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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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Mlinarec J, Boštjančić LL, Malenica N, Jurković A, Boland T, Yakovlev SS, Besendorfer V. Structure and Methylation of 35S rDNA in Allopolyploids Anemone multifida (2 n = 4 x = 32, BBDD) and Anemone baldensis (2 n = 6 x = 48, AABBDD) and Their Parental Species Show Evidence of Nucleolar Dominance. FRONTIERS IN PLANT SCIENCE 2022; 13:908218. [PMID: 35874014 PMCID: PMC9296772 DOI: 10.3389/fpls.2022.908218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/07/2022] [Indexed: 05/26/2023]
Abstract
Transcriptional silencing of 35S rDNA loci inherited from one parental species is occurring relatively frequently in allopolyploids. However, molecular mechanisms by which it is selected for transcriptional silencing remain unclear. We applied NGS, silver staining and bisulfite sequencing to study the structure, expression and methylation landscape of 35S rDNA in two allopolyploids of common origin, allotetraploid Anemone multifida (2n = 4x = 32, genome composition BBDD) and allohexaploid A. baldensis (2n = 6x = 48, AABBDD), and their genome donors, A. sylvestris (2n = 16, AA), A. cylindrica (2n = 16, BB) and A. parviflora (2n = 16, DD). The size of the recovered 35S rDNA units varied from 10,489 bp in A. cylindrica to 12,084 bp in A. sylvestris. Anemone showed an organization typical of most ribosomal 35S rDNA composed of NTS, ETS, rRNA genes, TTS and TIS with structural features of plant IGS sequences and all functional elements needed for rRNA gene activity. The NTS was more variable than the ETS and consisted of SRs which are highly variable among Anemone. Five to six CpG-rich islands were found within the ETS. CpG island located adjacent to the transcription initiation site (TIS) was highly variable regarding the sequence size and methylation level and exhibited in most of the species lower levels of methylation than CpG islands located adjacent to the 18S rRNA gene. Our results uncover hypomethylation of A. sylvestris- and A. parviflora-derived 35S rDNA units in allopolyploids A. multifida and A. baldensis. Hypomethylation of A. parviflora-derived 35S rDNA was more prominent in A. baldensis than in A. multifida. We showed that A. baldensis underwent coupled A. sylvestris-derived 35S rDNA array expansion and A. parviflora-derived 35S rDNA copy number decrease that was accompanied by lower methylation level of A. sylvestris-derived 35S rDNA units in comparison to A. parviflora-derived 35S rDNA units. These observations suggest that in A. baldensis nucleolar dominance is directed toward A. sylvestris-derived chromosomes. This work broadens our current knowledge of the 35S rDNA organization in Anemone and provides evidence of the progenitor-specific 35S rDNA methylation in nucleolar dominance.
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Affiliation(s)
| | - Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
- Department of Computer Science, ICube, UMR 7357, CNRS, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, Strasbourg, France
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
| | - Todd Boland
- Memorial University of Newfoundland’s Botanical Gardens, St. John’s, NL, Canada
| | - Sonja Siljak Yakovlev
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Horvatovac, Croatia
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Orooji F, Mirzaghaderi G, Kuo YT, Fuchs J. Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:917310. [PMID: 35812971 PMCID: PMC9261981 DOI: 10.3389/fpls.2022.917310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Nigella is a small genus belonging to the Ranunculaceae family which is presumably originated and distributed in Aegean and the adjacent Western-Irano-Turanian region. Comparative repeat analysis of N. sativa, N. damascena and N. bucharica was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven Nigella species using the in silico identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of N. sativa, N. damascena and N. bucharica genomes, respectively. Roughly, half of the genomes are retrotransposons (class I transposons), while DNA transposons (class II transposons) contributed to only about 2% of the genomes. The analyzed Nigella species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in N. sativa, one in N. damascena and four in N. bucharica were identified, which were mostly (peri)centromeric and represented about 1% of each genome. A high variation in number and position of 45S rDNA loci were found among Nigella species. Interestingly, in N. hispanica, each chromosome revealed at least one 45S rDNA site and one of them occurs in hemizygous condition. Based on the chromosome numbers, genome size and (peri)centromeric satellites, three karyotype groups were observed: Two with 2n = 2x = 12 and a karyotype formula of 10m + 2t (including N. sativa, N. arvensis, N. hispanica as the first group and N. damascena and N. orientalis as the second group) and a more distant group with 2n = 2x = 14 and a karyotype formula of 8m + 2st + 4t (including N. integrifolia and N. bucharica). These karyotype groups agreed with the phylogenetic analysis using ITS and rbcL sequences. We conclude that variation in (peri)centromeric sequences, number and localization of rDNA sites as well as chromosome number (dysploidy) are involved in the diversification of the genus Nigella.
