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Teixeira GA, de Aguiar HJAC, Petitclerc F, Orivel J, Lopes DM, Barros LAC. Evolutionary insights into the genomic organization of major ribosomal DNA in ant chromosomes. INSECT MOLECULAR BIOLOGY 2021; 30:340-354. [PMID: 33586259 DOI: 10.1111/imb.12699] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The major rDNA genes are composed of tandem repeats and are part of the nucleolus organizing regions (NORs). They are highly conserved and therefore useful in understanding the evolutionary patterns of chromosomal locations. The evolutionary dynamics of the karyotype may affect the organization of rDNA genes within chromosomes. In this study, we physically mapped 18S rDNA genes in 13 Neotropical ant species from four subfamilies using fluorescence in situ hybridization. Furthermore, a survey of published rDNA cytogenetic data for 50 additional species was performed, which allowed us to detect the evolutionary patterns of these genes in ant chromosomes. Species from the Neotropical, Palearctic, and Australian regions, comprising a total of 63 species from 19 genera within six subfamilies, were analysed. Most of the species (48 out of 63) had rDNA genes restricted to a single chromosome pair in their intrachromosomal regions. The position of rDNA genes within the chromosomes appears to hinder their dispersal throughout the genome, as translocations and ectopic recombination are uncommon in intrachromosomal regions because they can generate meiotic abnormalities. Therefore, rDNA genes restricted to a single chromosome pair seem to be a plesiomorphic feature in ants, while multiple rDNA sites, observed in distinct subfamilies, may have independent origins in different genera.
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Affiliation(s)
- G A Teixeira
- Programa de Pós-graduação em Biologia Celular e Estrutural, Universidade Federal de Viçosa, Viçosa, Brazil
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - H J A C de Aguiar
- Universidade Federal do Amapá, Campus Binacional, BR 156, n° 3051, Bairro Universidade, Oiapoque, 68980-000, Brazil
| | - F Petitclerc
- CNRS, UMR EcoFoG, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - J Orivel
- CNRS, UMR EcoFoG, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - D M Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - L A C Barros
- Universidade Federal do Amapá, Campus Binacional, BR 156, n° 3051, Bairro Universidade, Oiapoque, 68980-000, Brazil
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52
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Schubert I. Boon and Bane of DNA Double-Strand Breaks. Int J Mol Sci 2021; 22:ijms22105171. [PMID: 34068283 PMCID: PMC8153287 DOI: 10.3390/ijms22105171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs), interrupting the genetic information, are elicited by various environmental and endogenous factors. They bear the risk of cell lethality and, if mis-repaired, of deleterious mutation. This negative impact is contrasted by several evolutionary achievements for DSB processing that help maintaining stable inheritance (correct repair, meiotic cross-over) and even drive adaptation (immunoglobulin gene recombination), differentiation (chromatin elimination) and speciation by creating new genetic diversity via DSB mis-repair. Targeted DSBs play a role in genome editing for research, breeding and therapy purposes. Here, I survey possible causes, biological effects and evolutionary consequences of DSBs, mainly for students and outsiders.
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Affiliation(s)
- Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, D-06466 Seeland, Germany
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53
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Flynn JM, Long M, Wing RA, Clark AG. Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis. Mol Biol Evol 2021; 37:1362-1375. [PMID: 31960929 DOI: 10.1093/molbev/msaa010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The factors that drive the rapid changes in abundance of tandem arrays of highly repetitive sequences, known as satellite DNA, are not well understood. Drosophila virilis has one of the highest relative amounts of simple satellites of any organism that has been studied, with an estimated >40% of its genome composed of a few related 7-bp satellites. Here, we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the highly abundant AAACTAC satellite family arose from a related satellite in the branch leading to the virilis phylad 4.5-11 Ma before exploding in abundance in some species of the clade. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. By analyzing multiple strains of D. virilis, we saw that the abundances of two centromere-proximal satellites are anticorrelated along a geographical gradient, which we suggest could be caused by ongoing conflicts at the centromere. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes including selection, meiotic drive, and constraints on satellite sequence and abundance.
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Rod A Wing
- School of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
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54
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Rifkin JL, Beaudry FEG, Humphries Z, Choudhury BI, Barrett SCH, Wright SI. Widespread Recombination Suppression Facilitates Plant Sex Chromosome Evolution. Mol Biol Evol 2021; 38:1018-1030. [PMID: 33095227 PMCID: PMC7947811 DOI: 10.1093/molbev/msaa271] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with preexisting recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant Rumex hastatulus. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographic range. We identified the shared and neo-sex chromosomes using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosomes are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homolog indicates that low recombination rates mainly preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing by repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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55
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Ta TD, Waminal NE, Nguyen TH, Pellerin RJ, Kim HH. Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna. Genes Genomics 2021; 43:237-249. [PMID: 33655486 PMCID: PMC7966213 DOI: 10.1007/s13258-021-01051-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2n = 28, but dysploid species like Senna tora have also been observed. OBJECTIVE To understand the dynamics of these TRs and their impact on S. tora dysploidization. METHODS We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships. RESULTS Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora, but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea. StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora, was either absent or localized at the subtelomeric or pericentromeric regions in other species. CONCLUSIONS These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in "carrying" repeats during genome reshuffling.
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Affiliation(s)
- Thanh Dat Ta
- Department of Chemistry and Life Science, Bioscience Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Chemistry and Life Science, Bioscience Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Thi Hong Nguyen
- Department of Chemistry and Life Science, Bioscience Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Chemistry and Life Science, Bioscience Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyun Hee Kim
- Department of Chemistry and Life Science, Bioscience Institute, Sahmyook University, Seoul, 01795, Republic of Korea.
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56
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Kim NS. Advancement of chromosome science in the genomics era. Genes Genomics 2021; 43:195-198. [PMID: 33630270 PMCID: PMC7905199 DOI: 10.1007/s13258-021-01058-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 12/04/2022]
Affiliation(s)
- Nam-Soo Kim
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Korea.
