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Xavier A, Yadav R, Gowda V. Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers. AMERICAN JOURNAL OF BOTANY 2024:e16334. [PMID: 38825815 DOI: 10.1002/ajb2.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/04/2024]
Abstract
PREMISE Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known. METHODS A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models. RESULTS The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution. CONCLUSIONS Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.
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Affiliation(s)
- Aleena Xavier
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Ritu Yadav
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
| | - Vinita Gowda
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, 462066, Madhya Pradesh, India
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Shafir A, Halabi K, Escudero M, Mayrose I. A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny. THE NEW PHYTOLOGIST 2023; 238:1733-1744. [PMID: 36759331 DOI: 10.1111/nph.18805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes, ES-41012, Seville, Spain
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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Stepanenko A, Chen G, Hoang PTN, Fuchs J, Schubert I, Borisjuk N. The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units. FRONTIERS IN PLANT SCIENCE 2022; 13:819750. [PMID: 35310643 PMCID: PMC8928438 DOI: 10.3389/fpls.2022.819750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The freshwater plant water lettuce (Pistia stratiotes L.) grows in warm climatic zones and is used for phytoremediation and biomass production. P. stratiotes belongs to the Araceae, an ecologically and structurally diverse early monocot family, but the phylogenetic relationships among Araceae members are poorly understood. Ribosomal DNAs (rDNAs), including the 35S and 5S rDNA, encode the RNA components of ribosomes and are widely used in phylogenetic and evolutionary studies of various plant taxa. Here, we comprehensively characterized the chromosomal locations and molecular organization of 35S and 5S rDNA genes in water lettuce using karyological and molecular methods. Fluorescence in situ hybridization revealed a single location for the 35S and 5S rDNA loci, each on a different pair of the species' 28 chromosomes. Molecular cloning and nucleotide sequencing of 35S rDNA of P. stratiotes, the first representative Araceae sensu stricto in which such a study was performed, displayed typical structural characteristics. The full-length repeat showed high sequence conservation of the regions producing the 18S, 5.8S, and 25S rRNAs and divergence of the internal transcribed spacers ITS1 and ITS2 as well as the large intergenic spacer (IGS). Alignments of the deduced sequence of 18S rDNA with the sequences available for other Araceae and representatives of other clades were used for phylogenetic analysis. Examination of 11 IGS sequences revealed significant intra-genomic length variability due to variation in subrepeat number, with four types of units detected within the 35S rDNA locus of the P. stratiotes genome (estimated size 407 Mb/1C). Similarly, the 5S rDNA locus harbors gene units comprising a conserved 119-bp sequence encoding 5S rRNA and two types of non-transcribed spacer (NTS) sequences. Type I was classified into four subtypes, which apparently originated via progressive loss of subrepeats within the duplicated NTS region containing the 3' part of the 5S rRNA gene. The minor Type II NTS is shorter than Type I and differs in nucleotide composition. Some DNA clones containing two or three consecutive 5S rDNA repeats harbored 5S rDNA genes with different types of NTSs, confirming the mosaic composition of the 5S rDNA locus.
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Affiliation(s)
- Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Phuong T. N. Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Faculty of Biology, Dalat University, Đà Lạt, Vietnam
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
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Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae. PLANTS 2021; 10:plants10122639. [PMID: 34961110 PMCID: PMC8704351 DOI: 10.3390/plants10122639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022]
Abstract
Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.