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Affiliation(s)
- Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Mitrenina EY, Erst AS, Peruzzi L, Skaptsov MV, Ikeda H, Nikulin VY, Wang W. Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae). PHYTOKEYS 2021; 187:207-227. [PMID: 35068976 PMCID: PMC8741716 DOI: 10.3897/phytokeys.187.75715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Comparative karyomorphological analyses of six out of the eight white-flowered species of Eranthissect.Shibateranthis have been carried out. All studied specimens of E.byunsanensis, E.lobulata, E.pinnatifida, and E.stellata had a somatic chromosome number 2n = 16 with basic chromosome number x = 8. On the contrary, E.tanhoensis and E.sibirica had a basic chromosome number x = 7. The specimens of E.tanhoensis were diploid with 2n = 14, while the specimens of E.sibirica were polyploid with 2n = 42. Monoploid chromosome sets of the investigated diploid species had 4-5 metacentric chromosomes and 2-4 submetacentric/subtelocentric/acrocentric chromosomes. The highest level of interchromosomal asymmetry, estimated via CVCL, was found in E.byunsanensis and E.pinnatifida. The highest levels of intrachromosomal asymmetry (MCA) and heterogeneity in centromere position (CVCI) were found in E.lobulata and E.byunsanensis, while E.sibirica had the most symmetric karyotype. A multivariate PCoA analysis of basic karyotype parameters (2n, x, THL, CVCL, MCA, and CVCI) highlighted no overlap among species accessions, which was also confirmed by LDA. The average absolute monoploid DNA content (1Cx) of the 23 investigated samples of six Eranthis species varied from 9.26 ± 0.25 pg in E.sibirica to 15.93 ± 0.32 pg in E.stellata. Overall karyological affinity was highlighted between E.lobulata and E.stellata, on one side, and between E.byunsanensis and E.pinnatifida, on the other side. Interestingly, there was no significant correlation between total haploid (monoploid) chromosome length (THL) and 1Cx values in these species.
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Affiliation(s)
- Elizaveta Yu. Mitrenina
- Laboratory of Herbarium, National Research Tomsk State University, Tomsk, RussiaNational Research Tomsk State UniversityTomskRussia
| | - Andrey S. Erst
- Laboratory of Herbarium, National Research Tomsk State University, Tomsk, RussiaNational Research Tomsk State UniversityTomskRussia
- Laboratory of Herbarium, Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaLaboratory of Herbarium, Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of SciencesNovosibirskRussia
| | - Lorenzo Peruzzi
- Department of Biology, Botany Unit, University of Pisa, Pisa, ItalyUniversity of PisaPisaItaly
| | - Mikhail V. Skaptsov
- South-Siberian Botanical Garden, Altai State University, Barnaul, RussiaAltai State UniversityBarnaulRussia
| | - Hiroshi Ikeda
- The University Museum, The University of Tokyo, Tokyo, JapanThe University of TokyoTokyoJapan
| | - Vyacheslav Yu. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, RussiaFederal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of SciencesVladivostokRussia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany of the Chinese Academy of Sciences, Beijing, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany of the Chinese Academy of SciencesBeijingChina
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Astuti G, Marconi G, Pupillo P, Peruzzi L. Anemonoides × lipsiensis comb. nov. (Ranunculaceae), new for the Italian flora. ITALIAN BOTANIST 2019. [DOI: 10.3897/italianbotanist.7.35004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The hybrid Anemonoidesnemorosa × A.ranunculoides is recorded for the first time in Italy at the southern periphery of Bologna (N Italy, Emilia-Romagna). Its status is supported by both morphological features and chromosome number (2n = 31). For this taxon, a new nomenclatural combination is proposed.
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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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Li QJ, Wang X, Wang JR, Su N, Zhang L, Ma YP, Chang ZY, Zhao L, Potter D. Efficient Identification of Pulsatilla (Ranunculaceae) Using DNA Barcodes and Micro-Morphological Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1196. [PMID: 31649688 PMCID: PMC6794950 DOI: 10.3389/fpls.2019.01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/30/2019] [Indexed: 05/04/2023]
Abstract
Pulsatilla (Ranunculaceae) comprises about 40 species, many of which have horticultural and/or medicinal importance. However, the recognition and identification of wild Pulsatilla species is difficult due to the presence of complex morphological characters. DNA barcoding is a powerful molecular tool capable of rapidly and accurately distinguishing between species. Here, we assessed the effectiveness of four commonly used DNA barcoding loci-rbcL (R), trnH-psbA ( T ), matK (M), and ITS (I)-to identify species of Pulsatilla from a comprehensive sampling group. Among the four barcoding single loci, the nuclear ITS marker showed the highest interspecific distances and the highest rate of correct identification. Among the eleven combinations, the chloroplast multi-locus R+T and R+M+T combinations were found to have the best species discrimination rate, followed by R+M. Overall, we propose that the R+M+T combination and the ITS marker on its own are, respectively, the best multi- and single-locus barcodes for discriminating among species of Pulsatilla. The phylogenetic analysis was able to distinguish species of Pulsatilla to the subgenus level, but the analysis also showed relatively low species resolution. This may be caused by incomplete lineage sorting and/or hybridization events in the evolutionary history of the genus, or by the resolution limit of the candidate barcodes. We also investigated the leaf epidermis of eight representative species using scanning electronic microscopy. The resulting micro-morphological characters were valuable for identification of related species. Using additional genome fragments, or even whole chloroplast genomes combined with micro-morphological data may permit even higher resolution of species in Pulsatilla.