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57
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Xiong Z, Gaeta RT, Edger PP, Cao Y, Zhao K, Zhang S, Pires JC. Chromosome inheritance and meiotic stability in allopolyploid Brassica napus. G3-GENES GENOMES GENETICS 2021; 11:6044140. [PMID: 33704431 PMCID: PMC8022990 DOI: 10.1093/g3journal/jkaa011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022]
Abstract
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A–C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors were non-uniformly distributed across the genome in resynthesized B. napus, and in particular homoeologs sharing synteny along their entire length exhibited multivalents at diakinesis and polysomic inheritance at telophase I. Natural B. napus appeared to resolve meiotic errors mainly by suppressing homoeologous pairing, resolving nonhomologous centromere associations and 45S rDNA associations before diakinesis, and reducing homoeologous cross-overs.
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Affiliation(s)
- Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China.,Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Robert T Gaeta
- Bayer's Crop Science Division, Chesterfield, MO 63017, USA
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Department of Horticulture, Michigan State University, East Lansing, MI 48823, USA
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - Siqi Zhang
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, PR China
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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58
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Chromosome change and karyotype differentiation–implications in speciation and plant systematics. THE NUCLEUS 2021. [DOI: 10.1007/s13237-020-00343-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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59
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Waminal NE, Pellerin RJ, Kang SH, Kim HH. Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy. FRONTIERS IN PLANT SCIENCE 2021; 12:629898. [PMID: 33643358 PMCID: PMC7902697 DOI: 10.3389/fpls.2021.629898] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 05/16/2023]
Abstract
Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7-5,833 bp and 325-2.89 × 106, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.
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Affiliation(s)
- Nomar Espinosa Waminal
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
| | - Remnyl Joyce Pellerin
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Hyun Hee Kim
- Department of Chemistry and Life Science, BioScience Institute, Sahmyook University, Seoul, South Korea
- *Correspondence: Hyun Hee Kim
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60
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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. FRONTIERS IN PLANT SCIENCE 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] [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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61
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Ferraz ME, Fonsêca A, Pedrosa-Harand A. Multiple and independent rearrangements revealed by comparative cytogenetic mapping in the dysploid Leptostachyus group (Phaseolus L., Leguminosae). Chromosome Res 2020; 28:395-405. [PMID: 33191473 DOI: 10.1007/s10577-020-09644-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 10/23/2022]
Abstract
Polyploidy and dysploidy have been reported as the main events in karyotype evolution of plants. In the genus Phaseolus L. (2n = 22), a small monophyletic group of three species, the Leptostachyus group, presents a dysploid karyotype with 2n = 20. It was shown in Phaseolus leptostachyus that the dysploidy was caused by a nested chromosome fusion (NCF) accompanied by several translocations, suggesting a high rate of karyotype evolution in the group. To verify if this karyotype restructuring was a single event or occurred progressively during the evolution of this group, we analysed P. macvaughii, sister to Phaseolus micranthus + P. leptostachyus. Twenty-four genomic clones of P. vulgaris previously mapped on P. leptostachyus, in addition to the 5S and 35S rDNA probes, were used for fluorescence in situ hybridization. Only a single rearrangement was common to the two species: the nested chromosome fusion (NCF) involving chromosomes 10 and 11. The translocation of chromosome 2 is not the same found in P. leptostachyus, and pericentric inversions in chromosomed 3 and 4 were exclusive of P. macvaughii. The other rearrangements observed in P. leptostachyus were not shared with this species, suggesting that they occurred after the separation of these lineages. The presence of private rearrangements indicates a progressive accumulation of karyotype changes in the Leptostachyus group instead of an instant genome-wide repatterning.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Artur Fonsêca
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil.
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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63
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Carta A, Bedini G, Peruzzi L. A deep dive into the ancestral chromosome number and genome size of flowering plants. THE NEW PHYTOLOGIST 2020; 228:1097-1106. [PMID: 32421860 DOI: 10.1111/nph.16668] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 05/22/2023]
Abstract
Chromosome number and genome variation in flowering plants have stimulated growing speculation about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal. We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 000 taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5000 taxa. Our analyses revealed an ancestral haploid chromosome number for angiosperms of n = 7, a diploid status, and an ancestral 1C of 1.73 pg. For 160 families, inferred ancestral n are provided for the first time. Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, 1C genome size also increases (or decreases) significantly in late-branching lineages. Therefore, no evidence exists of a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.
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Affiliation(s)
- Angelino Carta
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Gianni Bedini
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Lorenzo Peruzzi
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
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64
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Lukhtanov VA, Dincă V, Friberg M, Vila R, Wiklund C. Incomplete Sterility of Chromosomal Hybrids: Implications for Karyotype Evolution and Homoploid Hybrid Speciation. Front Genet 2020; 11:583827. [PMID: 33193715 PMCID: PMC7594530 DOI: 10.3389/fgene.2020.583827] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022] Open
Abstract
Heterozygotes for major chromosomal rearrangements such as fusions and fissions are expected to display a high level of sterility due to problems during meiosis. However, some species, especially plants and animals with holocentric chromosomes, are known to tolerate chromosomal heterozygosity even for multiple rearrangements. Here, we studied male meiotic chromosome behavior in four hybrid generations (F1–F4) between two chromosomal races of the Wood White butterfly Leptidea sinapis differentiated by at least 24 chromosomal fusions/fissions. Previous work showed that these hybrids were fertile, although their fertility was reduced as compared to crosses within chromosomal races. We demonstrate that (i) F1 hybrids are highly heterozygous with nearly all chromosomes participating in the formation of trivalents at the first meiotic division, and (ii) that from F1 to F4 the number of trivalents decreases and the number of bivalents increases. We argue that the observed process of chromosome sorting would, if continued, result in a new homozygous chromosomal race, i.e., in a new karyotype with intermediate chromosome number and, possibly, in a new incipient homoploid hybrid species. We also discuss the segregational model of karyotype evolution and the chromosomal model of homoploid hybrid speciation.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Magne Friberg
- Biodiversity Unit, Department of Biology, Lund University, Lund, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Zhang Z, Meng F, Sun P, Yuan J, Gong K, Liu C, Wang W, Wang X. An updated explanation of ancestral karyotype changes and reconstruction of evolutionary trajectories to form Camelina sativa chromosomes. BMC Genomics 2020; 21:705. [PMID: 33045990 PMCID: PMC7549213 DOI: 10.1186/s12864-020-07081-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/18/2020] [Indexed: 11/20/2022] Open
Abstract
Background Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage I (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa chromosomes are currently unknown. Here, we managed to adopt a telomere-centric theory proposed previously to explain the karyotype evolution in C. sativa. Results By characterizing the homology between A. lyrata and C. sativa chromosomes, we inferred ancestral diploid karyotype of C. sativa (ADK), including 7 ancestral chromosomes, and reconstructed the evolutionary trajectories leading to the formation of extant C. sativa genome. The process involved 2 chromosome fusions. We found that sub-genomes Cs-G1 and Cs-G2 may share a closer common ancestor than Cs-G3. Together with other lines of evidence from Arabidopsis, we propose that the Brassicaceae plants, even the eudicots, follow a chromosome fusion mechanism favoring end-end joining of different chromosomes, rather than a mechanism favoring the formation circular chromosomes and nested chromosome fusion preferred by the monocots. Conclusions The present work will contribute to understanding the formation of C. sativa chromosomes, providing insight into Brassicaceae karyotype evolution.
