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Kobrlová L, Čížková J, Zoulová V, Vejvodová K, Hřibová E. First insight into the genomes of the Pulmonaria officinalis group (Boraginaceae) provided by repeatome analysis and comparative karyotyping. BMC PLANT BIOLOGY 2024; 24:859. [PMID: 39266954 PMCID: PMC11395855 DOI: 10.1186/s12870-024-05497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/07/2024] [Indexed: 09/14/2024]
Abstract
BACKGROUND The genus Pulmonaria (Boraginaceae) represents a taxonomically complex group of species in which morphological similarity contrasts with striking karyological variation. The presence of different numbers of chromosomes in the diploid state suggests multiple hybridization/polyploidization events followed by chromosome rearrangements (dysploidy). Unfortunately, the phylogenetic relationships and evolution of the genome, have not yet been elucidated. Our study focused on the P. officinalis group, the most widespread species complex, which includes two morphologically similar species that differ in chromosome number, i.e. P. obscura (2n = 14) and P. officinalis (2n = 16). Ornamental cultivars, morphologically similar to P. officinalis (garden escapes), whose origin is unclear, were also studied. Here, we present a pilot study on genome size and repeatome dynamics of these closely related species in order to gain new information on their genome and chromosome structure. RESULTS Flow cytometry confirmed a significant difference in genome size between P. obscura and P. officinalis, corresponding to the number of chromosomes. Genome-wide repeatome analysis performed on genome skimming data showed that retrotransposons were the most abundant repeat type, with a higher proportion of Ty3/Gypsy elements, mainly represented by the Tekay lineage. Comparative analysis revealed no species-specific retrotransposons or striking differences in their copy number between the species. A new set of chromosome-specific cytogenetic markers, represented by satellite DNAs, showed that the chromosome structure in P. officinalis was more variable compared to that of P. obscura. Comparative karyotyping supported the hybrid origin of putative hybrids with 2n = 15 collected from a mixed population of both species and outlined the origin of ornamental garden escapes, presumably derived from the P. officinalis complex. CONCLUSIONS Large-scale genome size analysis and repeatome characterization of the two morphologically similar species of the P. officinalis group improved our knowledge of the genome dynamics and differences in the karyotype structure. A new set of chromosome-specific cytogenetic landmarks was identified and used to reveal the origin of putative hybrids and ornamental cultivars morphologically similar to P. officinalis.
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Affiliation(s)
- Lucie Kobrlová
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Veronika Zoulová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kateřina Vejvodová
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic.
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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Decena MÁ, Sancho R, Inda LA, Pérez-Collazos E, Catalán P. Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses. FRONTIERS IN PLANT SCIENCE 2024; 15:1419255. [PMID: 39049853 PMCID: PMC11266827 DOI: 10.3389/fpls.2024.1419255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024]
Abstract
Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the "polyploid genome shock hypothesis" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.
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Affiliation(s)
- María Ángeles Decena
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Rubén Sancho
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Centro de Investigaciones Tecnológicas y Agroalimentarias de Aragón (CITA), Zaragoza, Spain
| | - Ernesto Pérez-Collazos
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) Universidad de Zaragoza), Unidad Asociada al Consejo Superior de Investigaciones Científicas (CSIC), Zaragoza, Spain
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Kalfusová R, Herklotz V, Kumke K, Houben A, Kovařík A, Ritz CM, Lunerová J. Epigenetic histone H3 phosphorylation marks discriminate between univalent- and bivalent-forming chromosomes during canina asymmetrical meiosis. ANNALS OF BOTANY 2024; 133:435-446. [PMID: 38127060 PMCID: PMC11006542 DOI: 10.1093/aob/mcad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND AND AIMS Dogroses (Rosa sect. Caninae) are mostly pentaploid, bearing 2n = 5x = 35 chromosomes in somatic cells. They evolved a unique form of asymmetrical meiosis characterized by two types of chromosomes: (1) chromosomes forming bivalents and distributed in the normal sexual way; and (2) chromosomes occurring as univalents and transferred by a female gamete only. In the mature pollen of pentaploid species, seven bivalent-derived chromosomes are transmitted to offspring, and 21 unpaired univalent chromosomes are eliminated during microsporogenesis. To discriminate between bivalent- and univalent-forming chromosomes, we studied histone H3 phosphorylation patterns regulating meiotic chromosome condensation and segregation. METHODS We analysed histone modification patterns during male canina meiosis in two representative dogrose species, 5x Rosa canina and 5x Rosa rubiginosa, by immunohistochemical and molecular cytogenetics