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Ferraz ME, Fonsêca A, Pedrosa-Harand A. Multiple and independent rearrangements revealed by comparative cytogenetic mapping in the dysploid Leptostachyus group (Phaseolus L., Leguminosae). Chromosome Res 2020; 28:395-405. [PMID: 33191473 DOI: 10.1007/s10577-020-09644-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 10/23/2022]
Abstract
Polyploidy and dysploidy have been reported as the main events in karyotype evolution of plants. In the genus Phaseolus L. (2n = 22), a small monophyletic group of three species, the Leptostachyus group, presents a dysploid karyotype with 2n = 20. It was shown in Phaseolus leptostachyus that the dysploidy was caused by a nested chromosome fusion (NCF) accompanied by several translocations, suggesting a high rate of karyotype evolution in the group. To verify if this karyotype restructuring was a single event or occurred progressively during the evolution of this group, we analysed P. macvaughii, sister to Phaseolus micranthus + P. leptostachyus. Twenty-four genomic clones of P. vulgaris previously mapped on P. leptostachyus, in addition to the 5S and 35S rDNA probes, were used for fluorescence in situ hybridization. Only a single rearrangement was common to the two species: the nested chromosome fusion (NCF) involving chromosomes 10 and 11. The translocation of chromosome 2 is not the same found in P. leptostachyus, and pericentric inversions in chromosomed 3 and 4 were exclusive of P. macvaughii. The other rearrangements observed in P. leptostachyus were not shared with this species, suggesting that they occurred after the separation of these lineages. The presence of private rearrangements indicates a progressive accumulation of karyotype changes in the Leptostachyus group instead of an instant genome-wide repatterning.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Artur Fonsêca
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil.
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Carta A, Bedini G, Peruzzi L. A deep dive into the ancestral chromosome number and genome size of flowering plants. THE NEW PHYTOLOGIST 2020; 228:1097-1106. [PMID: 32421860 DOI: 10.1111/nph.16668] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 05/22/2023]
Abstract
Chromosome number and genome variation in flowering plants have stimulated growing speculation about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal. We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 000 taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5000 taxa. Our analyses revealed an ancestral haploid chromosome number for angiosperms of n = 7, a diploid status, and an ancestral 1C of 1.73 pg. For 160 families, inferred ancestral n are provided for the first time. Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, 1C genome size also increases (or decreases) significantly in late-branching lineages. Therefore, no evidence exists of a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.
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Affiliation(s)
- Angelino Carta
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Gianni Bedini
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Lorenzo Peruzzi
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
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Kim SH, Yang J, Park J, Yamada T, Maki M, Kim SC. Comparison of Whole Plastome Sequences between Thermogenic Skunk Cabbage Symplocarpus renifolius and Nonthermogenic S. nipponicus (Orontioideae; Araceae) in East Asia. Int J Mol Sci 2019; 20:E4678. [PMID: 31547213 PMCID: PMC6801674 DOI: 10.3390/ijms20194678] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 01/10/2023] Open
Abstract
Symplocarpus, a skunk cabbage genus, includes two sister groups, which are drastically different in life history traits and thermogenesis, as follows: The nonthermogenic summer flowering S. nipponicus and thermogenic early spring flowering S. renifolius. Although the molecular basis of thermogenesis and complete chloroplast genome (plastome) of thermogenic S. renifolius have been well characterized, very little is known for that of S. nipponicus. We sequenced the complete plastomes of S. nipponicus sampled from Japan and Korea and compared them with that of S. renifolius sampled from Korea. The nonthermogenic S. nipponicus plastomes from Japan and Korea had 158,322 and 158,508 base pairs, respectively, which were slightly shorter than the thermogenic plastome of S. renifolius. No structural or content rearrangements between the species pairs were found. Six highly variable noncoding regions (psbC/trnS, petA/psbJ, trnS/trnG, trnC/petN, ycf4/cemA, and rpl3/rpl22) were identified between S. nipponicus and S. renifolius and 14 hot-spot regions were also identified at the subfamily level. We found a similar total number of SSR (simple sequence repeat) motifs in two accessions of S. nipponicus sampled from Japan and Korea. Phylogenetic analysis supported the basal position of subfamily Orontioideae and the monophyly of genus Symplocarpus, and also revealed an unexpected evolutionary relationship between S. nipponicus and S. renifolius.
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Affiliation(s)
- Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea.
