1
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Zhou R, Qin X, Hou J, Liu Y. Research progress on Brassicaceae plants: a bibliometrics analysis. Front Plant Sci 2024; 15:1285050. [PMID: 38357268 PMCID: PMC10864531 DOI: 10.3389/fpls.2024.1285050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
The Brassicaceae is a worldwide family that produces ornamental flowers, edible vegetables, and oilseed plants, with high economic value in agriculture, horticulture, and landscaping. This study used the Web of Science core dataset and the CiteSpace bibliometric tool to quantitatively visualize the number of publications, authors, institutions, and countries of 3139 papers related to Brassicaceae plants from 2002 to 2022. The keywords and references were divided into two phases: Phase 1 (2002-2011) and Phase 2 (2012-2022) for quantitative and qualitative analysis. The results showed: An average annual publication volume of 149 articles, with an overall fluctuating upward trend; the research force was mainly led by Professor Ihsan A. Al-shehbaz from Missouri Botanical Garden; and the United States had the highest number of publications. In the first phase, research focused on the phylogeny of Brassicaceae plants, while the second phase delved into diverse research based on previous studies, research in areas such as polyploidy, molecular technique, physiology, and hyperaccumulator has been extended. Based on this research, we propounded some ideas for future studies on Brassicaceae plants and summarized the research gaps.
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Affiliation(s)
- Ruixue Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xinsheng Qin
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Junjun Hou
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yining Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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2
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Shen F, Xu S, Shen Q, Bi C, Lysak MA. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits. Nat Commun 2023; 14:4102. [PMID: 37491530 PMCID: PMC10368706 DOI: 10.1038/s41467-023-39800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/29/2023] [Indexed: 07/27/2023] Open
Abstract
Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMOGS-OX, IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qi Shen
- Genome Research Center, Leeuwenhoek Biotechnology Inc., Hong Kong, China
- Shangji Biotechnology Inc., Tianjin, China
- PheniX, Plant Phenomics Research Centre, Nanjing Agricultural University, Nanjing, China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Martin A Lysak
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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3
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. New Phytol 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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4
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Weiss-Schneeweiss H, Jang TS. Formamide-Free Genomic In Situ Hybridization (ff-GISH). Methods Mol Biol 2023; 2672:257-264. [PMID: 37335482 DOI: 10.1007/978-1-0716-3226-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization allows for the mapping of various sequence types in the genomes and is thus widely used in structural, functional, and evolutionary studies. One particular type of in situ hybridization that specifically allows to map whole parental genomes in diploid and polyploid hybrids is genomic in situ hybridization (GISH). The efficiency of GISH, i.e., the specificity of hybridization of genomic DNA probes to the parental subgenomes in hybrids depends, among others, on the age of the polyploids and the similarity of the parental genomes, specifically their repetitive DNA fractions. Typically, high levels of overall repeat similarity between the parental genomes result in lower efficiency of GISH. Here, we present the formamide-free GISH (ff-GISH) protocol that can be applied to diploid and polyploid hybrids of both monocots and dicots. ff-GISH allows higher efficiency of the labeling of the putative parental genomes compared to the standard GISH protocol and allows discrimination of parental chromosome sets that share up to 80-90% repeat similarity. This modified method is nontoxic, is simple, and lends itself to modifications. It can also be used for standard FISH and mapping of individual sequence types in chromosomes/genomes.
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Affiliation(s)
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
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5
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Wang Y, Chen Y, Wei Q, Chen X, Wan H, Sun C. Characterization of repetitive sequences in Dendrobium officinale and comparative chromosomal structures in Dendrobium species using FISH. Gene 2022; 846:146869. [PMID: 36075328 DOI: 10.1016/j.gene.2022.146869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Tandem repeats are one of the most conserved features in the eukaryote genomes. Dendrobium is the third largest genus in family Orchidaceae compromising over 1,200 species. However, the organization of repetitive sequences in Dendrobium species remains unclear. In this study, we performed the identification and characterization of the tandem repeats in D. officinale genome using graph-based clustering and Fluorescence in situ hybridization (FISH). Six major clusters including five satellite DNAs (DofSat1-5) and one 5S rDNA repeat (Dof5S) were identified as tandem repeats. The tandem organization of DofSat5 was verified by PCR amplification and southern blotting. The chromosomal locations of the repetitive DNAs in D. officinale were investigated by FISH using the tandem repeats and oligos probes. The results showed that each of the DofSat5, 5S and 45S rDNA had one pair of strong signals on D. officinale chromosomes. The distribution of repetitive DNAs along chromosomes was also investigated based on genomic in situ hybridization (GISH) among four Dendrobium species. The results suggested complex chromosomal fusion/segmentation and rearrangements during the evolution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differentiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.