approaches. Immunostaining of meiotic cells included α-tubulin, histone H3 phosphorylation (H3S10p, H3S28p and H3T3p) and methylation (H3K4me3 and H3K27me3) marks. In addition, fluorescent in situ hybridization was carried out with an 18S rDNA probe. KEY RESULTS In the first meiotic division, univalent chromosomes underwent equational division into chromatids, while homologues in bivalents were segregated as regular dyads. In diakinesis, bivalent chromosomes displayed strong H3 phosphorylation signals in proximal regions, spreading to the rest of the chromosome. In contrast, in univalents, the H3 phosphorylation signals were weaker, occurring mostly outside proximal regions largely overlapping with the H3K4me3 signals. Reduced phosphorylation was associated with relative under-condensation of the univalent chromosomes, particularly at early diakinesis. CONCLUSIONS We hypothesize that the absence of pairing and/or recombination in univalent chromosomes negatively affects the histone H3 phosphorylation of their chromatin and perhaps the loading of meiotic-specific cohesins. This apparently destabilizes cohesion of sister chromatids, leading to their premature split in the first meiotic division.
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Affiliation(s)
- Radka Kalfusová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Veit Herklotz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Christiane M Ritz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technical University Dresden, D-01069, Dresden, Germany
| | - Jana Lunerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
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Reichel K, Herklotz V, Smolka A, Nybom H, Kellner A, De Riek J, Smulders MJM, Wissemann V, Ritz CM. Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L. PLoS One 2023; 18:e0292634. [PMID: 37797054 PMCID: PMC10553836 DOI: 10.1371/journal.pone.0292634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.
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Affiliation(s)
- Katja Reichel
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Alisia Smolka
- Institute of Biology, Dahlem Center of Plant Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Alexandra Kellner
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jan De Riek
- Flanders Research Institute for Agricultural, Fisheries and Food Research (ILVO), Plant Sciences Unit, Melle, Belgium
| | | | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum for Natural History Görlitz, Senckenberg–Member of the Leibniz Association, Görlitz, Germany
- International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Technical University Dresden, Zittau, Germany
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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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Kolarčik V, Mirková M, Mikoláš V. Reproduction Modes and Conservation Implications in Three Polyploid Sorbus Stenoendemics in Eastern Slovakia (Central Europe). PLANTS (BASEL, SWITZERLAND) 2023; 12:373. [PMID: 36679086 PMCID: PMC9863969 DOI: 10.3390/plants12020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
The remarkable species diversity of the genus Sorbus is a result of polyploidization and frequent hybridization between interacting species of different cytotypes. Moreover, hybridization is possible between several parental taxa. Gametophytic apomixis, which is common among polyploid Sorbus taxa, indicates the role of clonal reproduction in the evolutionary stabilization of hybridogeneous genotypes. The precise determination of the origin of seeds and their quantitative evaluation may elucidate inter-cytotype interactions, the potential role of mixed-cytotype populations in evolutionary success, and the long-term survival of some hybrid species. We investigated the reproduction modes of selected species of Sorbus in mixed-cytotype populations in eastern Slovakia, Central Europe. We determined the pollen quality, seed production rate, and the ploidy level of mature trees, as well as the origin of the embryo and endosperm in seeds of the stenoendemics S. amici-petri, S. dolomiticola, and S. hornadensis. The tetraploids S. amici-petri and S. hornadensis are characterized by regular and highly stainable pollen grains and reproduce predominantly via pseudogamous apomixis. In contrast, triploid S. dolomiticola usually has oval, heterogenous, and weakly stainable pollen grains, suggesting male meiotic irregularities. Although seeds originate via pseudogamous apomixis in S. dolomiticola as well, the ploidy level of sperm cells participating in the fertilization of central cells is usually determined by co-occurring species of different cytotypes. This suggests that maintaining mating partners is necessary for the long-term survival of a triploid species. We documented rare BIII hybrids and the residual sexuality in tetraploids. The distribution of seeds of meiotic and apomeiotic origins in S. amici-petri shows bimodal characteristics; however, genotypes with predominantly sexual seed types are rare. Reproduction modes documented in polyploid stenoendemics of Sorbus and inferred microevolutionary intercytotype relationships highlight the mixed-cytotype populations as the source of biodiversity in apomictic plant complexes. We suggest that conservation efforts should focus on maintaining the species and cytotypic diversity of Sorbus populations, especially when it comes to the conservation of triploid species.