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, Kyungpook National University, Daegu, Gyeongsangbuk-do 41566, Korea.
| | | | - Takayuki Yamada
- Botanical Gardens, Tohoku University, Sendai 980-0862, Japan.
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Sendai 980-0862, Japan.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea.
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Marinho MAO, Souza G, Felix LP, De Carvalho R. Comparative cytogenetics of the ACPT clade (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae): a very diverse group of the suborder Cactineae, Caryophyllales. PROTOPLASMA 2019; 256:805-814. [PMID: 30604246 DOI: 10.1007/s00709-018-01334-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
The clade ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) is the most diverse lineage of the subordem Cactineae. The relationships between these families are still uncertain, with different topologies suggested by phylogenetic analyses with several combinations of markers. Different basic numbers (x) have been suggested for each family and for the subord, often in a contestable way. Comparative cytogenetic has helped to understand the evolutionary relationships of phylogenetically poorly resolved groups, as well as their mechanisms of karyotype evolution. The karyotype evolution in representatives of Cactineae was analyzed, focusing on the ACPT clade, through the analysis of chromosome number in a phylogenetic bias. The phylogeny obtained showed a well-resolved topology with support for the monophyly of the five families. Although a chromosomal number is known for less than 30% of the Cactineae species, the analyses revealed a high karyotype variability, from 2n = 8 to 2n = 110. The analysis of character reconstruction of the ancestral haploid numbers (p) suggested p = 12 for Cactineae, with distinct basic numbers for the clade family ACPT: Cactaceae and Montiaceae (p = 11), Talinaceae (p = 12), and Anacampserotaceae and Portulacaceae (p = 9). Talinaceae, Anacampserotaceae, and Cactaceae were stable, while Portulaca and Montiaceae were karyotypically variable. The chromosome evolution of this group was mainly due to events of descending disploidy and poliploidy. Our data confirm that the low phylogenetic resolution among the families of the ACPT clade is due to a divergence of this clade in a short period of time. However, each of these families can be characterized by basic chromosome numbers and unique karyotype evolution events.
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Affiliation(s)
- Maria Angélica Oliveira Marinho
- Graduate Program in Botany, Department of Biology, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco, 52171-900, Brazil.
| | - Gustavo Souza
- Laboratory of Cytogenetics and Evolution of Plants, Department of Botany, Universidade Federal de Pernambuco, Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Leonardo P Felix
- Center of Agrarian Sciences, Universidade Federal da Paraíba, Campus II, Areia, Paraíba, 58397-000, Brazil
| | - Reginaldo De Carvalho
- Graduate Program in Botany, Department of Biology, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco, 52171-900, Brazil
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McCarthy EW, Landis JB, Kurti A, Lawhorn AJ, Chase MW, Knapp S, Le Comber SC, Leitch AR, Litt A. Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae). BMC PLANT BIOLOGY 2019; 19:162. [PMID: 31029077 PMCID: PMC6486959 DOI: 10.1186/s12870-019-1771-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/10/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns. RESULTS Predicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana, perhaps due to the influence of pollinators. CONCLUSIONS Young polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana.
