploid cytotypes. Twenty-four species studied are diploid, 16 tetraploid and two hexaploid, whereas ten species possess two, and two species possess three ploidy levels. Di- and tetraploids are distributed across most of the distribution area of Knautia, while hexaploids were sampled in the Balkan and Iberian Peninsulas and the Alps. CONCLUSIONS We show that the frequency of polyploidisation is unevenly distributed in Knautia both in a geographic and phylogenetic context. Monoploid GS varies considerably among three evolutionary lineages (sections) of Knautia, but also within sections Trichera and Tricheroides, as well as within some of the species. Although the exact causes of this variation remain elusive, we demonstrate that monoploid GS increases significantly towards the limits of the genus' distribution.
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Affiliation(s)
- Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020, Innsbruck, Austria
| | - Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 20/II, HR-10000, Zagreb, Croatia
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria.
| | - Friedrich Ehrendorfer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020, Innsbruck, Austria
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18
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Hwang YJ, Song CM, Younis A, Kim CK, Kang YI, Lim KB. Morphological characterization under different ecological habitats and physical mapping of 5S and 45S rDNA in Lilium distichum with fluorescence in situ hybridization. REVISTA CHILENA DE HISTORIA NATURAL 2015. [DOI: 10.1186/s40693-015-0037-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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20
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Fredotović Ž, Šamanić I, Weiss-Schneeweiss H, Kamenjarin J, Jang TS, Puizina J. Triparental origin of triploid onion, Allium × cornutum (Clementi ex Visiani, 1842), as evidenced by molecular, phylogenetic and cytogenetic analyses. BMC PLANT BIOLOGY 2014; 14:24. [PMID: 24418109 PMCID: PMC3899691 DOI: 10.1186/1471-2229-14-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/08/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND Reconstruction of the parental origins of cultivated plants from wild relatives, especially after long periods of domestication, is not a trivial task. However, recent advances in molecular phylogenetics, among other approaches, have proved to be very informative in analyses of the origin and evolution of polyploid genomes. An established minor garden crop, triploid onion Allium × cornutum (Clementi ex Visiani, 1842) (2n = 3x = 24), is widespread in southeastern Asia and Europe. Our previous cytogenetic analyses confirmed its highly heterozygous karyotype and indicated its possible complex triparental genome origin. Allium cepa L. and Allium roylei Stearn were suggested as two putative parental species of A. × cornutum, whereas the third parental species remained hitherto unknown. RESULTS Here we report the phylogenetic analyses of the internal transcribed spacers ITS1-5.8S-ITS2 of 35S rDNA and the non-transcribed spacer (NTS) region of 5S rDNA of A. × cornutum and its relatives of the section Cepa. Both ITS and NTS sequence data revealed intra-individual variation in triploid onion, and these data clustered into the three main clades, each with high sequence homology to one of three other species of section Cepa: A. cepa, A. roylei, and unexpectedly, the wild Asian species Allium pskemense B. Fedtsh. Allium pskemense is therefore inferred to be the third, so far unknown, putative parental species of triploid onion Allium × cornutum. The 35S and 5S rRNA genes were found to be localised on somatic chromosomes of A. × cornutum and its putative parental species by double fluorescent in situ hybridisation (FISH). The localisation of 35S and 5S rDNA in A. × cornutum chromosomes corresponded to their respective positions in the three putative parental species, A. cepa, A. pskemense, and A. roylei. GISH (genomic in situ hybridisation) using DNA of the three putative parental diploids corroborated the results of the phylogenetic study. CONCLUSIONS The combined molecular, phylogenetic and cytogenetic data obtained in this study provided evidence for a unique triparental origin of triploid onion A. × cornutum with three putative parental species, A. cepa, A. pskemense, and A. roylei.