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Affiliation(s)
- Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovakia
| | - Mária Mirková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovakia
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Garcia S, Pascual-Díaz JP, Krumpolcová A, Kovarík A. Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol. Methods Mol Biol 2023; 2672:501-512. [PMID: 37335496 DOI: 10.1007/978-1-0716-3226-0_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable interest for biologists, in general. Ribosomal RNA genes have also been largely used to establish phylogenetic relationships, and to identify allopolyploid or homoploid hybridization.Here, we demonstrate how high-throughput sequencing data, through graph clustering implemented in RepeatExplorer2 pipeline ( https://repeatexplorer-elixir.cerit-sc.cz/galaxy/ ), can be helpful to decipher the genomic organization of 5S rRNA genes. We show that the linear shapes of cluster graphs are reminiscent to the linked organization of 5S and 35S rDNA (L-type arrangement) while the circular graphs correspond to their separate arrangement (S-type). We further present a simplified protocol based on the paper by (Garcia et al., Front Plant Sci 11:41, 2020) about the use of graph clustering of 5S rDNA homoeologs (S-type) to identify hybridization events in the species history. We found that the graph complexity (i.e., graph circularity in this case) is related to ploidy and genome complexity, with diploids typically showing circular-shaped graphs while allopolyploids and other interspecific hybrids display more complex graphs, with usually two or more interconnected loops representing intergenic spacers. When a three-genomic comparative clustering analysis from a given hybrid (homoploid/allopolyploid) and its putative progenitor species (diploids) is performed, it is possible to identify the corresponding homoeologous 5S rRNA gene families, and to elucidate the contribution of each putative parental genome to the 5S rDNA pool of the hybrid. Thus, the analysis of 5S rDNA cluster graphs by RepeatExplorer, together with information coming from other sources (e.g., morphology, cytogenetics) is a complementary approach for the determination of allopolyploid or homoploid hybridization and even ancient introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alice Krumpolcová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ales Kovarík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Tynkevich YO, Novikov AV, Chorney II, Volkov RA. Organization of the 5S rDNA Intergenic Spacer and Its Use in the Molecular Taxonomy of the Genus Aconitum L. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722060111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Targueta CP, Gatto KP, Vittorazzi SE, Recco-Pimentel SM, Lourenço LB. High diversity of 5S ribosomal DNA and evidence of recombination with the satellite DNA PcP190 in frogs. Gene 2022; 851:147015. [DOI: 10.1016/j.gene.2022.147015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/25/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
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10
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Moreno-Aguilar MF, Inda LA, Sánchez-Rodríguez A, Arnelas I, Catalán P. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. FRONTIERS IN PLANT SCIENCE 2022; 13:901733. [PMID: 35845705 PMCID: PMC9284676 DOI: 10.3389/fpls.2022.901733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
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Affiliation(s)
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Instituto Agroalimentario de Aragón, Universidad de Zaragoza, Centro de Investigación y Tecnología Agroalimentaria, Zaragoza, Spain
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Itziar Arnelas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Unidad Asociada al CSIC, Zaragoza, Spain
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11
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He J, Zhao Y, Zhang S, He Y, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes (Basel) 2022; 13:894. [PMID: 35627279 PMCID: PMC9141308 DOI: 10.3390/genes13050894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosomal DNA (rDNA) is an excellent cytogenetic marker owing to its tandem arrangement and high copy numbers. However, comparative studies have focused more on the number of rDNA site variations within the Chrysanthemum genus, and studies on the types of rDNA sites with the same experimental procedures at the species levels are lacking. To further explore the number and types of rDNA site variations, we combined related data to draw ideograms of the rDNA sites of Chrysanthemum accessions using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Latent variations (such as polymorphisms of 45S rDNA sites and co-localized 5S-45S rDNA) also occurred among the investigated accessions. Meanwhile, a significant correlation was observed between the number of 5S rDNA sites and chromosome number. Additionally, the clumped and concentrated geographical distribution of different ploidy Chrysanthemum accessions may significantly promote the karyotype evolution. Based on the results above, we identified the formation mechanism of rDNA variations. Furthermore, these findings may provide a reliable method to examine the sites and number of rDNA variations among Chrysanthemum and its related accessions and allow researchers to further understand the evolutionary and phylogenetic relationships of the Chrysanthemum genus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (J.H.); (Y.Z.); (S.Z.); (Y.H.); (J.J.); (S.C.); (W.F.); (Z.G.); (Y.L.); (Z.W.); (F.C.)