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Affiliation(s)
- Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Present address: Department of Biological Sciences, SUNY Cortland, Cortland, NY 13045 USA
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102 Australia
| | | | - Steven C. Le Comber
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
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Pimentel M, Escudero M, Sahuquillo E, Minaya MÁ, Catalán P. Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene? PeerJ 2017; 5:e3815. [PMID: 28951814 PMCID: PMC5611942 DOI: 10.7717/peerj.3815] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/26/2017] [Indexed: 11/24/2022] Open
Abstract
The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
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Affiliation(s)
- Manuel Pimentel
- Evolutionary Biology Research Group (GIBE), Department of Biology, University of A Coruña, A Coruña, Galicia, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Andalucía, Spain
| | - Elvira Sahuquillo
- Evolutionary Biology Research Group (GIBE), Department of Biology, University of A Coruña, A Coruña, Galicia, Spain
| | - Miguel Ángel Minaya
- Department of Molecular Microbiology and Immunology, St. Louis University, Saint Louis, MO, United States of America
| | - Pilar Catalán
- High Polytechnic School of Huesca, University of Zaragoza, Huesca, Aragón, Spain.,Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
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Mota L, Torices R, Loureiro J. The Evolution of Haploid Chromosome Numbers in the Sunflower Family. Genome Biol Evol 2016; 8:3516-3528. [PMID: 27797951 PMCID: PMC5203788 DOI: 10.1093/gbe/evw251] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2016] [Indexed: 12/15/2022] Open
Abstract
Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events; however, it did not find evidence for a paleopolyploidization at the base of this family, which has previously been hypothesized on the basis of sequence data from a limited number of species. The obtained results and potential causes of these discrepancies are discussed.
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Affiliation(s)
- Lucie Mota
- Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Rubén Torices
- Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Department of Functional and Evolutionary Ecology, Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - João Loureiro
- Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Mandáková T, Gloss AD, Whiteman NK, Lysak MA. How diploidization turned a tetraploid into a pseudotriploid. AMERICAN JOURNAL OF BOTANY 2016; 103:1187-96. [PMID: 27206460 DOI: 10.3732/ajb.1500452] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/10/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Despite being highly fertile and occupying a large geographic region, the North American heartleaf bittercress (Cardamine cordifolia; Brassicaceae) has a puzzling triploid-like chromosome number (2n = 3x = 24). As most triploids are sterile, we embarked on a detailed analysis of the C. cordifolia genome to elucidate its origin and structure. METHODS Mitotic and meiotic chromosome complement of C. cordifolia was analyzed by comparative chromosome painting using chromosome-specific BAC contigs of Arabidopsis thaliana. Resulting chromosome patterns were documented by multicolor fluorescence microscopy and compared with known ancestral and extant Brassicaceae genomes. KEY RESULTS We discovered that C. cordifolia is not a triploid hybrid but a diploidized tetraploid with the prevalence of regular, diploid-like meiotic pairing. The ancestral tetraploid chromosome number (2n = 32) was reduced to a triploid-like number (2n = 24) through four terminal chromosome translocations. CONCLUSIONS The structure of the pseudotriploid C. cordifolia genome results from a stepwise diploidization process after whole-genome duplication. We showed that translocation-based descending dysploidy (from n = 16 to n = 12) was mediated by the formation of five new chromosomes. The genome of C. cordifolia represents the diploidization process in statu nascendi and provides valuable insights into mechanisms of postpolyploidy rediploidization in land plants. Our data further suggest that chromosome number alone does not need to be a reliable proxy of species' evolutionary past and that the same chromosome number may originate either by polyploidization (hybridization) or due to descending dysploidy.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Noah K Whiteman
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Martin A Lysak
- Plant Cytogenomics Research Group, CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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Lakshmanan PS, Van Laere K, Eeckhaut T, Van Huylenbroeck J, Van Bockstaele E, Khrustaleva L. Karyotype analysis and visualization of 45S rRNA genes using fluorescence in situ hybridization in aroids (Araceae). COMPARATIVE CYTOGENETICS 2015; 9:145-60. [PMID: 26140158 PMCID: PMC4488963 DOI: 10.3897/compcytogen.v9i2.4366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/09/2015] [Indexed: 05/04/2023]
Abstract
Karyotype analysis and FISH mapping using 45S rDNA sequences on 6 economically important plant species Anthuriumandraeanum Linden ex André, 1877, Monsteradeliciosa Liebmann, 1849, Philodendronscandens Koch & Sello, 1853, Spathiphyllumwallisii Regel, 1877, Syngoniumauritum (Linnaeus, 1759) Schott, 1829 and Zantedeschiaelliottiana (Knight, 1890) Engler, 1915 within the monocotyledonous family Araceae (aroids) were performed. Chromosome numbers varied between 2n=2x=24 and 2n=2x=60 and the chromosome length varied between 15.77 µm and 1.87 µm. No correlation between chromosome numbers and genome sizes was observed for the studied genera. The chromosome formulas contained only metacentric and submetacentric chromosomes, except for Philodendronscandens in which also telocentric and subtelocentric chromosomes were observed. The highest degree of compaction was calculated for Spathiphyllumwallisii (66.49Mbp/µm). B-chromosome-like structures were observed in Anthuriumandraeanum. Their measured size was 1.87 times smaller than the length of the shortest chromosome. After FISH experiments, two 45S rDNA sites were observed in 5 genera. Only in Zantedeschiaelliottiana, 4 sites were seen. Our results showed clear cytogenetic differences among genera within Araceae, and are the first molecular cytogenetics report for these genera. These chromosome data and molecular cytogenetic information are useful in aroid breeding programmes, systematics and evolutionary studies.