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Affiliation(s)
- Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jiaqing Yuan
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Ke Gong
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Weijie Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China. .,Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
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Liu Y, Su H, Zhang J, Shi L, Liu Y, Zhang B, Bai H, Liang S, Gao Z, Birchler JA, Han F. Rapid Birth or Death of Centromeres on Fragmented Chromosomes in Maize. THE PLANT CELL 2020; 32:3113-3123. [PMID: 32817254 PMCID: PMC7534475 DOI: 10.1105/tpc.20.00389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/17/2020] [Accepted: 08/18/2020] [Indexed: 05/04/2023]
Abstract
Comparative genomics has revealed common occurrences in karyotype evolution such as chromosomal end-to-end fusions and insertions of one chromosome into another near the centromere, as well as many cases of de novo centromeres that generate positional polymorphisms. However, how rearrangements such as dicentrics and acentrics persist without being destroyed or lost remains unclear. Here, we sought experimental evidence for the frequency and timeframe for inactivation and de novo formation of centromeres in maize (Zea mays). The pollen from plants with supernumerary B chromosomes was gamma-irradiated and then applied to normal maize silks of a line without B chromosomes. In ∼8,000 first-generation seedlings, we found many B-A translocations, centromere expansions, and ring chromosomes. We also found many dicentric chromosomes, but a fraction of these show only a single primary constriction, which suggests inactivation of one centromere. Chromosomal fragments were found without canonical centromere sequences, revealing de novo centromere formation over unique sequences; these were validated by immunolocalization with Thr133-phosphorylated histone H2A, a marker of active centromeres, and chromatin immunoprecipitation-sequencing with the CENH3 antibody. These results illustrate the regular occurrence of centromere birth and death after chromosomal rearrangement during a narrow window of one to potentially only a few cell cycles for the rearranged chromosomes to be recognized in this experimental regime.
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Affiliation(s)
- Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lindan Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Bai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi Gao
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400
| | - James A Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211-7400
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Hasterok R, Wang K, Jenkins G. Progressive refinement of the karyotyping of Brachypodium genomes. THE NEW PHYTOLOGIST 2020; 227:1668-1675. [PMID: 31774178 DOI: 10.1111/nph.16342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/05/2019] [Indexed: 05/23/2023]
Abstract
Brachypodium distachyon is a weedy grass species that is firmly established as a model for the comparative and functional genomics of temperate cereals and grasses. Its simple, nuclear genome of five chromosomes contrasts it with other relatives of the genus with different, and usually higher, basic chromosome numbers and ploidy levels. This variation in karyotypic structure affords the possibility of reconstructing evolutionary pathways that have shaped the genome structure of extant species. This Tansley insight documents how key refinements in molecular cytogenetic approaches, from simple fluorescence in situ hybridization to comparative chromosome barcoding, have enabled genome structure studies and yielded valuable information about the drivers of karyotypic reorganization and evolution in the model grass genus Brachypodium.
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Affiliation(s)
- Robert Hasterok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou Fujian, 350002, China
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Edward Llwyd Building, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK
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Beaudry FEG, Wright SI. Chromosome Evolution: Infectious Sex Chromosomes in the African Monarch Butterfly. Curr Biol 2020; 30:R657-R659. [PMID: 32516618 DOI: 10.1016/j.cub.2020.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Why do some organisms have multiple sex chromosomes? New findings in an African butterfly suggest a prominent role for a bacterial parasite.
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Affiliation(s)
- Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Silva JC, Soares FAF, Sattler MC, Clarindo WR. Repetitive sequences and structural chromosome alterations promote intraspecific variations in Zea mays L. karyotype. Sci Rep 2020; 10:8866. [PMID: 32483238 PMCID: PMC7264354 DOI: 10.1038/s41598-020-65779-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 12/02/2022] Open
Abstract
LTR-retrotransposons, knobs and structural chromosome alterations contribute to shape the structure and organization of the Zea mays karyotype. Our initial nuclear DNA content data of Z. mays accessions revealed an intraspecific variation (2 C = 2.00 pg to 2 C = 6.10 pg), suggesting differences in their karyotypes. We aimed to compare the karyotypes of three Z. mays accessions in search of the differences and similarities among them. Karyotype divergences were demonstrated among the accessions, despite their common chromosome number (2n = 20) and ancestral origin. Cytogenomic analyses showed that repetitive sequences and structural chromosome alterations play a significant role in promoting intraspecific nuclear DNA content variation. In addition, heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower nuclear 2 C value. Besides this, translocation was also observed in the short arm of chromosome 1. Differently, higher 2 C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphism involving the number and position of the 180-bp knob sequence was found among the accessions. Taken together, we provide insights on the pivotal role played by repetitive sequences and structural chromosome alterations in shaping the karyotype of Z. mays.
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Affiliation(s)
- Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil.
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
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Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol 2020; 4:820-830. [PMID: 32313176 PMCID: PMC7269912 DOI: 10.1038/s41559-020-1156-z] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/19/2020] [Indexed: 01/24/2023]
Abstract
Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.