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12
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Scoppola A, Cardoni S, Marcussen T, Simeone MC. Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae ( Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation. PLANTS (BASEL, SWITZERLAND) 2022; 11:1294. [PMID: 35631718 PMCID: PMC9147628 DOI: 10.3390/plants11101294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 05/11/2022] [Indexed: 01/02/2023]
Abstract
Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual pansies occur in Italy, four of which are morphologically very similar and belong to the informal 'V. tricolor species complex': V. arvensis (2n = 34), V. hymettia (2n = 16), V. kitaibeliana (2n = 16), and V. tricolor (2n = 26). Their field recognition is difficult and reflects a long-debated taxonomy often resulting in doubtful records in field inventories and across European herbaria. The current lack of comprehensive intra- and interspecific comparative studies and a relative scarcity of appropriate genetic markers coupled with unambiguous cytological descriptions are hindering clear taxa circumscription and phylogenetic inferences within this group. In this work, we tested DNA sequence variation of three highly variable plastid markers and High-Throughput Sequencing (HTS) of the nuclear ribosomal 5S-IGS region in an attempt to decipher species identity within the V. tricolor species complex and to obtain an insight on their genome organization and evolution. Our results document the close relationships within this species group, a reliable molecular resolution for V. tricolor, and the common ancestry of V. arvensis and the poorly differentiated V. kitaibeliana and V. hymettia. Evidence of an important inter-population geographical divergence was recorded in V. tricolor and V. arvensis, pointing at the existence of different eco-cytotypes within these entities. Overall diversity patterns and the occurrence of two to four differently diverging 5S-IGS lineages are discussed in the light of the acknowledged taxonomy and genomic evolutive trajectories of sect. Melanium.
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Affiliation(s)
- Anna Scoppola
- Department of Agricultural and Forestry Sciences (DAFNE), Tuscia University, Via S. Camillo de Lellis, 01100 Viterbo, Italy; (A.S.); (M.C.S.)
| | - Simone Cardoni
- Department of Agricultural and Forestry Sciences (DAFNE), Tuscia University, Via S. Camillo de Lellis, 01100 Viterbo, Italy; (A.S.); (M.C.S.)
| | - Thomas Marcussen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066, NO-0316 Oslo, Norway;
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Sciences (DAFNE), Tuscia University, Via S. Camillo de Lellis, 01100 Viterbo, Italy; (A.S.); (M.C.S.)
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Tynkevich YO, Shelyfist AY, Kozub LV, Hemleben V, Panchuk II, Volkov RA. 5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy. FRONTIERS IN PLANT SCIENCE 2022; 13:852406. [PMID: 35498650 PMCID: PMC9043955 DOI: 10.3389/fpls.2022.852406] [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: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.
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Affiliation(s)
- Yurij O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Antonina Y. Shelyfist
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Liudmyla V. Kozub
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Irina I. Panchuk
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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15
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Herklotz V, Kovařík A, Wissemann V, Lunerová J, Vozárová R, Buschmann S, Olbricht K, Groth M, Ritz CM. Power and Weakness of Repetition - Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization ( Rosa and Fragaria). FRONTIERS IN PLANT SCIENCE 2021; 12:738119. [PMID: 34950159 PMCID: PMC8688825 DOI: 10.3389/fpls.2021.738119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a "repeatomic fingerprint," and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.
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Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Sebastian Buschmann
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | | | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technische Universität Dresden, International Institute (IHI) Zittau, Zittau, Germany
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Roshka NM, Cherevatov OV, Volkov RA. Molecular Organization and Polymorphism of 5S rDNA in Carpathian Bees. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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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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