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Affiliation(s)
- Prabhu Shankar Lakshmanan
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University (UGent), Coupure links 653, 9000 Ghent, Belgium
- Center of Molecular Biotechnology, Department of Genetics and Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy (TIMACAD), 49, Timiryazevskaya str., 127550 Moscow, Russia
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium
| | - Tom Eeckhaut
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium
| | - Johan Van Huylenbroeck
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium
| | - Erik Van Bockstaele
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University (UGent), Coupure links 653, 9000 Ghent, Belgium
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Department of Genetics and Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy (TIMACAD), 49, Timiryazevskaya str., 127550 Moscow, Russia
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Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I. The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers. THE NEW PHYTOLOGIST 2015; 206:19-26. [PMID: 25423910 DOI: 10.1111/nph.13191] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Anna Rice
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lior Glick
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shiran Abadi
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Moshe Einhorn
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Naama M Kopelman
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ayelet Salman-Minkov
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jonathan Mayzel
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ofer Chay
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. ANNALS OF BOTANY 2014; 114:1651-63. [PMID: 25274549 PMCID: PMC4649684 DOI: 10.1093/aob/mcu189] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/07/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. METHODS Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. KEY RESULTS Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). CONCLUSIONS Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.
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Affiliation(s)
- Andreas Fleischmann
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Todd P Michael
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | - Aretuza Sousa
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Johann Greilhuber
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Kai F Müller
- Institute for Evolution and Biodiversity, University of Muenster, Hüfferstrasse 1, D 48149 Münster, Germany
| | - Günther Heubl
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
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18
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Henriquez CL, Arias T, Pires JC, Croat TB, Schaal BA. Phylogenomics of the plant family Araceae. Mol Phylogenet Evol 2014; 75:91-102. [DOI: 10.1016/j.ympev.2014.02.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 02/15/2014] [Accepted: 02/18/2014] [Indexed: 11/16/2022]
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19
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Glick L, Mayrose I. ChromEvol: Assessing the Pattern of Chromosome Number Evolution and the Inference of Polyploidy along a Phylogeny. Mol Biol Evol 2014; 31:1914-22. [DOI: 10.1093/molbev/msu122] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Turco A, Medagli P, Albano A, D’Emerico S. Karyomorphometry on three polyploid species of Arum L. (Araceae, Aroideae). COMPARATIVE CYTOGENETICS 2014; 8:71-80. [PMID: 24744834 PMCID: PMC3978243 DOI: 10.3897/compcytogen.v8i1.6444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/28/2014] [Indexed: 06/03/2023]
Abstract
In this study three polyploid Arum Linnaeus, 1753 species from Southern Italy were chromosomally investigated. Arum italicum Miller, 1768 was found to have 2n = 84 chromosomes and a karyotype composed of numerous asymmetric chromosomes. Arum maculatum Linnaeus, 1753 and Arum apulum (Carano) P. C. Boyce, 1993 were found to have 2n = 56 chromosomes. In the examined taxa some chromosome pairs were characterized by the presence of weakly coloured Feulgen-stained segments. The karyotype morphology of Arum italicum was found to be similar to that of Arum maculatum, but the more asymmetrical karyotype and numerous weakly coloured Feulgen-stained segments observed in the former suggest the existence of more extensive rearrangements. In contrast, Arum apulum was observed to have a symmetrical karyotype. The A1, A2 and SYi karyotype asymmetry indices are presented. The relationships between these taxa in terms of karyotype morphology and evolution are discussed.