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Affiliation(s)
- Yunzhu Wang
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yue Chen
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyang Chen
- Seed Management Terminal of Zhejiang, Hangzhou 310021, China.
| | - Hongjian Wan
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Chongbo Sun
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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6
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Ru Y, Mandáková TM, Lysak MA, Koch MA. The evolutionary history of Cardamine bulbifera shows a successful rapid postglacial Eurasian range expansion in the absence of sexual reproduction. Ann Bot 2022; 130:245-263. [PMID: 35789248 PMCID: PMC9445599 DOI: 10.1093/aob/mcac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Sexual reproduction is known to drive plant diversification and adaptation. Here we investigate the evolutionary history and spatiotemporal origin of a dodecaploid (2n = 12x = 96) Eurasian deciduous woodland species, Cardamine bulbifera, which reproduces and spreads via vegetative bulb-like structures only. The species has been among the most successful range-expanding understorey woodland plants in Europe, which raises the question of the genetic architecture of its gene pool, since its hexaploid (2n = 6x = 48) but putatively outcrossing closest relative, C. quinquefolia, displays a smaller distribution range in Eastern Europe towards the Caucasus region. Cardamine bulbifera belongs to a small monophyletic clade of four species comprising also C. abchasica (2n = 2x = 16) and C. bipinnata (unknown ploidy) from the Caucasus region. METHODS We sequenced the genomes of the two polyploids and their two putative ancestors using Illumina short-read sequencing technology (×7-8 coverage). Covering the entire distribution range, genomic data were generated for 67 samples of the two polyploids (51 samples of C. bulbifera, 16 samples of C. quinquefolia) and 6 samples of the putative diploid taxa (4 samples of C. abchasica, 2 samples of C. bipinnata) to unravel the evolutionary origin of the polyploid taxa using phylogenetic reconstructions of biparentally and maternally inherited genetic sequence data. Ploidy levels of C. bulbifera and C. quinquefolia were analysed by comparative chromosome painting. We used genetic assignment analysis (STRUCTURE) and approximate Bayesian computation (ABC) modelling to test whether C. bulbifera represents genetically differentiated lineages and addressed the hypothesis of its hybrid origin. Comparative ecological modelling was applied to unravel possible niche differentiation among the two polyploid species. KEY RESULTS Cardamine bulbifera was shown to be a non-hybridogenous, auto-dodecaploid taxon of early Pleistocene origin, but with a history of past gene flow with its hexaploid sister species C. quinquefolia, likely during the last glacial maximum in shared refuge areas in Eastern Europe towards Western Turkey and the Crimean Peninsula region. The diploid Caucasian endemic C. abchasica is considered an ancestral species, which also provides evidence for the origin of the species complex in the Caucasus region. Cardamine bulbifera successfully expanded its distribution range postglacially towards Central and Western Europe accompanied by a transition to exclusively vegetative propagation. CONCLUSIONS A transition to vegetative propagation in C. bulbifera is hypothesized as the major innovation to rapidly expand its distribution range following postglacially progressing woodland vegetation throughout Europe. Preceding and introgressive gene flow from its sister species C. quinquefolia in the joint refuge area is documented. This transition and ecological differentiation may have been triggered by preceding introgressive gene flow from its sister species in the joint East European refuge areas.
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Affiliation(s)
- Yalu Ru
- Centre for Organismal Studies Heidelberg (COS), Department of Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Terezie M Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
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7
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Han TS, Hu ZY, Du ZQ, Zheng QJ, Liu J, Mitchell-Olds T, Xing YW. Adaptive responses drive the success of polyploid yellowcresses ( Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot. Plant Divers 2022; 44:455-467. [PMID: 36187546 PMCID: PMC9512641 DOI: 10.1016/j.pld.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R. elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Zheng-Yan Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Qiang Du
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | | | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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8
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. Plants (Basel) 2022; 11:plants11020204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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9
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Bayat S, Lysak MA, Mandáková T. Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae). Plant J 2021; 108:1768-1785. [PMID: 34661331 DOI: 10.1111/tpj.15542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.
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Affiliation(s)
- Soheila Bayat
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Martin A Lysak
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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10
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Maravilla AJ, Rosato M, Rosselló JA. Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review. Plants (Basel) 2021; 10:2541. [PMID: 34834904 PMCID: PMC8621592 DOI: 10.3390/plants10112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.
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Affiliation(s)
| | | | - Josep A. Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/Quart 80, E-46008 València, Spain; (A.J.M.); (M.R.)