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Affiliation(s)
- Qiu-jie Li
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer, China
| | - Yue-ping Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
- *Correspondence: Liang Zhao,
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
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Mlinarec J, Skuhala A, Jurković A, Malenica N, McCann J, Weiss-Schneeweiss H, Bohanec B, Besendorfer V. The Repetitive DNA Composition in the Natural Pesticide Producer Tanacetum cinerariifolium: Interindividual Variation of Subtelomeric Tandem Repeats. FRONTIERS IN PLANT SCIENCE 2019; 10:613. [PMID: 31156676 PMCID: PMC6532368 DOI: 10.3389/fpls.2019.00613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the T. cinerariifolium genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome. T. cinerariifolium exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in T. cinerariifolium. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of T. cinerariifolium chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in T. cinerariifolium and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | - Ana Skuhala
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Jamie McCann
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | | | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
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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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Fonsêca A, Ferraz ME, Pedrosa-Harand A. Speeding up chromosome evolution in Phaseolus: multiple rearrangements associated with a one-step descending dysploidy. Chromosoma 2015; 125:413-21. [PMID: 26490170 DOI: 10.1007/s00412-015-0548-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022]
Abstract
The genus Phaseolus L. has been subject of extensive cytogenetic studies due to its global economic importance. It is considered karyotypically stable, with most of its ca. 75 species having 2n = 22 chromosomes, and only three species (Phaseolus leptostachyus, Phaseolus macvaughii, and Phaseolus micranthus), which form the Leptostachyus clade, having 2n = 20. To test whether a simple chromosomal fusion was the cause of this descending dysploidy, mitotic chromosomes of P. leptostachyus (2n = 20) were comparatively mapped by fluorescent in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and ribosomal DNA (rDNA) probes. Our results corroborated the conservation of the 5S and 45S rDNA sites on ancestral chromosomes 10 and 6, respectively. The reduction from x = 11 to x = 10 was the result of the insertion of chromosome 10 into the centromeric region of chromosome 11, supporting a nested chromosome fusion (NCF) as the main cause of this dysploidy. Additionally, the terminal region of the long arm of chromosome 6 was translocated to this larger chromosome. Surprisingly, the NCF was accompanied by several additional translocations and inversions previously unknown for the genus, suggesting that the dysploidy may have been associated to a burst of genome reorganization in this otherwise stable, diploid plant genus.
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Affiliation(s)
- Artur Fonsêca
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil.
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Garmendia A, Ferriol M, Juarez J, Zając A, Kałużny K, Merle H. A rare case of a natural contact zone in Morocco between an autopolyploid and an allopolyploid of Centaurea aspera with sterile tetraploid hybrids. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:746-757. [PMID: 25363815 DOI: 10.1111/plb.12284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/24/2014] [Indexed: 06/04/2023]
Abstract
A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed.
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Affiliation(s)
- A Garmendia
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
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Reis AC, Sousa SM, Vale AA, Pierre PMO, Franco AL, Campos JMS, Vieira RF, Viccini LF. Lippia alba (Verbenaceae): A new tropical autopolyploid complex? AMERICAN JOURNAL OF BOTANY 2014; 101:1002-1012. [PMID: 24920764 DOI: 10.3732/ajb.1400149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
• Premise of the study: Tropical regions have high species diversity, and polyploidization is a major mechanism of speciation in plants. However, few cases of natural polyploidy have been reported in tropical regions. Lippia alba, is a tropical, aromatic shrub with a wide distribution, extensive morphological plasticity, and several chemotypes. The species has long been recognized as a diploid with 2n = 30 chromosomes. Recently, two variations in chromosome number (2n = 60; 2n = 12-60) have been reported, suggesting the occurrence of polyploidy within the species.• Methods: Flow cytometry was used to investigate the genome size in 106 accessions from 14 Brazilian States. Conventional and molecular cytogenetic techniques and pollen viability analysis were employed to characterize each chromosome number observed.• Key results: The DNA 1C-value varied from 1.17 to 3.45 pg, showing a large variation in genome size. Five distinct chromosome numbers were observed (2n = 30, 38, 45, 60, 90); three are cytogenetically described here for the first time. The 5S rDNA signals varied proportionally according to each chromosome number, but 45S rDNA sites did not. High rates of meiotic irregularity were observed, mainly in cytotypes with higher chromosome numbers.• Conclusions: The data provide new support for the occurrence of a polyploid series in Lippia alba. We provide a hypothesis for how this complex may have arisen. Other cryptic polyploid complexes may remain undiscovered in tropical regions.
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Affiliation(s)
- Aryane C Reis
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Saulo M Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Aline A Vale
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Patrícia M O Pierre
- Universidade Federal de Santa Catarina, Campus Universitário Curitibanos, Rodovia Ulisses Gaboardi-km 3 89520-000, Curitibanos, SC, Brazil
| | - Ana L Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - José Marcello S Campos
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Roberto F Vieira
- Embrapa Recursos Genéticos e Biotecnologia, CEP 70.770-900, Distrito Federal, Brasília, Brazil
| | - Lyderson F Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
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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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