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Ovesna J, Chrpova J, Kolarikova L, Svoboda P, Hanzalova A, Palicova J, Holubec V. Exploring Wild Hordeum spontaneum and Hordeum marinum Accessions as Genetic Resources for Fungal Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:3258. [PMID: 37765425 PMCID: PMC10534467 DOI: 10.3390/plants12183258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Crop Wild Relatives (CWRs), as potential sources of new genetic variants, are being extensively studied to identify genotypes that will be able to confer resistance to biotic stresses. In this study, a collection of barley wild relatives was assessed in the field, and their phenotypic variability was evaluated using a Barley Description List, reflecting the identified ecosites. Overall, the CWRs showed significant field resistance to various fungal diseases. To further investigate their resistance, greenhouse tests were performed, revealing that several CWRs exhibited resistance against Fusarium culmorum, Pyrenophora teres, and Puccinia hordei G.H. Otth. Additionally, to characterize the genetic diversity within the collection, DNA polymorphisms at 21 loci were examined. We successfully employed barley-specific SSR markers, confirming their suitability for identifying H. spontaneum and even H. marinum, i.e., perennial species. The SSR markers efficiently clustered the investigated collection according to species and ecotypes, similarly to the phenotypic assessment. Moreover, SSR markers associated with disease resistance revealed different alleles in comparison to those found in resistant barley cultivars. Overall, our findings highlight that this evaluated collection of CWRs represents a valuable reservoir of genetic variability and resistance genes that can be effectively utilized in breeding programs.
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Affiliation(s)
- Jaroslava Ovesna
- Crop Research Institute, 161 06 Prague, Czech Republic; (L.K.); (P.S.); (A.H.)
| | - Jana Chrpova
- Crop Research Institute, 161 06 Prague, Czech Republic; (L.K.); (P.S.); (A.H.)
| | | | | | | | | | - Vojtech Holubec
- Crop Research Institute, 161 06 Prague, Czech Republic; (L.K.); (P.S.); (A.H.)
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Kuang L, Shen Q, Chen L, Ye L, Yan T, Chen ZH, Waugh R, Li Q, Huang L, Cai S, Fu L, Xing P, Wang K, Shao J, Wu F, Jiang L, Wu D, Zhang G. The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies. PLANT COMMUNICATIONS 2022; 3:100333. [PMID: 35643085 PMCID: PMC9482977 DOI: 10.1016/j.xplc.2022.100333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/24/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.
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Affiliation(s)
- Liuhui Kuang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Lingzhen Ye
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK; The Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Qi Li
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lu Huang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Liangbo Fu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Pengwei Xing
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jiari Shao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Feibo Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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Yin B, Sun G, Sun D, Ren X. Phylogenetic analysis of two single-copy nuclear genes revealed origin of tetraploid barley Hordeum marinum. PLoS One 2020; 15:e0235475. [PMID: 32603381 PMCID: PMC7326175 DOI: 10.1371/journal.pone.0235475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/16/2020] [Indexed: 01/31/2023] Open
Abstract
Sea barley Hordeum marinum is an important germplasm resource. However, the origin of this tetraploid H. marinum subsp. gussoneanum is still unclear, which has caused great perplexity to the exploration and utilization of germplasm resources. We used two single-copy nuclear genes, thioredoxin-like gene (TRX) and waxy1 gene encoding granule-bound starch synthase (WAXY1) to analyze 41 accessions of Hordeum marinum. The phylogenies of different genes told different story of evolution of tetraploids of H. marinum subsp. gussoneanum. The phylogenetic trees showed that two distinct copies of sequences from both genes were detected for some accessions of the tetraploids of H. marinum subsp. gussoneanum, and diploid marinum might also contribute to the origin and evolution of the tetraploid gussoneanum. Our findings suggested that tetraploid more likely originated from the diploids of H. marinum subsp. gussoneanum and another ancestor that might be an extinct unknown diploid species. Homogenization of gene in tetraploids also occurred after polyploidization as both TRX and WAXY1 sequences in some accessions of tetraploid H. marinum subsp. gussoneanum cannot be distinguished, indicating the complicated evolution of this tetraploid.