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Affiliation(s)
- Željana Fredotović
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Ivica Šamanić
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juraj Kamenjarin
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Tae-Soo Jang
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jasna Puizina
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
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Jang TS, Emadzade K, Parker J, Temsch EM, Leitch AR, Speta F, Weiss-Schneeweiss H. Chromosomal diversification and karyotype evolution of diploids in the cytologically diverse genus Prospero (Hyacinthaceae). BMC Evol Biol 2013; 13:136. [PMID: 23819574 PMCID: PMC3728210 DOI: 10.1186/1471-2148-13-136] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/27/2013] [Indexed: 11/18/2022] Open
Abstract
Background Prospero (Hyacinthaceae) provides a unique system to assess the impact of genome rearrangements on plant diversification and evolution. The genus exhibits remarkable chromosomal variation but very little morphological differentiation. Basic numbers of x = 4, 5, 6 and 7, extensive polyploidy, and numerous polymorphic chromosome variants were described, but only three species are commonly recognized: P. obtusifolium, P. hanburyi, and P. autumnale s.l., the latter comprising four diploid cytotypes. The relationship between evolutionary patterns and chromosomal variation in diploids, the basic modules of the extensive cytological diversity, is presented. Results Evolutionary inferences were derived from fluorescence in situ hybridization (FISH) with 5S and 35S rDNA, genome size estimations, and phylogenetic analyses of internal transcribed spacer (ITS) of 35S rDNA of 49 diploids in the three species and all cytotypes of P. autumnale s.l. All species and cytotypes possess a single 35S rDNA locus, interstitial except in P. hanburyi where it is sub-terminal, and one or two 5S rDNA loci (occasionally a third in P. obtusifolium) at fixed locations. The localization of the two rDNA types is unique for each species and cytotype. Phylogenetic data in the P. autumnale complex enable tracing of the evolution of rDNA loci, genome size, and direction of chromosomal fusions: mixed descending dysploidy of x = 7 to x = 6 and independently to x = 5, rather than successive descending dysploidy, is proposed. Conclusions All diploid cytotypes are recovered as well-defined evolutionary lineages. The cytogenetic and phylogenetic approaches have provided excellent phylogenetic markers to infer the direction of chromosomal change in Prospero. Evolution in Prospero, especially in the P. autumnale complex, has been driven by differentiation of an ancestral karyotype largely unaccompanied by morphological change. These new results provide a framework for detailed analyses of various types of chromosomal rearrangements and karyotypic variation in polyploids.
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Affiliation(s)
- Tae-Soo Jang
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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Tayalé A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 2013; 140:79-96. [PMID: 23751271 DOI: 10.1159/000351318] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.
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Affiliation(s)
- A Tayalé
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Hersch-Green EI. Polyploidy in Indian paintbrush (Castilleja; Orobanchaceae) species shapes but does not prevent gene flow across species boundaries. AMERICAN JOURNAL OF BOTANY 2012; 99:1680-90. [PMID: 23032815 DOI: 10.3732/ajb.1200253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF STUDY A difference in chromosome numbers (ploidy variation) between species is usually considered a major barrier to gene flow. Therefore, it is surprising that little is known about whether ploidy variation, both within and among species, influences spatial patterns of interspecific hybridization. The role that polyploidy plays in structuring gene flow patterns between three co-occurring Indian paintbrush (Castilleja) species is investigated. • METHODS Reciprocal hand pollinations were performed in populations where the three species co-occur with and without variable plants (previous data tested the ancestral "hybrid" history of these variable plants). I measured fruit set, seed production, seed germination, and the DNA content of parent plants and 26 synthesized F(1) hybrids. Data were combined with pollinator fidelity data to estimate the contribution of individual barriers to reproductive isolation. • KEY RESULTS Interspecific gene flow could occur in all directions, but barriers were weaker for conspecific vs. heterospecific crosses. Species were nearly fixed for different ploidy levels, but some deviations occurred, primarily in populations with variable plants. Interspecific gene flow could occur across ploidy levels, but it was more likely when species had the same number of chromosomes or when resulting F(1) hybrids had even numbers of chromosomes. Postzygotic reproductive barriers were generally weaker than pollinator fidelity. • CONCLUSIONS Polyploidy likely plays a large role in shaping contemporary and historical patterns of gene flow among these species. This study suggests that differences in chromosome numbers among closely related, compatible species might help structure spatial patterns of hybridization.
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Affiliation(s)
- Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931 USA.