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Affiliation(s)
- Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Alexander Brandt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Kai Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | | | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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71
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Vitales D, Álvarez I, Garcia S, Hidalgo O, Nieto Feliner G, Pellicer J, Vallès J, Garnatje T. Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae). ANNALS OF BOTANY 2020; 125:611-623. [PMID: 31697800 PMCID: PMC7103019 DOI: 10.1093/aob/mcz183] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae). METHODS Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number. KEY RESULTS By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species. CONCLUSIONS Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
- For correspondence. Email
| | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Jaume Pellicer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
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Báez M, Souza G, Guerra M. Does the chromosomal position of 35S rDNA sites influence their transcription? A survey on Nothoscordum species (Amaryllidaceae). Genet Mol Biol 2020; 43:e20180194. [PMID: 31469154 PMCID: PMC7197985 DOI: 10.1590/1678-4685-gmb-2018-0194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/21/2019] [Indexed: 11/22/2022] Open
Abstract
35S ribosomal DNA (rDNA) sites are the regions where the ribosomal genes 18S, 5.8S and 25S, responsible for the formation of the nucleoli, are found. The fact that rDNA sites have non-random distribution on chromosomes suggests that their positions may influence their transcription. To identify if the preferentially transcribed rDNA sites occupy specific position, six species (nine cytotypes) of the genus Nothoscordum were analyzed using two different techniques to impregnate the nucleolar organizer regions (NORs) with silver nitrate. Both techniques strongly stained NORs, but one of them also stained the proximal region of all chromosomes, suggesting the existence of another group of argentophilic proteins in this region. In species with rDNA sites in acrocentric and metacentric chromosomes, sites located on the short arms of the acrocentric chromosomes were preferentially activated. On the other hand, in species with rDNA sites restricted to the short arms of the acrocentrics, all of them were activated, whereas in those species with sites restricted to the terminal region of metacentric chromosomes, the frequency of active sites was always lower than expected. This indicate that, at least in Nothoscordum, the transcription of an rDNA site is influenced by its chromosomal position, and may explain, at least partially, the strongly non-random distribution of these sites in plant and animal chromosomes.
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Affiliation(s)
- Mariana Báez
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução de Plantas, Recife, PE, Brazil
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Šťáhlavský F, Forman M, Just P, Denič F, Haddad CR, Opatova V. Cytogenetics of entelegyne spiders (Arachnida, Araneae) from southern Africa. COMPARATIVE CYTOGENETICS 2020; 14:107-138. [PMID: 32194919 PMCID: PMC7066264 DOI: 10.3897/compcytogen.v14i1.48667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Spiders represent one of the most studied arachnid orders. They are particularly intriguing from a cytogenetic point of view, due to their complex and dynamic sex chromosome determination systems. Despite intensive research on this group, cytogenetic data from African spiders are still mostly lacking. In this study, we describe the karyotypes of 38 species of spiders belonging to 16 entelegyne families from South Africa and Namibia. In the majority of analysed families, the observed chromosome numbers and morphology (mainly acrocentric) did not deviate from the family-level cytogenetic characteristics based on material from other continents: Tetragnathidae (2n♂ = 24), Ctenidae and Oxyopidae (2n♂ = 28), Sparassidae (2n♂ = 42), Gnaphosidae, Trachelidae and Trochanteriidae (2n♂ = 22), and Salticidae (2n♂ = 28). On the other hand, we identified interspecific variability within Hersiliidae (2n♂ = 33 and 35), Oecobiidae (2n♂ = 19 and 25), Selenopidae (2n♂ = 26 and 29) and Theridiidae (2n♂ = 21 and 22). We examined the karyotypes of Ammoxenidae and Gallieniellidae for the first time. Their diploid counts (2n♂ = 22) correspond to the superfamily Gnaphosoidea and support their placement in this lineage. On the other hand, the karyotypes of Prodidominae (2n♂ = 28 and 29) contrast with all other Gnaphosoidea. Similarly, the unusually high diploid number in Borboropactus sp. (2n♂ = 28) within the otherwise cytogenetically uniform family Thomisidae (mainly 2n♂ = 21-24) supports molecular data suggesting a basal position of the genus in the family. The implementation of FISH methods for visualisation of rDNA clusters facilitated the detection of complex dynamics of numbers of these loci. We identified up to five loci of the 18S rDNA clusters in our samples. Three different sex chromosome systems (X0, X1X20 and X1X2X30) were also detected among the studied taxa.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Martin Forman
- Department of Genetics and Microbiology, Charles University, Faculty of Science, Viničná 5, CZ-12844 Praha, Czech Republic
| | - Pavel Just
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Filip Denič
- Department of Genetics and Microbiology, Charles University, Faculty of Science, Viničná 5, CZ-12844 Praha, Czech Republic
| | - Charles R. Haddad
- Department of Zoology and Entomology, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Vera Opatova
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, CZ-12844 Praha, Czech Republic
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74
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Teixeira GA, Barros LAC, Lopes DM, de Aguiar HJAC. Cytogenetic variability in four species of Gnamptogenys Roger, 1863 (Formicidae: Ectatomminae) showing chromosomal polymorphisms, species complex, and cryptic species. PROTOPLASMA 2020; 257:549-560. [PMID: 31813009 DOI: 10.1007/s00709-019-01451-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Gnamptogenys includes 138 described species that are widely distributed, with high diversity, in the Neotropics. Some Neotropical species have taxonomic issues, as is the case with Gnamptogenys striatula, for which morphological variations have been observed between different populations. For the ant species with taxonomic issues, classical and molecular cytogenetic studies have assisted in the resolution of these issues. Cytogenetic studies of Gnamptogenys are scarce and have only been reported for 14 taxa. These reports have rarely presented chromosomal morphology. Considering the importance of the taxonomic revision of some species, such as G. striatula, the present study cytogenetically characterized four species of Gnamptogenys: G. striatula, G. moelleri, G. regularis, and G. triangularis, discussing their phylogenetic and biogeographic characteristics. The number of chromosomes ranged from 2n = 26 to 2n = 44, with distinct karyotypes at both species and population levels. All four species presented a pair of 18S rDNA gene markers that coincided with GC-rich regions. In the case of G. striatula from the Atlantic rainforest, a chromosomal polymorphism was observed, with chromosomal translocations being the likely origin of this polymorphism. Two populations of G. striatula showed karyotype differences, thus corroborating previous morphological data indicating the existence of a species complex in this taxon. In addition, G. regularis showed a polymorphism involving a chromosome pair bearing ribosomal genes, possibly caused by unequal crossing-over. Although G. moelleri has a well-defined taxonomy, a population from the eastern Amazon rainforest presented a divergent karyotype from the Atlantic rainforest populations, suggesting the existence of a cryptic species in this taxon.