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11
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Watson JM, Trieb J, Troestl M, Renfrew K, Mandakova T, Fulnecek J, Shippen DE, Riha K. A hypomorphic allele of telomerase uncovers the minimal functional length of telomeres in Arabidopsis. Genetics 2021; 219:6339584. [PMID: 34849882 DOI: 10.1093/genetics/iyab126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/23/2021] [Indexed: 12/23/2022] Open
Abstract
Despite the essential requirement of telomeric DNA for genome stability, the length of telomere tracts between species substantially differs, raising the question of the minimal length of telomeric DNA necessary for proper function. Here, we address this question using a hypomorphic allele of the telomerase catalytic subunit, TERT. We show that although this construct partially restored telomerase activity to a tert mutant, telomeres continued to shorten over several generations, ultimately stabilizing at a bimodal size distribution. Telomeres on two chromosome arms were maintained at a length of 1 kb, while the remaining telomeres were maintained at 400 bp. The longest telomeres identified in this background were also significantly longer in wild-type populations, suggesting cis-acting elements on these arms either promote telomerase processivity or recruitment. Genetically disrupting telomerase processivity in this background resulted in immediate lethality. Thus, telomeres of 400 bp are both necessary and sufficient for Arabidopsis viability. As this length is the estimated minimal length for t-loop formation, our data suggest that telomeres long enough to form a t-loop constitute the minimal functional length.
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Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Johanna Trieb
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Martina Troestl
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Kyle Renfrew
- Department of Biochemistry, Texas A&M University, College Station, TX 77840, USA
| | - Terezie Mandakova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Jaroslav Fulnecek
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Dorothy E Shippen
- Department of Biochemistry, Texas A&M University, College Station, TX 77840, USA
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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12
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Zhao Q, Meng Y, Wang P, Qin X, Cheng C, Zhou J, Yu X, Li J, Lou Q, Jahn M, Chen J. Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis. Plant J 2021; 107:1243-1259. [PMID: 34160852 DOI: 10.1111/tpj.15381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 05/22/2023]
Abstract
Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo-painting (COP) allowing visualization of fine-scale genome structures of eight Cucumis species from both African-origin and Asian-origin clades. Based on COP data, an evolutionary framework containing a genus-level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n = 12) evolved to extant Cucumis genomes by hybridizations and frequent lineage- and species-specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n = 12), Cucumis hystrix (n = 12) and cucumber (Cucumis sativus, n = 7), had highly shuffled genomes caused by large-scale inversions, centromere repositioning and chromothripsis-like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere-proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.
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Affiliation(s)
- Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ya Meng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Panqiao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junguo Zhou
- College of Horticulture and landscape, Henan Institute of Science and Technology, Xinxiang, 453000, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Molly Jahn
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Oh Y, Barbey CR, Chandra S, Bai J, Fan Z, Plotto A, Pillet J, Folta KM, Whitaker VM, Lee S. Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry ( Fragaria × ananassa). Front Plant Sci 2021; 12:639345. [PMID: 34017348 PMCID: PMC8129584 DOI: 10.3389/fpls.2021.639345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/16/2021] [Indexed: 06/01/2023]
Abstract
Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, FaFAD1. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing FaFAD1, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of FaFAD1 and determined the allele dosage of FaFAD1 that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus FaFAD1 that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence-absence variation of FaFAD1 was discovered among γ-D producers and non-producers. To explore the genomic structure of FaFAD1 in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the FaFAD1 region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of FaFAD1 presence and absence polymorphism in producing γ-D and proposes that both alleles of FaFAD1 are required to produce the highest content of fruity aroma in strawberry fruit.
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Affiliation(s)
- Youngjae Oh
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Christopher R. Barbey
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Saket Chandra
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Jinhe Bai
- Horticultural Research Laboratory, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Fort Pierce, FL, United States
| | - Zhen Fan
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Anne Plotto
- Horticultural Research Laboratory, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Fort Pierce, FL, United States
| | - Jeremy Pillet
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Kevin M. Folta
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Vance M. Whitaker
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Department of Horticultural Sciences, Institute of Food and Agricultural Sciences (IFAS) Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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14
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Šlenker M, Kantor A, Marhold K, Schmickl R, Mandáková T, Lysak MA, Perný M, Caboňová M, Slovák M, Zozomová-Lihová J. Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides. Front Plant Sci 2021; 12:659275. [PMID: 33995457 PMCID: PMC8115912 DOI: 10.3389/fpls.2021.659275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/10/2021] [Indexed: 05/19/2023]
Abstract
Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