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Affiliation(s)
- Bo Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Biology Department, Saint Mary’s University, Halifax, NS, Canada
| | - Daokun Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Zhang S, Zhu M, Shang Y, Wang J, Dawadundup, Zhuang L, Zhang J, Chu C, Qi Z. Physical organization of repetitive sequences and chromosome diversity of barley revealed by fluorescence in situ hybridization (FISH). Genome 2019; 62:329-339. [PMID: 30933665 DOI: 10.1139/gen-2018-0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fluorescence in situ hybridization (FISH) using oligonucleotides is a simple and convenient method for chromosome research. In this study, 34 of 46 previously developed oligonucleotides produced signals in barley. Together with two plasmid clones and one PCR-amplified cereal centromere repeat (CCS1) probe, 37 repetitive sequences were chromosomally located produced three types of signals covering different positions on the chromosomes. The centromeric and pericentric regions had a more complex genomic organization and sequence composition probably indicative of higher contents of heterochromatin. An efficient multi-plex probe containing eight oligonucleotides and a plasmid clone of 45S rDNA was developed. Thirty-three barley karyotypes were developed and compared. Among them, 11 irradiation-induced mutants of cultivar 08-49 showed no chromosomal variation, whereas 22 cultivar and landrace accessions contained 28 chromosomal polymorphisms. Chromosome 4H was the most variable and 6H was the least variable based on chromosome polymorphic information content (CPIC). Five polymorphic chromosomes (1H-2, 2H-1, 3H-3, 5H-2, and 6H-2) were dominant types, each occurring in more than 50% of accessions. The multi-plex probe should facilitate identification of further chromosomal polymorphisms in barley.
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Affiliation(s)
- Siyu Zhang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Minqiu Zhu
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.,b Changshu Institute of Technology, Changshu 215500, Jiangsu, China
| | - Yi Shang
- c Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China.,d Hybrid Rapeseed Research Center of Shaanxi Province, Yangling 712100, China
| | - Jiaqi Wang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dawadundup
- e Institute of Agriculture, Tibet Academy of Agricultural and Animal Science, Lhasa 850032, China
| | - Lifang Zhuang
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlong Zhang
- f Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Chenggen Chu
- g Texas A&M Agrilife Research, Amarillo, TX 79106, USA
| | - Zengjun Qi
- a National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Yurkevich OY, Samatadze TE, Levinskikh MA, Zoshchuk SA, Signalova OB, Surzhikov SA, Sychev VN, Amosova AV, Muravenko OV. Molecular Cytogenetics of Pisum sativum L. Grown under Spaceflight-Related Stress. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4549294. [PMID: 30627557 PMCID: PMC6304655 DOI: 10.1155/2018/4549294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 11/22/2018] [Indexed: 11/17/2022]
Abstract
The ontogenesis and reproduction of plants cultivated aboard a spacecraft occur inside the unique closed ecological system wherein plants are subjected to serious abiotic stresses. For the first time, a comparative molecular cytogenetic analysis of Pisum sativum L. (Fabaceae) grown on board the RS ISS during the Expedition-14 and Expedition-16 and also plants of their succeeding (F1 and F2) generations cultivated on Earth was performed in order to reveal possible structural chromosome changes in the pea genome. The karyotypes of these plants were studied by multicolour fluorescence in situ hybridization (FISH) with five different repeated DNA sequences (45S rDNA, 5S rDNA, PisTR-B/1, microsatellite motifs (AG)12, and (GAA)9) as probes. A chromosome aberration was revealed in one F1 plant. Significant changes in distribution of the examined repeated DNAs in karyotypes of the "space grown" pea plants as well as in F1 and F2 plants cultivated on Earth were not observed if compared with control plants. Additional oligo-(GAA)9 sites were detected on chromosomes 6 and 7 in karyotypes of F1 and F2 plants. The detected changes might be related to intraspecific genomic polymorphism or plant cell adaptive responses to spaceflight-related stress factors. Our findings suggest that, despite gradual total trace contamination of the atmosphere on board the ISS associated with the extension of the space station operating life, exposure to the space environment did not induce serious chromosome reorganizations in genomes of the "space grown" pea plants and generations of these plants cultivated on Earth.