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Affiliation(s)
- Gisele Amaro Teixeira
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | | | - Denilce Meneses Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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Glombik M, Bačovský V, Hobza R, Kopecký D. Competition of Parental Genomes in Plant Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:200. [PMID: 32158461 PMCID: PMC7052263 DOI: 10.3389/fpls.2020.00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/11/2020] [Indexed: 05/17/2023]
Abstract
Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.
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Affiliation(s)
- Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Roman Hobza
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
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76
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Pellestor F, Gatinois V. Chromoanagenesis: a piece of the macroevolution scenario. Mol Cytogenet 2020; 13:3. [PMID: 32010222 PMCID: PMC6988253 DOI: 10.1186/s13039-020-0470-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/05/2020] [Indexed: 01/04/2023] Open
Abstract
Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of “Hopeful Monsters” and the “Punctuated Equilibrium”. In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,INSERM 1183 «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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77
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Sankaranarayanan SR, Ianiri G, Coelho MA, Reza MH, Thimmappa BC, Ganguly P, Vadnala RN, Sun S, Siddharthan R, Tellgren-Roth C, Dawson TL, Heitman J, Sanyal K. Loss of centromere function drives karyotype evolution in closely related Malassezia species. eLife 2020; 9:e53944. [PMID: 31958060 PMCID: PMC7025860 DOI: 10.7554/elife.53944] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species. Malassezia species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified all eight centromeres in M. sympodialis as 3-5-kb long kinetochore-bound regions that span an AT-rich core and are depleted of the canonical histone H3. Centromeres of similar sequence features were identified as CENP-A-rich regions in Malassezia furfur, which has seven chromosomes, and histone H3 depleted regions in Malassezia slooffiae and Malassezia globosa with nine chromosomes each. Analysis of synteny conservation across centromeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of chromosome number reduction from an inferred nine-chromosome ancestral state: (a) chromosome breakage followed by loss of centromere DNA and (b) centromere inactivation accompanied by changes in DNA sequence following chromosome-chromosome fusion. We propose that AT-rich centromeres drive karyotype diversity in the Malassezia species complex through breakage and inactivation.
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Affiliation(s)
- Sundar Ram Sankaranarayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Md Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Promit Ganguly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | | | - Christian Tellgren-Roth
- National Genomics Infrastructure, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala UniversityUppsalaSweden
| | - Thomas L Dawson
- Skin Research Institute Singapore, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Department of Drug Discovery, Medical University of South Carolina, School of PharmacyCharlestonUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
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Burchardt P, Buddenhagen CE, Gaeta ML, Souza MD, Marques A, Vanzela ALL. Holocentric Karyotype Evolution in Rhynchospora Is Marked by Intense Numerical, Structural, and Genome Size Changes. FRONTIERS IN PLANT SCIENCE 2020; 11:536507. [PMID: 33072141 PMCID: PMC7533669 DOI: 10.3389/fpls.2020.536507] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/21/2020] [Indexed: 05/07/2023]
Abstract
Cyperaceae is a family of Monocotyledons comprised of species with holocentric chromosomes that are associated with intense dysploidy and polyploidy events. Within this family the genus Rhynchospora has recently become the focus of several studies that characterize the organization of the holocentric karyotype and genome structures. To broaden our understanding of genome evolution in this genus, representatives of Rhynchospora were studied to contrast chromosome features, C-CMA/DAPI band distribution and genome sizes. Here, we carried out a comparative analysis for 35 taxa of Rhynchospora, and generated new genome size estimates for 20 taxa. The DNA 2C-values varied up to 22-fold, from 2C = 0.51 pg to 11.32 pg, and chromosome numbers ranged from 2n = 4 to 61. At least 37% of our sampling exhibited 2n different from the basic number x = 5, and chromosome rearrangements were also observed. A large variation in C-CMA/DAPI band accumulation and distribution was observed as well. We show that genome variation in Rhynchospora is much larger than previously reported. Phylogenetic analysis showed that most taxa were grouped in clades corresponding to previously described taxonomic sections. Basic chromosome numbers are the same within every section, however, changes appeared in all the clades. Ancestral chromosome number reconstruction revealed n = 5 as the most likely ancestral complements, but n = 10 appears as a new possibility. Chromosome evolution models point to polyploidy as the major driver of chromosome evolution in Rhynchospora, followed by dysploidy. A negative correlation between chromosome size and diploid number open the discussion for holokinetic drive-based genome evolution. This study explores relationships between karyotype differentiation and genome size variation in Rhynchospora, and contrasts it against the phylogeny of this holocentric group.
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Affiliation(s)
- Paula Burchardt
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Marcos L. Gaeta
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | - Murilo D. Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- *Correspondence: André L. L. Vanzela, ; André Marques,
| | - André L. L. Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
- *Correspondence: André L. L. Vanzela, ; André Marques,
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79
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Chmúrčiaková N, Kašný M, Orosová M. Cytogenetics of Eudiplozoon nipponicum (Monogenea, Diplozoidae): Karyotype, spermatocyte division and 18S rDNA location. Parasitol Int 2019; 76:102031. [PMID: 31770588 DOI: 10.1016/j.parint.2019.102031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 10/25/2022]
Abstract
Ectoparasitic monogeneans of the family Diplozoidae have direct and monoxenous life cycle. The cytogenetics of monogeneans in general and diplozoids in particular, is a relatively underexplored area. This is why each new detailed description of a karyotype provides significant information about the evolution of monogenean chromosomes and contributes to a better understanding of phylogenetic relationships within this group. This study offers new data on the chromosomes of Eudiplozoon nipponicum, an invasive parasite of the common carp. This species' karyotype consists of seven pairs of telocentric chromosomes (2n = 14 t). After DAPI staining, we marked heterochromatin blocks on all chromosomes in the pericentromeric region. Silver staining (AgNO3) and staining with fluorescent dye YOYO-1 revealed the presence of one large active nucleolus. Fluorescent in situ hybridization with an 18S rDNA probe revealed one cluster of ribosomal genes at the terminal part of the long arms of chromosome pair No. 7. We compared our results with studies on the phylogenetic relationships of diplozoids which applied a combination of molecular methods and classical morphological characterization and found that the results of our cytogenetic analysis are consistent with the hypothesis that E. nipponicum is more basal member of the family Diplozoidae.