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Mlinarec J, Šatović Z, Malenica N, Ivančić-Baće I, Besendorfer V. Evolution of the tetraploid Anemone multifida (2n = 32) and hexaploid A. baldensis (2n = 48) (Ranunculaceae) was accompanied by rDNA loci loss and intergenomic translocation: evidence for their common genome origin. ANNALS OF BOTANY 2012; 110:703-12. [PMID: 22711694 PMCID: PMC3400456 DOI: 10.1093/aob/mcs128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 04/13/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS In the genus Anemone two small groups of taxa occur with the highest ploidy levels 2n = 6x = 48, belonging to the closely related clades: the montane/alpine Baldensis clade and the more temperate Multifida clade. To understand the formation of polyploids within these groups, the evolution of allohexaploid A. baldensis (AABBDD, 2n = 6x = 48) from Europe and allotetraploid Anemone multifida (BBDD, 2n = 4x = 32) from America was analysed. METHODS Internal transcribed spacer and non-transcribed spacer sequences were used as molecular markers for phylogenetic analyses. Cytogenetic studies, including genomic in situ hybridization with genomic DNA of potential parental species as probe, fluorescence in situ hybridization with 5S and 18S rDNA as probes and 18S rDNA restriction analyses, were used to identify the parental origin of chromosomes and to study genomic changes following polyploidization. KEY RESULTS This study shows that A. multifida (BBDD, 2n= 4x = 32) and A. baldensis (AABBDD, 2n = 6x = 48) are allopolyploids originating from the crosses of diploid members of the Multifida (donor of the A and B subgenomes) and Baldensis groups (donor of the D subgenome). The A and B subgenomes are closely related to the genomes of A. sylvestris, A. virginiana and A. cylindrica, indicating that these species or their progeny might be the ancestral donors of the B subgenome of A. multifida and A and B subgenomes of A. baldensis. Both polyploids have undergone genomic changes such as interchromosomal translocation affecting B and D subgenomes and changes at rDNA sites. Anemone multifida has lost the 35S rDNA loci characteristic of the maternal donor (B subgenome) and maintained only the rDNA loci of the paternal donor (D subgenome). CONCLUSIONS It is proposed that A. multifida and A. baldensis probably had a common ancestor and their evolution was facilitated by vegetation changes during the Quaternary, resulting in their present disjunctive distribution.
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Affiliation(s)
- J. Mlinarec
- Faculty of Science, University of Zagreb, Division of Biology, Department of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Z. Šatović
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, HR-10000 Zagreb, Croatia
| | - N. Malenica
- Faculty of Science, University of Zagreb, Division of Biology, Department of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - I. Ivančić-Baće
- Faculty of Science, University of Zagreb, Division of Biology, Department of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - V. Besendorfer
- Faculty of Science, University of Zagreb, Division of Biology, Department of Molecular Biology, Horvatovac 102a, HR-10000 Zagreb, Croatia
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Talukdar D. Meiotic consequences of selfing in grass pea (Lathyrus sativus L.) autotetraploids in the advanced generations: Cytogenetics of chromosomal rearrangement and detection of aneuploids. THE NUCLEUS 2012. [DOI: 10.1007/s13237-012-0059-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Mlinarec J, Satović Z, Mihelj D, Malenica N, Besendorfer V. Cytogenetic and phylogenetic studies of diploid and polyploid members of tribe Anemoninae (Ranunculaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:525-36. [PMID: 22188120 DOI: 10.1111/j.1438-8677.2011.00519.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The ancestry, phylogenetic differentiation and systematic classification of the worldwide-distributed genus Anemone have been debated for many years. In this paper 11 Anemone, three Pulsatilla species and Hepatica nobilis were subjected to detailed karyotype analysis with the aim of obtaining new cytogenetic data that will contribute to karyotype evolutionary studies of the tribe Anemoninae. The results are interpreted in a phylogenetic context, established from the intergenic nontranscribed spacer (NTS) of 5S rDNA and internal transcribed spacer (ITS) of 35S rDNA. One to three 35S and one to three 5S rDNA loci are present in diploid and polyploid taxa. The 35S rDNA loci are located terminally on the short arm of acrocentric chromosomes, while for 5S rDNA there is no preferential chromosomal position as it exhibits terminal, subterminal, interstitial or pericentromeric positions, and is located either on acrocentric or metacentric chromosomes. The karyotype of hexaploid A. baldensis (2n = 6x = 48) is presented for the first time, and A. sylvestris is proposed as one of its putative parental species. Chromosome fusion/translocation is proposed as the key mechanism involved in reduction of the basic chromosome number from 8 in the Anemone subgenus to 7 in the Anemonidium subgenus. The cytogenetic data obtained are mainly supported by ITS and NTS phylogeny. Diversification of the genus Anemone was accompanied by a large reduction of heterochromatin, from the Mediterranean anemones that have large amounts of heterochromatin to the New World anemones without any detectable heterochromatic blocks.