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Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga B. Signalova
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir N. Sychev
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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7
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Cuadrado Á, de Bustos A, Jouve N. On the allopolyploid origin and genome structure of the closely related species Hordeum secalinum and Hordeum capense inferred by molecular karyotyping. ANNALS OF BOTANY 2017; 120:245-255. [PMID: 28137705 PMCID: PMC5737408 DOI: 10.1093/aob/mcw270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/28/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS To provide additional information to the many phylogenetic analyses conducted within Hordeum , here the origin and interspecific affinities of the allotetraploids Hordeum secalinum and Hordeum capense were analysed by molecular karyotyping. METHODS Karyotypes were determined using genomic in situ hybridization (GISH) to distinguish the sub-genomes and , plus fluorescence in situ hybridization (FISH)/non-denaturing (ND)-FISH to determine the distribution of ten tandem repetitive DNA sequences and thus provide chromosome markers. KEY RESULTS Each chromosome pair in the six accessions analysed was identified, allowing the establishment of homologous and putative homeologous relationships. The low-level polymorphism observed among the H. secalinum accessions contrasted with the divergence recorded for the sub-genome of the H. capense accessions. Although accession H335 carries an intergenomic translocation, its chromosome structure was indistinguishable from that of H. secalinum . CONCLUSION Hordeum secalinum and H. capense accession H335 share a hybrid origin involving Hordeum marinum subsp. gussoneanum as the genome donor and an unidentified genome progenitor. Hordeum capense accession BCC2062 either diverged, with remodelling of the sub-genome, or its genome was donated by a now extinct ancestor. A scheme of probable evolution shows the intricate pattern of relationships among the Hordeum species carrying the genome (including all H. marinum taxa and the hexaploid Hordeum brachyantherum ).
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Affiliation(s)
- Ángeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcalá, 28871 Alcalá de Henares (Madrid), Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotechnology, University of Alcalá, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnology, University of Alcalá, 28871 Alcalá de Henares (Madrid), Spain
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Dou Q, Liu R, Yu F. Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae). COMPARATIVE CYTOGENETICS 2016; 10:465-481. [PMID: 28123672 PMCID: PMC5240503 DOI: 10.3897/compcytogen.v10i4.9666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 05/29/2023]
Abstract
Molecular karyotypes of Hordeum bogdanii Wilensky, 1918 (2n = 14), and Hordeum brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28), were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat) motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of Hordeum bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in Hordeum brevisubulatum. Although the distribution of repeats in the chromosomes of Hordeum brevisubulatum is different from that of Hordeum bogdanii, similar patterns between the two species imply that the autopolyploid origin of Hordeum brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.