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Affiliation(s)
- Marek Šlenker
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Kantor
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin A. Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Michaela Caboňová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
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15
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Bohutínská M, Alston M, Monnahan P, Mandáková T, Bray S, Paajanen P, Kolář F, Yant L. Novelty and convergence in adaptation to whole genome duplication. Mol Biol Evol 2021; 38:3910-3924. [PMID: 33783509 PMCID: PMC8382928 DOI: 10.1093/molbev/msab096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimised in an autotetraploid (within-species polyploid) to avoid mis-segregation. Here we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 million years diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodelling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organisation, stress signalling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Mark Alston
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Patrick Monnahan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Sian Bray
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Biosciences University of Nottingham, Nottingham, UK
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Life Sciences University of Nottingham, Nottingham, UK
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16
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Akiyama R, Sun J, Hatakeyama M, Lischer HEL, Briskine RV, Hay A, Gan X, Tsiantis M, Kudoh H, Kanaoka MM, Sese J, Shimizu KK, Shimizu‐Inatsugi R. Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. New Phytol 2021; 229:3587-3601. [PMID: 33222195 PMCID: PMC7986779 DOI: 10.1111/nph.17101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/09/2020] [Indexed: 05/09/2023]
Abstract
Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
| | - Jianqiang Sun
- Research Center for Agricultural Information TechnologyNational Agriculture and Food Research Organization3‐1‐1 KannondaiTsukubaIbaraki305‐8517Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Functional Genomics Center ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Swiss Institute of BioinformaticsQuartier Sorge – Batiment GenopodeLausanneCH‐1015Switzerland
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Swiss Institute of BioinformaticsQuartier Sorge – Batiment GenopodeLausanneCH‐1015Switzerland
- Interfaculty Bioinformatics UnitUniversity of BernBaltzerstrasse 6BernCH‐3012Switzerland
| | - Roman V. Briskine
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Functional Genomics Center ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
| | - Angela Hay
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Xiangchao Gan
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Miltos Tsiantis
- Department of Comparative Development and GeneticsMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 10Köln50829Germany
| | - Hiroshi Kudoh
- Center for Ecological ResearchKyoto UniversityHirano 2‐509‐3Otsu520‐2113Japan
| | - Masahiro M. Kanaoka
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoya464‐8602Japan
| | - Jun Sese
- Humanome Lab, Inc.L‐HUB 3F1‐4, Shumomiyabi‐choShinjukuTokyo162‐0822Japan
- Artificial Intelligence Research CenterAIST2‐3‐26 AomiKoto‐kuTokyo135‐0064Japan
- AIST‐Tokyo Tech RWBC‐OIL2‐12‐1 OkayamaMeguro‐kuTokyo152‐8550Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
- Kihara Institute for Biological Research (KIBR)Yokohama City University641‐12 MaiokaTotsuka‐wardYokohama244‐0813Japan
| | - Rie Shimizu‐Inatsugi
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 190ZurichCH‐8057Switzerland
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17
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Agrawal N, Gupta M, Banga SS, Heslop-Harrison JS(P. Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries. Front Plant Sci 2020; 11:598039. [PMID: 33414797 PMCID: PMC7783396 DOI: 10.3389/fpls.2020.598039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500-1,000 kb) with 1,997-5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.
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Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - JS (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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18
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Sun J, Shimizu-Inatsugi R, Hofhuis H, Shimizu K, Hay A, Shimizu KK, Sese J. A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents. Front Genet 2020; 11:567262. [PMID: 33133153 PMCID: PMC7573311 DOI: 10.3389/fgene.2020.567262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/18/2020] [Indexed: 12/03/2022] Open
Abstract
Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.
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Affiliation(s)
- Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Hugo Hofhuis
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Humanome Lab, Inc., Tokyo, Japan
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19
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Chen H, German DA, Al-Shehbaz IA, Yue J, Sun H. Phylogeny of Euclidieae (Brassicaceae) based on plastome and nuclear ribosomal DNA data. Mol Phylogenet Evol 2020; 153:106940. [PMID: 32818597 DOI: 10.1016/j.ympev.2020.106940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 01/19/2023]
Abstract
Euclidieae, a morphologically diverse tribe in the family Brassicaceae (Cruciferae), consists of 29 genera and more than 150 species distributed mainly in Asia. Prior phylogenetic analyses on Euclidieae are inadequate. In this study, sequence data from the plastid genome and nuclear ribosomal DNA of 72 species in 27 genera of Euclidieae were used to infer the inter- and intra-generic relationships within. The well-resolved and strongly supported plastome phylogenies revealed that Euclidieae could be divided into five clades. Both Cymatocarpus and Neotorularia are polyphyletic in nuclear and plastome phylogenies. Besides, the conflicts of systematic positions of three species of Braya and two species of Solms-laubachia s.l. indicated that hybridization and or introgression might have happened during the evolutionary history of the tribe. Results from divergence-time analyses suggested an early Miocene origin of Euclidieae, and it probably originated from the Central Asia, Pamir Plateau and West Himalaya. In addition, multiple ndh genes loss and pseudogenization were detected in eight species based on comparative genomic study.