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Affiliation(s)
- J Mlinarec
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.
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Weiss-Schneeweiss H, Blöch C, Turner B, Villaseñor JL, Stuessy TF, Schneeweiss GM. The promiscuous and the chaste: frequent allopolyploid speciation and its genomic consequences in American daisies (Melampodium sect. Melampodium; Asteraceae). Evolution 2011; 66:211-28. [PMID: 22220876 DOI: 10.1111/j.1558-5646.2011.01424.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyploidy, an important factor in eukaryotic evolution, is especially abundant in angiosperms, where it often acts in concert with hybridization to produce allopolyploids. The application of molecular phylogenetic techniques has identified the origins of numerous allopolyploids, but little is known on genomic and chromosomal consequences of allopolyploidization, despite their important role in conferring divergence of allopolyploids from their parental species. Here, using several plastid and nuclear sequence markers, we clarify the origin of tetra- and hexaploids in a group of American daisies, allowing characterization of genome dynamics in polyploids compared to their diploid ancestors. All polyploid species are allopolyploids. Among the four diploid gene pools, the propensity for allopolyploidization is unevenly distributed phylogenetically with a few species apparently more prone to participate, but the underlying causes remain unclear. Polyploid genomes are characterized by differential loss of ribosomal DNA loci (5S and 35S rDNA), known hotspots of chromosomal evolution, but show genome size additivity, suggesting limited changes beyond those affecting rDNA loci or the presence of processes counterbalancing genome reduction. Patterns of rDNA sequence conversion and provenance of the lost loci are highly idiosyncratic and differ even between allopolyploids of identical parentage, indicating that allopolyploids deriving from the same lower-ploid parental species can follow different evolutionary trajectories.
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Affiliation(s)
- Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
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Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus. Chromosoma 2011; 120:557-71. [DOI: 10.1007/s00412-011-0331-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/23/2011] [Accepted: 07/01/2011] [Indexed: 01/13/2023]
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REBERNIG CAROLINA, SCHNEEWEISS GERALDM, BARDY KATHARINAE, SCHÖNSWETTER PETER, VILLASEÑOR JOSEL, OBERMAYER RENATE, STUESSY TODF, WEISS-SCHNEEWEISS HANNA. Multiple Pleistocene refugia and Holocene range expansion of an abundant southwestern American desert plant species (Melampodium leucanthum, Asteraceae). Mol Ecol 2010; 19:3421-43. [DOI: 10.1111/j.1365-294x.2010.04754.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.
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Affiliation(s)
- Christian Parisod
- National Centre for Biosystematics, University of Oslo, 0318 Oslo, Norway.