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Affiliation(s)
- Quanwen Dou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Ruijuan Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Feng Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
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Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 2016; 24:231-42. [DOI: 10.1007/s10577-016-9518-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/31/2016] [Accepted: 02/01/2016] [Indexed: 01/05/2023]
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10
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Carmona A, de Bustos A, Jouve N, Cuadrado Á. Allopolyploidy and the complex phylogenetic relationships within the Hordeum brachyantherum taxon. Mol Phylogenet Evol 2016; 97:107-119. [PMID: 26790585 DOI: 10.1016/j.ympev.2016.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
Abstract
Hordeum brachyantherum Nevski includes two subspecies: the diploid (2×) subsp. californicum, and subsp. brachyantherum, which itself includes a tetraploid (4×) and a hexaploid (6×) cytotype. The phylogenetic relationships between these taxa and the origin of the polyploids remain controversial. To provide additional information to the many molecular phylogenetic analyses conducted within Hordeum, FISH-based karyotypes were produced for all subspecies/cytotypes within H. brachyantherum. Chromosomes of H. roshevitzii and H. marinum subsp. gussoneanum were also analysed since these species are potentially involved in the origin of the polyploids. For karyotyping, ten repetitive DNA sequences were screened to indentify repeats showing sufficient diversity in terms of copy number and localisation that they might serve as physical markers for distinguishing between each mitotic chromosome pair in all accessions. Genomic in situ hybridisation (GISH) was used to distinguish between subgenomes in polyploids. The karyotype maps allowed the assessment of the chromosomal diversity within species/cytotypes and the identification of possibly homoeologous chromosomes. The results show a wide divergence between the chromosomes of subsp. californicum and H. roshevitzii, and with their supposed derivatives in subsp. brachyantherum 4×. One of the three subgenomes of subsp. brachyantherum 6× is derived from subsp. gussoneanum with no genomic reorganisation (i.e., neither amplification nor loss of the repetitive DNA sequences analysed). It is generally accepted that subsp. brachyantherum 4× is the other progenitor of subsp. brachyantherum 6×, but the present results suggest this to be unlikely. The present findings thus show the cytogenetic diversity and genomic structure of H. brachyantherum, and reveal its complex evolutionary history, in which chromosomal diversification and allopolyploidy have played important roles.
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Affiliation(s)
- Alejandro Carmona
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Ángeles Cuadrado
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain.
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Brassac J, Blattner FR. Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci. Syst Biol 2015; 64:792-808. [PMID: 26048340 PMCID: PMC4538882 DOI: 10.1093/sysbio/syv035] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/02/2015] [Indexed: 11/20/2022] Open
Abstract
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.
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Affiliation(s)
- Jonathan Brassac
- Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany;
| | - Frank R Blattner
- Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
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12
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Garrido-Ramos MA. Satellite DNA in Plants: More than Just Rubbish. Cytogenet Genome Res 2015; 146:153-170. [PMID: 26202574 DOI: 10.1159/000437008] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.
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Milani D, Cabral-de-Mello DC. Microsatellite organization in the grasshopper Abracris flavolineata (Orthoptera: Acrididae) revealed by FISH mapping: remarkable spreading in the A and B chromosomes. PLoS One 2014; 9:e97956. [PMID: 24871300 PMCID: PMC4037182 DOI: 10.1371/journal.pone.0097956] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/27/2014] [Indexed: 12/12/2022] Open
Abstract
With the aim of acquiring deeper knowledge about repetitive DNAs chromosomal organization in grasshoppers, we used fluorescent in situ hybridization (FISH) to map the distribution of 16 microsatellite repeats, including mono-, di-, tri- and tetra-nucleotides, in the chromosomes of the species Abracris flavolineata (Acrididae), which harbors B chromosome. FISH revealed two main patterns: (i) exclusively scattered signals, and (ii) scattered and specific signals, forming evident blocks. The enrichment was observed in both euchromatic and heterochromatic areas and only the motif (C)30 was absent in heterochromatin. The A and B chromosomes were enriched with all the elements that were mapped, being observed in the B chromosome more distinctive blocks for (GA)15 and (GAG)10. For A complement distinctive blocks were noticed for (A)30, (CA)15, (CG)15, (GA)15, (CAC)10, (CAA)10, (CGG)10, (GAA)10, (GAC)10 and (GATA)8. These results revealed an intense spreading of microsatellites in the A. flavolineata genome that was independent of the A+T or G+C enrichment in the repeats. The data indicate that the microsatellites compose the B chromosome and could be involved in the evolution of this element in this species, although no specific relationship with any A chromosome was observed to discuss about its origin. The systematic analysis presented here contributes to the knowledge of repetitive DNA chromosomal organization among grasshoppers including the B chromosomes.
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Affiliation(s)
- Diogo Milani
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro, São Paulo, Brazil
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