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Affiliation(s)
- Nikola Chmúrčiaková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Martina Orosová
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01 Košice, Slovakia.
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80
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Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution. Int J Mol Sci 2019; 20:ijms20225557. [PMID: 31703351 PMCID: PMC6888173 DOI: 10.3390/ijms20225557] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/17/2022] Open
Abstract
The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodiumdistachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time.
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81
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Centromere repositioning causes inversion of meiosis and generates a reproductive barrier. Proc Natl Acad Sci U S A 2019; 116:21580-21591. [PMID: 31597736 PMCID: PMC6815110 DOI: 10.1073/pnas.1911745116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mutations in inner kinetochore components induce centromere repositioning without alteration in the centromeric DNA sequence, revealing a feedback mechanism underlying the high epigenetic stability of the centromere. This also provides a desirable experimental system to explore the functional significance of centromere positioning in meiosis. We discovered that in a heterozygotic meiosis, a repositioned centromere generates a reproductive barrier, suggesting a functional role of evolutionary new centromeres in speciation; furthermore, in a homozygotic meiosis, chromosomes carrying repositioned centromeres frequently undergo the 2 stages of meiotic segregation in an inverted order, demonstrating high flexibility in the meiotic process. The chromosomal position of each centromere is determined epigenetically and is highly stable, whereas incremental cases have supported the occurrence of centromere repositioning on an evolutionary time scale (evolutionary new centromeres, ENCs), which is thought to be important in speciation. The mechanisms underlying the high stability of centromeres and its functional significance largely remain an enigma. Here, in the fission yeast Schizosaccharomyces pombe, we identify a feedback mechanism: The kinetochore, whose assembly is guided by the centromere, in turn, enforces centromere stability. Upon going through meiosis, specific inner kinetochore mutations induce centromere repositioning—inactivation of the original centromere and formation of a new centromere elsewhere—in 1 of the 3 chromosomes at random. Repositioned centromeres reside asymmetrically in the pericentromeric regions and cells carrying them are competent in mitosis and homozygotic meiosis. However, when cells carrying a repositioned centromere are crossed with those carrying the original centromere, the progeny suffer severe lethality due to defects in meiotic chromosome segregation. Thus, repositioned centromeres constitute a reproductive barrier that could initiate genetic divergence between 2 populations with mismatched centromeres, documenting a functional role of ENCs in speciation. Surprisingly, homozygotic repositioned centromeres tend to undergo meiosis in an inverted order—that is, sister chromatids segregate first, and homologous chromosomes separate second—whereas the original centromeres on other chromosomes in the same cell undergo meiosis in the canonical order, revealing hidden flexibility in the perceived rigid process of meiosis.
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82
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Báez M, Vaio M, Dreissig S, Schubert V, Houben A, Pedrosa-Harand A. Together But Different: The Subgenomes of the Bimodal Eleutherine Karyotypes Are Differentially Organized. FRONTIERS IN PLANT SCIENCE 2019; 10:1170. [PMID: 31649686 PMCID: PMC6791338 DOI: 10.3389/fpls.2019.01170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Bimodal karyotypes are characterized by the presence of two sets of chromosomes of contrasting size. Eleutherine bulbosa (2n = 12) presents a bimodal karyotype with a large chromosome pair, which has a pericentric inversion in permanent heterozygosity with suppressed recombination, and five pairs of three to four times smaller chromosomes. Aiming to understand whether high copy number sequence composition differs between both chromosome sets, we investigated the repetitive DNA fraction of E. bulbosa and compared it to the chromosomal organization of the related Eleutherine latifolia species, not containing the pericentric inversion. We also compared the repetitive sequence proportions between the heteromorphic large chromosomes of E. bulbosa and between E. bulbosa and E. latifolia to understand the influence of the chromosome inversion on the dynamics of repetitive sequences. The most abundant repetitive families of the genome showed a similar chromosomal distribution in both homologs of the large pair and in both species, apparently not influenced by the species-specific inversions. The repeat families Ebusat1 and Ebusat4 are localized interstitially only on the large chromosome pair, while Ebusat2 is located in the centromeric region of all chromosomes. The four most abundant retrotransposon lineages are accumulated in the large chromosome pair. Replication timing and distribution of epigenetic and transcriptional marks differ between large and small chromosomes. The differential distribution of retroelements appears to be related to the bimodal condition and is not influenced by the nonrecombining chromosome inversions in these species. Thus, the large and small chromosome subgenomes of the bimodal Eleutherine karyotype are differentially organized and probably evolved by repetitive sequences accumulation on the large chromosome set.
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Affiliation(s)
- Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Magdalena Vaio
- Laboratory of Genetics, Department of Plant Biology, College of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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83
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Karyo-morphological consistency and heterochromatin distribution pattern in diploid and colchitetraploids of Vigna radiata and V. mungo. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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84
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Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids. Sci Rep 2019; 9:12298. [PMID: 31444367 DOI: 10.1038/s41598-019-48639-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oats. These maps greatly improve coverage from older marker systems. Seven linkage groups in the tetraploid showed much stronger homology and synteny with the A genome diploids than did the other seven, implying an allopolyploid hybrid origin of A. barbata from distinct A and B genome diploid ancestors. Inferred homeologies within A. barbata revealed that the A and B genomes are differentiated by several translocations between chromosomes within each subgenome. However, no translocation exchanges were observed between A and B genomes. Comparison to a consensus map of ACD hexaploid A. sativa (2n = 42) revealed that the A and D genomes of A. sativa show parallel rearrangements when compared to the A genomes of the diploids and tetraploids. While intergenomic translocations are well known in polyploid Avena, our results are most parsimoniously explained if translocations also occurred in the A, B and D genome diploid ancestors of polyploid Avena.