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32
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Rebernig CA, Weiss-Schneeweiss H, Schneeweiss GM, Schönswetter P, Obermayer R, Villaseñor JL, Stuessy TF. Quaternary range dynamics and polyploid evolution in an arid brushland plant species (Melampodium cinereum, Asteraceae). Mol Phylogenet Evol 2010; 54:594-606. [DOI: 10.1016/j.ympev.2009.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 10/02/2009] [Accepted: 10/06/2009] [Indexed: 12/19/2022]
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Garcia S, Garnatje T, Pellicer J, McArthur ED, Siljak-Yakovlev S, Vallès J. Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae). Genome 2009; 52:1012-24. [DOI: 10.1139/g09-077] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenus Tridentatae ( Artemisia , Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploid-polyploid species pairs. In addition, genome sizes and heterochromatin patterns were compared between these populations. The linked 5S and 35S rRNA genes are confirmed as characteristic for Artemisia, and a pattern at the diploid level of three rDNA loci located at telomeric positions proved to be typical. Loss of rDNA loci was observed in some polyploids, whereas others showed additivity with respect to their diploid relatives. Genome downsizing was observed in all polyploids. Banding patterns differed depending on the pair of species analysed, but some polyploid populations showed an increased number of heterochromatic bands. FISH and fluorochrome banding were useful in determining the systematic position of Artemisia bigelovii , for which a differential pattern was found as compared with the rest of the group. Additionally, FISH was used to detect the presence of the Arabidopsis-type telomere repeat for the first time in Artemisia.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Teresa Garnatje
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Jaume Pellicer
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - E. Durant McArthur
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Sonja Siljak-Yakovlev
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Joan Vallès
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
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Wang B, Ding Z, Liu W, Pan J, Li C, Ge S, Zhang D. Polyploid evolution in Oryza officinalis complex of the genus Oryza. BMC Evol Biol 2009; 9:250. [PMID: 19828030 PMCID: PMC2770061 DOI: 10.1186/1471-2148-9-250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 10/14/2009] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. RESULTS Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis. CONCLUSION C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids.
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Affiliation(s)
- Baosheng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Zhuoya Ding
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100039, PR China
| | - Jin Pan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
| | - Changbao Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
| | - Daming Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China
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Allopolyploid origin of Mediterranean species inHelictotrichon(Poaceae) and its consequences for karyotype repatterning and homogenisation of rDNA repeat units. SYST BIODIVERS 2009. [DOI: 10.1017/s1477200009003041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Blöch C, Weiss-Schneeweiss H, Schneeweiss GM, Barfuss MHJ, Rebernig CA, Villaseñor JL, Stuessy TF. Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae). Mol Phylogenet Evol 2009; 53:220-33. [PMID: 19272456 DOI: 10.1016/j.ympev.2009.02.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 02/23/2009] [Indexed: 11/19/2022]
Abstract
Chromosome evolution (including polyploidy, dysploidy, and structural changes) as well as hybridization and introgression are recognized as important aspects in plant speciation. A suitable group for investigating the evolutionary role of chromosome number changes and reticulation is the medium-sized genus Melampodium (Millerieae, Asteraceae), which contains several chromosome base numbers (x=9, 10, 11, 12, 14) and a number of polyploid species, including putative allopolyploids. A molecular phylogenetic analysis employing both nuclear (ITS) and plastid (matK) DNA sequences, and including all species of the genus, suggests that chromosome base numbers are predictive of evolutionary lineages within Melampodium. Dysploidy, therefore, has clearly been important during evolution of the group. Reticulate evolution is evident with allopolyploids, which prevail over autopolyploids and several of which are confirmed here for the first time, and also (but less often) on the diploid level. Within sect. Melampodium, the complex pattern of bifurcating phylogenetic structure among diploid taxa overlain by reticulate relationships from allopolyploids has non-trivial implications for intrasectional classification.
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Affiliation(s)
- Cordula Blöch
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
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37
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Wang L, Abbott RJ, Zheng W, Chen P, Wang Y, Liu J. History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau:Aconitum gymnandrum(Ranunculaceae). Mol Ecol 2009; 18:709-21. [PMID: 19175501 DOI: 10.1111/j.1365-294x.2008.04055.x] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Liuyang Wang
- Institute of Molecular Ecology, MOE Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China
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Paun O, Forest F, Fay MF, Chase MW. Hybrid speciation in angiosperms: parental divergence drives ploidy. THE NEW PHYTOLOGIST 2009; 182:507-518. [PMID: 19220761 PMCID: PMC2988484 DOI: 10.1111/j.1469-8137.2009.02767.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (that is, as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed.