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Affiliation(s)
- Alessio Turco
- Dept. of Biological and Environmental Sciences and Technologies, University of the Salento, Via prov.le Lecce-Monteroni 6, Lecce, Italy
| | - Pietro Medagli
- Dept. of Biological and Environmental Sciences and Technologies, University of the Salento, Via prov.le Lecce-Monteroni 6, Lecce, Italy
| | - Antonella Albano
- Dept. of Biological and Environmental Sciences and Technologies, University of the Salento, Via prov.le Lecce-Monteroni 6, Lecce, Italy
| | - Saverio D’Emerico
- Dept. of Plant Biology, University of Bari “Aldo Moro”, Via Orabona 4, Bari, Italy
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Sousa A, Cusimano N, Renner SS. Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae). ANNALS OF BOTANY 2014; 113:669-80. [PMID: 24500949 PMCID: PMC3936593 DOI: 10.1093/aob/mct302] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/29/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Since the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family. METHODS A phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24. KEY RESULTS The best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites. CONCLUSIONS The combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.
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Pellicer J, Kelly LJ, Leitch IJ, Zomlefer WB, Fay MF. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae. THE NEW PHYTOLOGIST 2014; 201:1484-1497. [PMID: 24299166 DOI: 10.1111/nph.12617] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/30/2013] [Indexed: 05/22/2023]
Abstract
• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.
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Affiliation(s)
- Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Laura J Kelly
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Wendy B Zomlefer
- Department of Plant Biology, 2502 Plant Sciences, University of Georgia, Athens, GA, 30602-7271, USA
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae). Heredity (Edinb) 2014; 112:562-8. [PMID: 24398885 DOI: 10.1038/hdy.2013.143] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 12/22/2022] Open
Abstract
Changes in chromosome number and structure are important contributors to adaptation, speciation and macroevolution. In flowering plants, polyploidy and subsequent reductions in chromosome number by fusion are major sources of chromosomal evolution, but chromosome number increase by fission has been relatively unexplored. Here, we use comparative linkage mapping with gene-based markers to reconstruct chromosomal synteny within the model flowering plant genus Mimulus (monkeyflowers). Two sections of the genus with haploid numbers ≥ 14 have been inferred to be relatively recent polyploids because they are phylogenetically nested within numerous taxa with low base numbers (n=8-10). We combined multiple data sets to build integrated genetic maps of the M. guttatus species complex (section Simiolus, n=14) and the M. lewisii group (section Erythranthe; n=8), and then aligned the two integrated maps using >100 shared markers. We observed strong segmental synteny between M. lewisii and M. guttatus maps, with essentially 1-to-1 correspondence across each of 16 chromosomal blocks. Assuming that the M. lewisii (and widespread) base number of 8 is ancestral, reconstruction of 14 M. guttatus chromosomes requires at least eight fission events (likely shared by Simiolus and sister section Paradanthus (n=16)), plus two fusion events. This apparent burst of fission in the yellow monkeyflower lineages raises new questions about mechanisms and consequences of chromosomal fission in plants. Our comparative maps also provide insight into the origins of a chromosome exhibiting centromere-associated female meiotic drive and create a framework for transferring M. guttatus genome resources across the entire genus.