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85
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Mwathi MW, Schiessl SV, Batley J, Mason AS. "Doubled-haploid" allohexaploid Brassica lines lose fertility and viability and accumulate genetic variation due to genomic instability. Chromosoma 2019; 128:521-532. [PMID: 31377850 DOI: 10.1007/s00412-019-00720-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023]
Abstract
Microspore culture stimulates immature pollen grains to develop into plants via tissue culture and is used routinely in many crop species to produce "doubled haploids": homozygous, true-breeding lines. However, microspore culture is also often used on material that does not have stable meiosis, such as interspecific hybrids. In this case, the resulting progeny may lose their "doubled haploid" homozygous status as a result of chromosome missegregation and homoeologous exchanges. However, little is known about the frequency of these effects. We assessed fertility, meiosis and genetic variability in self-pollinated progeny sets (the MDL2 population) resulting from first-generation plants (the MDL1 population) derived from microspores of a near-allohexaploid interspecific hybrid from the cross (Brassica napus × B. carinata) × B. juncea. Allelic inheritance and copy number variation were predicted using single nucleotide polymorphism marker data from the Illumina Infinium 60K Brassica array. Seed fertility and viability decreased substantially from the MDL1 to the MDL2 generation. In the MDL2 population, 87% of individuals differed genetically from their MDL1 parent. These genetic differences resulted from novel homoeologous exchanges between chromosomes, chromosome loss and gain, and segregation and instability of pre-existing karyotype abnormalities. Novel karyotype change was extremely common, with 2.2 new variants observed per MDL2 individual. Significant differences between progeny sets in the number of novel genetic variants were also observed. Meiotic instability clearly has the potential to dramatically change karyotypes (often without detectable effects on the presence or absence of alleles) in putatively homozygous, microspore-derived lines, resulting in loss of fertility and viability.
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Affiliation(s)
- Margaret W Mwathi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Sarah V Schiessl
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Annaliese S Mason
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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Hloušková P, Mandáková T, Pouch M, Trávníček P, Lysak MA. The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing. ANNALS OF BOTANY 2019; 124:103-120. [PMID: 31220201 PMCID: PMC6676390 DOI: 10.1093/aob/mcz036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/28/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.
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Affiliation(s)
- Petra Hloušková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Milan Pouch
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
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87
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Li N, Xu C, Zhang A, Lv R, Meng X, Lin X, Gong L, Wendel JF, Liu B. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. THE NEW PHYTOLOGIST 2019; 223:979-992. [PMID: 30919978 DOI: 10.1111/nph.15820] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome-wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome-wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome-wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.
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Affiliation(s)
- Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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88
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Chakraborty A, Panda SK, Mohakud NK, Roy D, Padhi S, Koh SW, Hande MP, Banerjee B. A Child with Partial Trisomy 4 (q26 - qterminal) Resulting from Paternally Inherited Translocation (4:18) Associated with Multiple Congenital Anomalies and Death. Genome Integr 2019; 10:1. [PMID: 31160964 PMCID: PMC6540766 DOI: 10.4103/genint.genint_4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Parental balanced reciprocal translocations can result in partial aneuploidy in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and cytogenetic characterization in a 9-day-old male child with partial trisomy of chromosome 4. Karyotyping of the proband and parents was performed along with multicolor fluorescence in situ hybridization (mFISH) of paternal chromosomes. Conventional cytogenetic analysis by karyotyping showed 47,XY,der(18),t(4;18)(q26;q22),+4 in proband, and the paternal karyotype was found as 47,XY,der(18),t(4;18)(q26;q22). mFISH analysis on paternal chromosomal preparations confirmed both region and origin of the balanced translocation. In this study, karyotyping helped us to identify both numerical and structural anomalies in the proband, and mFISH helped us to confirm our cytogenetic findings. Therefore, cytogenetic screening of both partners is recommended before pregnancy to rule out or confirm the presence of any numerical or structural anomaly in one, both, or none of the partners.
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Affiliation(s)
- Abhik Chakraborty
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Santosh Kumar Panda
- Department of Paediatrics, Kalinga Institute of Medical Sciences, KIIT University, Bhubaneswar, Odisha, India
| | - Nirmal Kumar Mohakud
- Department of Paediatrics, Kalinga Institute of Medical Sciences, KIIT University, Bhubaneswar, Odisha, India
| | - Debarshi Roy
- Division of Cytogenetics, inDNA Life Sciences Private Limited, Bhubaneswar, Odisha, India
| | - Swatishree Padhi
- Division of Cytogenetics, inDNA Life Sciences Private Limited, Bhubaneswar, Odisha, India
| | - Shu Wen Koh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Birendranath Banerjee
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India.,Division of Cytogenetics, inDNA Life Sciences Private Limited, Bhubaneswar, Odisha, India
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89
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Luo X, Liu J. Fluorescence In Situ Hybridization (FISH) Analysis of the Locations of the Oligonucleotides 5S rDNA, (AGGGTTT) 3, and (TTG) 6 in Three Genera of Oleaceae and Their Phylogenetic Framework. Genes (Basel) 2019; 10:genes10050375. [PMID: 31108932 PMCID: PMC6562466 DOI: 10.3390/genes10050375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022] Open
Abstract
We report the cytogenetic map for a collection of species in the Oleaceae, and test similarities among the karyotypes relative to their known species phylogeny. The oligonucleotides 5S ribosomal DNA (rDNA), (AGGGTTT)3, and (TTG)6 were used as fluorescence in situ hybridization (FISH) probes to locate the corresponding chromosomes in three Oleaceae genera: Fraxinus pennsylvanica, Syringa oblata, Ligustrum lucidum, and Ligustrum × vicaryi. Forty-six small chromosomes were identified in four species. (AGGGTTT)3 signals were observed on almost all chromosome ends of four species, but (AGGGTTT)3 played no role in distinguishing the chromosomes but displayed intact chromosomes and could thus be used as a guide for finding chromosome counts. (TTG)6 and 5S rDNA signals discerned several chromosomes located at subterminal or central regions. Based on the similarity of the signal pattern (mainly in number and location and less in intensity) of the four species, the variations in the 5S rDNA and (TTG)6 distribution can be ordered as L. lucidum < L. × vicaryi < F. pennsylvanica < S. oblata. Variations have observed in the three genera. The molecular cytogenetic data presented here might serve as a starting point for further larger-scale elucidation of the structure of the Oleaceae genome, and comparison with the known phylogeny of Oleaceae family.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
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90
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Susek K, Bielski W, Czyż KB, Hasterok R, Jackson SA, Wolko B, Naganowska B. Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution. Genes (Basel) 2019; 10:genes10040259. [PMID: 30939837 PMCID: PMC6523792 DOI: 10.3390/genes10040259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.