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Affiliation(s)
- Ovidiu Paun
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
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Kovarik A, Werlemark G, Leitch AR, Souckova-Skalicka K, Lim YK, Khaitová L, Koukalova B, Nybom H. The asymmetric meiosis in pentaploid dogroses (Rosa sect. Caninae) is associated with a skewed distribution of rRNA gene families in the gametes. Heredity (Edinb) 2008; 101:359-67. [PMID: 18648391 DOI: 10.1038/hdy.2008.63] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In pentaploid dogroses, Rosa section Caninae (2n=5x=35), the pollen transmits one basic genome (x=7) derived from the seven segregating bivalents, whereas the egg transmits four basic genomes (4x=28) one set derived from the segregation of seven bivalents and three sets of univalent-forming chromosomes. Chromosomes from all five genomes carry 18-5.8-26S nuclear ribosomal DNA (rDNA) sites. This mode of sexual reproduction, known as permanent odd polyploidy, can potentially lead to the independent evolution of rDNA on bivalent- and univalent-forming chromosomes. To test this hypothesis, we analyzed rRNA gene families in pollen and somatic leaf tissue of R. canina, R. rubiginosa and R. dumalis. Six major rRNA gene families (alpha, beta, beta' gamma, delta and epsilon) were identified based on several highly polymorphic sites in the internal transcribed spacers (ITSs). At least two of the major rRNA gene families were found in each species indicating that rDNAs have not been homogenized across subgenomes. A comparison of ITS1 sequences from leaf and pollen showed differences: the shared beta rRNA gene family was more abundant among pollen clones compared to leaf clones and must constitute a major part of the rDNA loci on bivalent-forming chromosomes. The gamma and delta families were underrepresented in pollen genomes and are probably located predominantly (or solely) on the univalents. The results support the hypothesis that pentaploid dogroses inherited a bivalent-forming genome from a common proto-canina ancestor, a likely donor of the beta rDNA family. Allopolyploidy with distantly related species is likely to have driven evolution of Rosa section Caninae.
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Affiliation(s)
- A Kovarik
- Laboratory of Molecular Epigenetics, Academy of Sciences of the Czech Republic, v.v.i., Institute of Biophysics, Brno, Czech Republic.
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Rosato M, Castro M, Rosselló JA. Relationships of the woody Medicago species (section Dendrotelis) assessed by molecular cytogenetic analyses. ANNALS OF BOTANY 2008; 102:15-22. [PMID: 18413655 PMCID: PMC2712417 DOI: 10.1093/aob/mcn055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND AND AIMS The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy. METHODS Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis. KEY RESULTS The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions. CONCLUSIONS FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular cytogenetic data do not suggest the hypothesis that M. arborea and M. strasseri were involved in the origin of M. citrina. FISH mapping can be used as an efficient tool to determine the genomic contribution of M. citrina in somatic hybrids with other medic species.
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Affiliation(s)
- Marcela Rosato
- Jardí Botànic, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain
| | - Mercedes Castro
- Facultad de Agronomia, Universidad Central de Venezuela, Apartado 4579, 2101 Maracay, Venezuela
| | - Josep A. Rosselló
- Jardí Botànic, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain
- For correspondence. E-mail
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Weiss-Schneeweiss H, Tremetsberger K, Schneeweiss GM, Parker JS, Stuessy TF. Karyotype diversification and evolution in diploid and polyploid South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data. ANNALS OF BOTANY 2008; 101:909-18. [PMID: 18285356 PMCID: PMC2710225 DOI: 10.1093/aob/mcn023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 01/11/2008] [Accepted: 01/21/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Changes in chromosome structure and number play an important role in plant evolution. A system well-suited to studying different modes of chromosome evolution is the genus Hypochaeris (Asteraceae) with its centre of species' diversity in South America. All South American species uniformly have a chromosome base number of x = 4 combined with variation in rDNA number and distribution, and a high frequency of polyploidy. The aim of this paper is to assess directions and mechanisms of karyotype evolution in South American species by interpreting both newly obtained and previous data concerning rDNA localization in a phylogenetic context. METHODS Eleven Hypochaeris species from 18 populations were studied using fluorescence in situ hybridization (FISH) with 35S and 5S rDNA probes. A phylogenetic framework was established from neighbour-net analysis of amplified fragment length polymorphism (AFLP) fingerprint data. KEY RESULTS A single 5S rDNA locus is invariably found on the short arm of chromosome 2. Using 35S rDNA loci, based on number (one or two) and localization (interstitial on the long arm of chromosome 2, but sometimes lacking, and terminal or interstitial on the short arm of chromosome 3, only very rarely lacking), seven karyotype groups can be distinguished; five of these include polyploids. Karyotype groups with more than one species do not form monophyletic groups. CONCLUSIONS Early evolution of Hypochaeris in South America was characterized by considerable karyotype differentiation resulting from independent derivations from an ancestral karyotype. There was marked diversification with respect to the position and evolution of the 35S rDNA locus on chromosome 3, probably involving inversions and/or transpositions, and on chromosome 2 (rarely 3) concerning inactivation and loss. Among these different karyotype assemblages, the apargioides group and its derivatives constitute by far the majority of species.