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Affiliation(s)
- Hongliang Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Laboratory of Systematics & Evolutionary Botany and Biodiversity, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Lenin Ave. 61, Barnaul 656049, Russia
| | | | - Jipei Yue
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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20
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Bi Y, Zhao Q, Yan W, Li M, Liu Y, Cheng C, Zhang L, Yu X, Li J, Qian C, Wu Y, Chen J, Lou Q. Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. Plant J 2020; 102:178-186. [PMID: 31692131 DOI: 10.1111/tpj.14600] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 10/09/2019] [Accepted: 10/21/2019] [Indexed: 05/07/2023]
Abstract
Chromosome painting is a powerful technique for chromosome and genome studies. We developed a flexible chromosome painting technique based on multiplex PCR of a synthetic oligonucleotide (oligo) library in cucumber (Cucumis sativus L., 2n = 14). Each oligo in the library was associated with a universal as well as nested specific primers for amplification, which allow the generation of different probes from the same oligo library. We were also able to generate double-stranded labelled oligos, which produced much stronger signals than single-stranded labelled oligos, by amplification using fluorophore-conjugated primer pairs. Oligos covering cucumber chromosome 1 (Chr1) and chromosome 4 (Chr4) consisting of eight segments were synthesized in one library. Different oligo probes generated from the library painted the corresponding chromosomes/segments unambiguously, especially on pachytene chromosomes. This technique was then applied to study the homoeologous relationships among cucumber, C. hystrix and C. melo chromosomes based on cross-species chromosome painting using Chr4 probes. We demonstrated that the probe was feasible to detect interspecies chromosome homoeologous relationships and chromosomal rearrangement events. Based on its advantages and great convenience, we anticipate that this flexible oligo-painting technique has great potential for the studies of the structure, organization, and evolution of chromosomes in any species with a sequenced genome.
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Affiliation(s)
- Yunfei Bi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenkai Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengxue Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuxi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuntao Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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21
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Akiyama R, Milosavljevic S, Leutenegger M, Shimizu-Inatsugi R. Trait-dependent resemblance of the flowering phenology and floral morphology of the allopolyploid Cardamine flexuosa to those of the parental diploids in natural habitats. J Plant Res 2020; 133:147-155. [PMID: 31925575 PMCID: PMC7026219 DOI: 10.1007/s10265-019-01164-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 12/08/2019] [Indexed: 05/24/2023]
Abstract
Allopolyploids possess complete sets of genomes derived from different parental species and exhibit a range of variation in various traits. Reproductive traits may play a key role in the reproductive isolation between allopolyploids and their parental species, thus affecting the thriving of allopolyploids. However, empirical data, especially in natural habitats, comparing reproductive trait variation between allopolyploids and their parental species remain rare. Here, we documented the flowering phenology and floral morphology of the allopolyploid wild plant Cardamine flexuosa and its diploid parents C. amara and C. hirsuta in their native range in Switzerland. The flowering of C. flexuosa started at an intermediate time compared with those of the parents and the flowering period of C. flexuosa overlapped with those of the parents. Cardamine flexuosa resembled C. hirsuta in the size of flowers and petals and the length/width ratio of petals, while it resembled C. amara in the length/width ratio of flowers. These results provide empirical evidence of the trait-dependent variation of allopolyploid phenotypes in natural habitats at the local scale. They also suggest that the variation in some reproductive traits in C. flexuosa is associated with self-fertilization. Therefore, it is helpful to consider the mating system in furthering the understanding of the processes that may have shaped trait variation in polyploids in nature.
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Stefan Milosavljevic
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Matthias Leutenegger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrase 190, 8057, Zurich, Switzerland.
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22
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Garcia S, Wendel JF, Borowska-Zuchowska N, Aïnouche M, Kuderova A, Kovarik A. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. Front Plant Sci 2020; 11:41. [PMID: 32117380 PMCID: PMC7025596 DOI: 10.3389/fpls.2020.00041] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. RESULTS (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. CONCLUSION We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Jonathan F. Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States
| | - Natalia Borowska-Zuchowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France
| | - Alena Kuderova
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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23
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Šimoníková D, Němečková A, Karafiátová M, Uwimana B, Swennen R, Doležel J, Hřibová E. Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana ( Musa Spp.). Front Plant Sci 2019; 10:1503. [PMID: 31824534 DOI: 10.3389/fpls.2019.01503/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/29/2019] [Indexed: 05/24/2023]
Abstract
Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis "DH Pahang" to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Alžbeěta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- Banana Breeding, International Institute of Tropical Agriculture, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- Banana Breeding, International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
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24
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Mandáková T, Zozomová-Lihová J, Kudoh H, Zhao Y, Lysak MA, Marhold K. The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives. Ann Bot 2019; 124:209-220. [PMID: 30868165 PMCID: PMC6758578 DOI: 10.1093/aob/mcz019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/24/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. METHODS Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. KEY RESULTS All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. CONCLUSIONS Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Judita Zozomová-Lihová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Japan
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Centre for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Martin A Lysak
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Karol Marhold
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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25
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Leostrin AV, Mayorov SR. Current State and Distribution of Alien Weedy Cardamine occulta Hornem. (Brassicaceae) in European Russia. Russ J Biol Invasions 2019. [DOI: 10.1134/s207511171903007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Šimoníková D, Němečková A, Karafiátová M, Uwimana B, Swennen R, Doležel J, Hřibová E. Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana ( Musa Spp.). Front Plant Sci 2019; 10:1503. [PMID: 31824534 PMCID: PMC6879668 DOI: 10.3389/fpls.2019.01503] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/29/2019] [Indexed: 05/04/2023]
Abstract
Oligo painting FISH was established to identify all chromosomes in banana (Musa spp.) and to anchor pseudomolecules of reference genome sequence of Musa acuminata spp. malaccensis "DH Pahang" to individual chromosomes in situ. A total of 19 chromosome/chromosome-arm specific oligo painting probes were developed and were shown to be suitable for molecular cytogenetic studies in genus Musa. For the first time, molecular karyotypes of diploid M. acuminata spp. malaccensis (A genome), M. balbisiana (B genome), and M. schizocarpa (S genome) from the Eumusa section of Musa, which contributed to the evolution of edible banana cultivars, were established. This was achieved after a combined use of oligo painting probes and a set of previously developed banana cytogenetic markers. The density of oligo painting probes was sufficient to study chromosomal rearrangements on mitotic as well as on meiotic pachytene chromosomes. This advance will enable comparative FISH mapping and identification of chromosomal translocations which accompanied genome evolution and speciation in the family Musaceae.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Alžbeěta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- Banana Breeding, International Institute of Tropical Agriculture, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- Banana Breeding, International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- *Correspondence: Eva Hřibová,
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27
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Mandáková T, Guo X, Özüdoğru B, Mummenhoff K, Lysak MA. Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years. Plant J 2018; 96:748-760. [PMID: 30101476 DOI: 10.1111/tpj.14065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 05/22/2023]
Abstract
The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).