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Mandáková T, Kovařík A, Zozomová-Lihová J, Shimizu-Inatsugi R, Shimizu KK, Mummenhoff K, Marhold K, Lysak MA. The more the merrier: recent hybridization and polyploidy in cardamine. THE PLANT CELL 2013; 25:3280-95. [PMID: 24082009 PMCID: PMC3809532 DOI: 10.1105/tpc.113.114405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/26/2013] [Accepted: 09/12/2013] [Indexed: 05/19/2023]
Abstract
This article describes the use of cytogenomic and molecular approaches to explore the origin and evolution of Cardamine schulzii, a textbook example of a recent allopolyploid, in its ~110-year history of human-induced hybridization and allopolyploidy in the Swiss Alps. Triploids are typically viewed as bridges between diploids and tetraploids but rarely as parental genomes of high-level hybrids and polyploids. The genome of the triploid semifertile hybrid Cardamine × insueta (2n = 24, RRA) was shown to combine the parental genomes of two diploid (2n = 2x = 16) species, Cardamine amara (AA) and Cardamine rivularis (RR). These parental genomes have remained structurally stable within the triploid genome over the >100 years since its origin. Furthermore, we provide compelling evidence that the alleged recent polyploid C. schulzii is not an autohexaploid derivative of C. × insueta. Instead, at least two hybridization events involving C. × insueta and the hypotetraploid Cardamine pratensis (PPPP, 2n = 4x-2 = 30) have resulted in the origin of the trigenomic hypopentaploid (2n = 5x-2 = 38, PPRRA) and hypohexaploid (2n = 6x-2 = 46, PPPPRA). These data show that the semifertile triploid hybrid can promote a merger of three different genomes and demonstrate how important it is to reexamine the routinely repeated textbook examples using modern techniques.
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Affiliation(s)
- Terezie Mandáková
- Research Group Plant Cytogenomics, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500 Brno, Czech Republic
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265 Brno, Czech Republic
| | | | - Rie Shimizu-Inatsugi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801 Prague, Czech Republic
| | - Martin A. Lysak
- Research Group Plant Cytogenomics, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500 Brno, Czech Republic
- Address correspondence to
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25
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Pellicer J, Kelly L, Magdalena C, Leitch I. Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies). Genome 2013; 56:437-49. [DOI: 10.1139/gen-2013-0039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nymphaeales are the most species-rich lineage of the earliest diverging angiosperms known as the ANA grade (Amborellales, Nymphaeales, Austrobaileyales), and they have received considerable attention from morphological, physiological, and ecological perspectives. Although phylogenetic relationships between these three lineages of angiosperms are mainly well resolved, insights at the whole genome level are still limited because of a dearth of information. To address this, genome sizes and chromosome numbers in 34 taxa, comprising 28 species were estimated and analysed together with previously published data to provide an overview of genome size and chromosome diversity in Nymphaeales. Overall, genome sizes were shown to vary 10-fold and chromosome numbers and ploidy levels ranged from 2n = 2x = 18 to 2n = 16x = ∼224. Distinct patterns of genome diversity were apparent, reflecting the differential incidence of polyploidy, changes in repetitive DNA content, and chromosome rearrangements within and between genera. Using model-based approaches, ancestral genome size and basic chromosome numbers were reconstructed to provide insights into the dynamics of genome size and chromosome number evolution. Finally, by combining additional data from Amborellales and Austrobaileyales, a comprehensive overview of genome sizes and chromosome numbers in these early diverging angiosperms is presented.