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Affiliation(s)
- Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
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Ansari HA, Ellison NW, Williams WM. Molecular and cytogenetic evidence for an allotetraploid origin of Trifolium dubium (Leguminosae). Chromosoma 2007; 117:159-67. [PMID: 18058119 DOI: 10.1007/s00412-007-0134-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/18/2007] [Accepted: 10/23/2007] [Indexed: 11/28/2022]
Abstract
Suckling clover, Trifolium dubium Sibth., is a European grassland legume that has spread to many parts of the world. The present work shows that it is an allotetraploid (2n = 4x = 30) combining the genomes of T. campestre Schreb. (2n = 2x = 14) and T. micranthum Viv. (2n = 2x = 16), two diploid species of similar geographic distribution. T. dubium has two nuclear ITS sequences that closely match those of T. campestre and T. micranthum. Genomic in situ hybridisation using genomic DNA of T. campestre and T. micranthum as probes has differentiated the ancestral sets of chromosomes in T. dubium cells. Comparative fluorescence in situ hybridisation analyses of 5S and 18S-26S rDNA loci were also consistent with an allotetraploid structure of the T. dubium genome. A marked preponderance of ITS repeats from T. campestre over those from T. micranthum indicated that concerted evolution has resulted in partial homogenisation of these sequences by depletion of the T. micranthum-derived 18S-26S rDNA repeats. In parallel with this, the epigenetic phenomenon of nucleolar dominance has been observed in T. dubium such that the chromatin associated with the 18S-26S rDNA loci derived from T. campestre is decondensed (transcriptionally active), whilst that from T. micranthum remains highly condensed throughout the cell cycle. T. dubium, therefore, appears to have arisen by way of hybridisation between forms of the diploid species T. campestre and T. micranthum accompanied by chromosome doubling. The observed genomic changes in rDNA resulting from interspecific hybridisation provide evidence for the process of genome diploidisation in T. dubium.
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Affiliation(s)
- Helal A Ansari
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, New Zealand.
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Lim KY, Matyasek R, Kovarik A, Leitch A. Parental origin and genome evolution in the allopolyploid Iris versicolor. ANNALS OF BOTANY 2007; 100:219-24. [PMID: 17591610 PMCID: PMC2735315 DOI: 10.1093/aob/mcm116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 03/26/2007] [Accepted: 05/01/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND AIMS One of the classic examples of an allopolyploid is Iris versicolor, 'Blue Flag' (2n = 108), first studied by Edgar Anderson and later popularized by George Ledyard Stebbins in cytogenetics and evolutionary text-books. It is revisited here using modern molecular and cytogenetic tools to investigate its putative allopolyploid origin involving progenitors of I. virginica (2n = 70) and I. setosa (2n = 38). METHODS Genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and Southern hybridization with 5S and 18-26S ribosomal DNA (rDNA) probes were used to identify the parental origin of chromosomes, and to study the unit structure, relative abundance and chromosomal location of rDNA sequences. KEY RESULTS GISH shows that I. versicolor has inherited the sum of the chromosome complement from the two progenitor species. In I. versicolor all the 18-26S rDNA units and loci are inherited from the progenitor of I. virginica, those loci from the I. setosa progenitor are absent. In contrast 5S rDNA loci and units from both progenitors are found, although one of the two 5S loci expected from the I. setosa progenitor is absent. CONCLUSIONS These data confirm Anderson's hypothesis that I. versicolor is an allopolyploid involving progenitors of I. virginica and I. setosa. The number of 18-26S rDNA loci in I. versicolor is similar to that of progenitor I. virginica, suggestive of a first stage in genome diploidization. The locus loss is targeted at the I. setosa-origin subgenome, and this is discussed in relation to other polyploidy systems.
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Affiliation(s)
- K Yoong Lim
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK.
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