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Affiliation(s)
- Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Xinyi Guo
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
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28
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Mccann J, Jang TS, Macas J, Schneeweiss GM, Matzke NJ, Novák P, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae). Syst Biol 2018; 67:1010-1024. [PMID: 29562303 PMCID: PMC6193527 DOI: 10.1093/sysbio/syy024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 02/17/2018] [Accepted: 03/15/2018] [Indexed: 12/04/2022] Open
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multispecies coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, Melampodium strigosum, and its two allohexaploid derivatives, Melampodium pringlei and Melampodium sericeum, which share both parentage and the direction of the cross, to the Pleistocene ($<$1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids' genomes. The repetitive elements most affected by the postpolyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
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Affiliation(s)
- Jamie Mccann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Jiři Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, Czech Republic
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
- Herbarium and Department of Evolution, Ecology and Organismal Biology, 1315 Kinnear Road, The Ohio State University, Columbus, Ohio, USA
| | - José L Villaseñor
- Department of Botany, UNAM, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, MX-04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
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29
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He L, Braz GT, Torres GA, Jiang J. Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 2018; 127:505-513. [PMID: 30242479 DOI: 10.1007/s00412-018-0682-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
Analysis of chromosome pairing has been an important tool to assess the genetic similarity of homologous and homoeologous chromosomes in polyploids. However, it is technically challenging to monitor the pairing of specific chromosomes in polyploid species, especially for plant species with a large number of small chromosomes. We developed oligonucleotide-based painting probes for four different potato chromosomes. We demonstrate that these probes are robust enough to monitor a single chromosome throughout the prophase I of meiosis in polyploid Solanum species. Cultivated potato (Solanum tuberosum, 2n = 4x = 48) is an autotetraploid. We demonstrate that the four copies of each potato chromosome pair as a quadrivalent in 66-78% of the meiotic cells at the pachytene stage. Solanum demissum (2n = 6x = 72) is a hexaploid and has been controversial regarding its nature as an autopolyploid or allopolyploid. Interestingly, no hexavalent pairing was observed in meiosis. Instead, we observed three independent bivalents in 83-98% of the meiotic cells at late diakinesis and early metaphase I for the four chromosomes. These results suggest that S. demissum has evolved into a cytologically stable state with predominantly bivalent pairing in meiosis.
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Affiliation(s)
- Li He
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.,Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Guilherme T Braz
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.,Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Giovana A Torres
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Grusz AL, Sigel EM, Witherup C. Homoeologous chromosome pairing across the eukaryote phylogeny. Mol Phylogenet Evol 2017; 117:83-94. [PMID: 28602622 DOI: 10.1016/j.ympev.2017.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 11/21/2022]
Abstract
During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example. Specifically, we present an overview of the breakdown of homologous chromosome pairing in model eukaryotes and provide a discussion of various meiotic aberrations that result in the failure of homolog recognition, with a particular focus on lineages with a history of hybridization and polyploidization, across major eukaryotic clades. We then explore what is known about these processes in natural and non-model eukaryotic taxa, thereby exposing disparities in our understanding of this key trait among non-model groups.