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Affiliation(s)
- J. Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - L.J. Kelly
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- Queen Mary University of London, School of Biological and Chemical Science, London E1 4NS, UK
| | - C. Magdalena
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - I.J. Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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26
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Peruzzi L, Góralski G, Joachimiak AJ, Bedini G. Does actually mean chromosome number increase with latitude in vascular plants? An answer from the comparison of Italian, Slovak and Polish floras. COMPARATIVE CYTOGENETICS 2012; 6:371-377. [PMID: 24260677 PMCID: PMC3834573 DOI: 10.3897/compcytogen.v6i4.3955] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/22/2012] [Indexed: 05/30/2023]
Abstract
WE COMPARED CHROMOSOME NUMBER (CN) VARIATION AMONG VASCULAR FLORAS OF THREE DIFFERENT COUNTRIES WITH INCREASING LATITUDE IN THE BOREAL HEMISPHERE: Italy, Slovakia, Poland. Aim of the study was to verify whether the patterns of CN variation parallel the differences in latitudinal ranges. The three datasets comprised 3426 (Italy), 3493 (Slovakia) and 1870 (Poland) distinct cytotypes. Standard statistics (ANOVA, Kruskal-Wallis tests) evidenced significant differences among the three countries, mean CN increasing together with latitude. On the contrary, an inverse relation (r = -1) was evidenced among the frequency of odd CNs and latitude. Our results show that the hypothesis of a polyploid increase proportional with distance from the Equator seems to be confirmed, when territories from the same hemisphere are compared.
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Affiliation(s)
- Lorenzo Peruzzi
- Department of Biology, Botany Unit, University of Pisa, via L. Ghini 5, 56126, Pisa, Italy
| | - Grzegorz Góralski
- Department of Plant Cytology and Embryology, Jagiellonian University, Grodzka 52, 31-044 Cracow, Poland
| | - Andrzej J. Joachimiak
- Department of Plant Cytology and Embryology, Jagiellonian University, Grodzka 52, 31-044 Cracow, Poland
| | - Gianni Bedini
- Department of Biology, Botany Unit, University of Pisa, via L. Ghini 5, 56126, Pisa, Italy
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27
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Bedini G, Garbari F, Peruzzi L. Chromosome number variation of the Italian endemic vascular flora. State-of-the-art, gaps in knowledge and evidence for an exponential relationship among even ploidy levels. COMPARATIVE CYTOGENETICS 2012; 6:192-211. [PMID: 24260662 PMCID: PMC3833792 DOI: 10.3897/compcytogen.v6i2.3107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/17/2012] [Indexed: 06/01/2023]
Abstract
The Italian endemic vascular flora is composed of 1,286 specific and subspecific taxa. From the critical analysis of "Chrobase.it", 711 of them (about 55%) have been studied from a karyological point of view. These taxa belong to 52 out of 56 families and 204 out of 284 genera. These data suggest that endemic species are more studied than the flora as a whole. Mean chromosome number for Italian endemics is 2n = 30.68 ± 20.27 (median: 2n = 26, mode: 2n = 18). These values are very close to those known for the whole flora. Similar variation ranges, among endemics and species with wider distribution, are likely to reflect similar evolutionary trends. Known chromosome numbers in Italian endemics range from 2n = 8 to 2n = 182. About 9% of taxa show more than one cytotype and the frequency of Bs in the Italian endemic vascular flora is 3.3%. These values are slightly smaller compared with the whole Italian flora. Finally, for the basic chromosome numbers x = 7, 8, 9, the proportion of diploids (2n = 2x) to even polyploids (2n = 4x, 6x, 8x and 10x) can be described by the exponential function f(p) = e((5.539 - 0.637p)) (R(2) = 0.984).
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Affiliation(s)
- Gianni Bedini
- Dipartimento di Biologia, Unità di Botanica generale e sistematica, Università di Pisa, via Luca Ghini 5, 56126, Pisa, Italy
| | - Fabio Garbari
- Dipartimento di Biologia, Unità di Botanica generale e sistematica, Università di Pisa, via Luca Ghini 5, 56126, Pisa, Italy
| | - Lorenzo Peruzzi
- Dipartimento di Biologia, Unità di Botanica generale e sistematica, Università di Pisa, via Luca Ghini 5, 56126, Pisa, Italy
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