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31
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Shimizu‐Inatsugi R, Terada A, Hirose K, Kudoh H, Sese J, Shimizu KK. Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Mol Ecol 2016; 26:193-207. [DOI: 10.1111/mec.13738] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/27/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Rie Shimizu‐Inatsugi
- Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Aika Terada
- PRESTO Japan Science and Technology Agency 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
- Department of Computational Biology and Medical Science Graduate School of Frontier Sciences The University of Tokyo 5‐1‐5 Kashiwanoha Kashiwa Chiba 277‐8561 Japan
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
| | - Kyosuke Hirose
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
| | - Hiroshi Kudoh
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
| | - Jun Sese
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
- Artificial Intelligence Research Center AIST 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
- Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST) 2‐4‐7 Aomi Koto‐ku Tokyo 135‐0064 Japan
- Center for Ecological Research Kyoto University Hirano 2‐509‐3 Otsu 520‐2113 Japan
- Kihara Institute for Biological Research Yokohama City University 641‐12 Maioka, Totsuka‐ward Yokohama Kanagawa 244‐0813 Japan
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Mandáková T, Gloss AD, Whiteman NK, Lysak MA. How diploidization turned a tetraploid into a pseudotriploid. Am J Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lysak MA, Mandáková T, Schranz ME. Comparative paleogenomics of crucifers: ancestral genomic blocks revisited. Curr Opin Plant Biol 2016; 30:108-15. [PMID: 26945766 DOI: 10.1016/j.pbi.2016.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 05/03/2023]
Abstract
A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model.
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Affiliation(s)
- Martin A Lysak
- Plant Cytogenomics Group, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | - Terezie Mandáková
- Plant Cytogenomics Group, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University (WU), Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands.
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Marhold K, Šlenker M, Kudoh H, Zozomová-Lihová J. Cardamine occulta, the correct species name for invasive Asian plants previously classified as C. flexuosa, and its occurrence in Europe. PhytoKeys 2016; 62:57-72. [PMID: 27212882 PMCID: PMC4856903 DOI: 10.3897/phytokeys.62.7865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/02/2016] [Indexed: 05/24/2023]
Abstract
The nomenclature of Eastern Asian populations traditionally assigned to Cardamine flexuosa has remained unresolved since 2006, when they were found to be distinct from the European species Cardamine flexuosa. Apart from the informal designation "Asian Cardamine flexuosa", this taxon has also been reported under the names Cardamine flexuosa subsp. debilis or Cardamine hamiltonii. Here we determine its correct species name to be Cardamine occulta and present a nomenclatural survey of all relevant species names. A lectotype and epitype for Cardamine occulta and a neotype for the illegitimate name Cardamine debilis (replaced by Cardamine flexuosa subsp. debilis and Cardamine hamiltonii) are designated here. Cardamine occulta is a polyploid weed that most likely originated in Eastern Asia, but it has also been introduced to other continents, including Europe. Here data is presented on the first records of this invasive species in European countries. The first known record for Europe was made in Spain in 1993, and since then its occurrence has been reported from a number of European countries and regions as growing in irrigated anthropogenic habitats, such as paddy fields or flower beds, and exceptionally also in natural communities such as lake shores.
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Affiliation(s)
- Karol Marhold
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha 2, Czech Republic
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia
| | - Marek Šlenker
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia
| | | | - Judita Zozomová-Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovakia
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35
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Nguepjop JR, Tossim HA, Bell JM, Rami JF, Sharma S, Courtois B, Mallikarjuna N, Sane D, Fonceka D. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids. Front Plant Sci 2016; 7:1635. [PMID: 27847512 PMCID: PMC5088615 DOI: 10.3389/fpls.2016.01635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/17/2016] [Indexed: 05/02/2023]
Abstract
Cultivated peanut and synthetics are allotetraploids (2n = 4x = 40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the 10 homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, six in a likely disomic pattern and the three remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.
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Affiliation(s)
- Joel R. Nguepjop
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Hodo-Abalo Tossim
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Joseph M. Bell
- Département de Biologie et Physiologie Végétales, Université de Yaoundé IYaoundé, Cameroon
| | - Jean-François Rami
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Brigitte Courtois
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Djibril Sane
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Senegal
| | - Daniel Fonceka
- Centre d’Etudes Régional pour I’Amélioration de I’Adaptation à la SécheresseThies, Senegal
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
- *Correspondence: Daniel Fonceka,
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Wicker T, Wing RA, Schubert I. Recurrent sequence exchange between homeologous grass chromosomes. Plant J 2015; 84:747-59. [PMID: 26408412 DOI: 10.1111/tpj.13040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 05/10/2023]
Abstract
All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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Jang TS, Weiss-Schneeweiss H. Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids. Cytogenet Genome Res 2015; 146:325-31. [PMID: 26492445 DOI: 10.1159/000441210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH.
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Affiliation(s)
- Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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38
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Vallejo-Marín M, Buggs RJA, Cooley AM, Puzey JR. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 2015; 69:1487-1500. [PMID: 25929999 PMCID: PMC5033005 DOI: 10.1111/evo.12678] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
Whole genome duplication (polyploidization) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high‐depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington, 99362
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23185
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Chester M, Riley RK, Soltis PS, Soltis DE. Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae). Heredity (Edinb) 2015; 114:309-17. [PMID: 25370212 PMCID: PMC4815575 DOI: 10.1038/hdy.2014.101] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 12/16/2022] Open
Abstract
Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allopolyploids in nature. In this study we assess chromosomal composition in a natural neoallotetraploid, Tragopogon mirus, and compare it with T. miscellus, which is an allotetraploid of similar age (~40 generations old). We also assess whether parental gene losses in T. mirus correlate with entire or partial chromosome losses. Of 37 T. mirus individuals that were karyotyped, 23 (62%) were chromosomally additive of the parents, whereas the remaining 14 individuals (38%) had aneuploid compositions. The proportion of additive versus aneuploid individuals differed from that found previously in T. miscellus, in which aneuploidy was more common (69%; Fisher's exact test, P=0.0033). Deviations from parental chromosome additivity within T. mirus individuals also did not reach the levels observed in T. miscellus, but similar compensated changes were observed. The loss of T. dubius-derived genes in two T. mirus individuals did not correlate with any chromosomal changes, indicating a role for smaller-scale genetic alterations. Overall, these data for T. mirus provide a second example of prolonged chromosomal instability in natural neoallopolyploid populations.
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Affiliation(s)
- M Chester
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - R K Riley
- Department of Biology, University of Florida, Gainesville, FL, USA
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - P S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - D E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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Kolář F, Lučanová M, Záveská E, Fuxová G, Mandáková T, Španiel S, Senko D, Svitok M, Kolník M, Gudžinskas Z, Marhold K. Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of theArabidopsis arenosagroup (Brassicaceae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12479] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Filip Kolář
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
- Institute of Botany; Academy of Sciences of the Czech Republic; Zámek 1 CZ-252 43 Průhonice Czech Republic
| | - Magdalena Lučanová
- Institute of Botany; Academy of Sciences of the Czech Republic; Zámek 1 CZ-252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Eliška Záveská
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Gabriela Fuxová
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Terezie Mandáková
- Plant Cytogenomics Research Group; Central European Institute of Technology (CEITEC); Masaryk University; Kamenice 5 CZ-62500 Brno Czech Republic
| | - Stanislav Španiel
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Dušan Senko
- Institute of Botany; Slovak Academy of Sciences; Dúbravská cesta 9 SK-845 23 Bratislava Slovak Republic
| | - Marek Svitok
- Department of Biology and General Ecology; Faculty of Ecology and Environmental Sciences; Technical University in Zvolen; T. G. Masaryka 24 SK-960 53 Zvolen Slovak Republic
- Eawag Swiss Federal Institute of Aquatic Science and Technology; Department of Aquatic Ecology, Centre of Ecology; Evolution and Biogeochemistry; Seestrasse 79 CH-6047 Kastanienbaum Switzerland
| | - Martin Kolník
- Tematínska 4 SK-91501 Nové Mesto nad Váhom Slovak Republic
| | - Zigmantas Gudžinskas
- Nature Research Centre; Institute of Botany; Laboratory of Flora and Geobotany; Žaliųjų Ežerų Str. 49 LT-08406 Vilnius Lithuania
| | - Karol Marhold
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
- Institute of Botany; Slovak Academy of Sciences; Dúbravská cesta 9 SK-845 23 Bratislava Slovak Republic
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Hay AS, Pieper B, Cooke E, Mandáková T, Cartolano M, Tattersall AD, Ioio RD, McGowan SJ, Barkoulas M, Galinha C, Rast MI, Hofhuis H, Then C, Plieske J, Ganal M, Mott R, Martinez-Garcia JF, Carine MA, Scotland RW, Gan X, Filatov DA, Lysak MA, Tsiantis M. Cardamine hirsuta: a versatile genetic system for comparative studies. Plant J 2014; 78:1-15. [PMID: 24460550 DOI: 10.1111/tpj.12447] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/14/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
A major goal in biology is to identify the genetic basis for phenotypic diversity. This goal underpins research in areas as diverse as evolutionary biology, plant breeding and human genetics. A limitation for this research is no longer the availability of sequence information but the development of functional genetic tools to understand the link between changes in sequence and phenotype. Here we describe Cardamine hirsuta, a close relative of the reference plant Arabidopsis thaliana, as an experimental system in which genetic and transgenic approaches can be deployed effectively for comparative studies. We present high-resolution genetic and cytogenetic maps for C. hirsuta and show that the genome structure of C. hirsuta closely resembles the eight chromosomes of the ancestral crucifer karyotype and provides a good reference point for comparative genome studies across the Brassicaceae. We compared morphological and physiological traits between C. hirsuta and A. thaliana and analysed natural variation in stamen number in which lateral stamen loss is a species characteristic of C. hirsuta. We constructed a set of recombinant inbred lines and detected eight quantitative trait loci that can explain stamen number variation in this population. We found clear phylogeographic structure to the genetic variation in C. hirsuta, thus providing a context within which to address questions about evolutionary changes that link genotype with phenotype and the environment.
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Affiliation(s)
- Angela S Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
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