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Affiliation(s)
- Karolina Susek
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, 40-032 Katowice, Poland.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
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91
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Wang Z, Wang J, Pan Y, Lei T, Ge W, Wang L, Zhang L, Li Y, Zhao K, Liu T, Song X, Zhang J, Yu J, Hu J, Wang X. Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium. BMC Genomics 2019; 20:180. [PMID: 30845910 PMCID: PMC6407190 DOI: 10.1186/s12864-019-5566-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/25/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers among them. A telomere-centric reduction model was proposed previously to explain chromosome number reduction. With Brachpodium as an intermediate linking different major lineages of grasses and a model plant of the Pooideae plants, we wonder whether it mediated the evolution from ancestral grass karyotype to Triticeae karyotype. RESULTS By inferring the homology among Triticeae, rice, and Brachpodium chromosomes, we reconstructed the evolutionary trajectories of the Triticeae chromosomes. By performing comparative genomics analysis with rice as a reference, we reconstructed the evolutionary trajectories of Pooideae plants, including Ae. Tauschii (2n = 14, DD), barley (2n = 14), Triticum turgidum (2n = 4x = 28, AABB), and Brachypodium (2n = 10). Their extant Pooidea and Brachypodium chromosomes were independently produced after sequential nested chromosome fusions in the last tens of millions of years, respectively, after their split from rice. More frequently than would be expected by chance, in Brachypodium, the 'invading' and 'invaded' chromosomes are homoeologs, originating from duplication of a common ancestral chromosome, that is, with more extensive DNA-level correspondence to one another than random chromosomes, nested chromosome fusion events between homoeologs account for three of seven cases in Brachypodium (P-value≈0.00078). However, this phenomenon was not observed during the formation of other Pooideae chromosomes. CONCLUSIONS Notably, we found that the Brachypodium chromosomes formed through exclusively distinctive trajectories from those of Pooideae plants, and were well explained by the telomere-centric model. Our work will contribute to understanding the structural and functional innovation of chromosomes in different Pooideae lineages and beyond.
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Affiliation(s)
- Zhenyi Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuxin Pan
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Kanglu Zhao
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jiaqi Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jingjing Hu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
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92
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Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 2019; 20:29. [PMID: 30744646 PMCID: PMC6369560 DOI: 10.1186/s13059-019-1627-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.
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Affiliation(s)
- Caroline Pont
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France
| | - Stefanie Wagner
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Antoine Kremer
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade, 1350K, Copenhagen, Denmark
| | - Christophe Plomion
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Jerome Salse
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.
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93
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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94
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Sader MA, Amorim BS, Costa L, Souza G, Pedrosa-Harand A. The role of chromosome changes in the diversification of Passiflora L. (Passifloraceae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2018.1546777] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mariela A. Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Bruno S. Amorim
- Museu da Amazônia, MUSA, Manaus, Amazonas, 69099-415, Brazil
- Pós-Graduação em Biotecnologia e Recursos Naturais, Universidade do Estado do Amazonas, Manaus, Amazonas, 69058-807, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
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95
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Çanlı M. A new perspective to aberrations caused by barium and vanadium ions on Lens culinaris Medik. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:19-23. [PMID: 29783108 DOI: 10.1016/j.ecoenv.2018.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
This study investigates aberrations caused by barium and vanadium on meristematic cells of Lens culinaris Medik. Barium and vanadium ions at various concentrations (0.05 M, 0.1 M, 0.25 M, 0.5 M, and 1.0 M) were exposed to the seeds of the plant at fixed time interval (12 h). After seedlings, with a microscopic examination images were captured about the root tips. Those images showed that several abnormalities occurred on the plant such as chromosome breakings, chromosome dispersion, bridge chromosome, chromosome adherence, ring chromosome. Variety and number of abnormalities were counted and compared to each other statistically. The results show an increase in abnormalities caused by for both ions with increasing treatment time. Chromosome adherence and chromosome breaking have reverse relationship in which number of occurrence for one of them decreases with increase on other one. Fish bone and chromosome adherence have a positive relationship in which number of one increases with the raise in other's number. Exposed metals have caused formation of ligands with proteins which can prevent the persistence of metal ions in DNA protein cross-links that are involved in DNA formation process.
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Affiliation(s)
- Murat Çanlı
- Mucur Vocational School, Department of Chemistry and Chemical Processing Technologies, Ahi Evran University, TR-40500 Mucur, Kırşehir, Turkey.
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96
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Lusinska J, Majka J, Betekhtin A, Susek K, Wolny E, Hasterok R. Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum. ANNALS OF BOTANY 2018; 122:445-459. [PMID: 29893795 PMCID: PMC6110338 DOI: 10.1093/aob/mcy086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs). METHODS Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones. KEY RESULTS All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement. CONCLUSIONS mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.
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Affiliation(s)
- Joanna Lusinska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Majka
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Susek
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- For correspondence. E-mail
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97
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Pellestor F, Gatinois V. Chromothripsis, a credible chromosomal mechanism in evolutionary process. Chromosoma 2018; 128:1-6. [DOI: 10.1007/s00412-018-0679-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/17/2023]
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98
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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99
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Alam SMI, Sarre SD, Gleeson D, Georges A, Ezaz T. Did Lizards Follow Unique Pathways in Sex Chromosome Evolution? Genes (Basel) 2018; 9:E239. [PMID: 29751579 PMCID: PMC5977179 DOI: 10.3390/genes9050239] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 02/02/2023] Open
Abstract
Reptiles show remarkable diversity in modes of reproduction and sex determination, including high variation in the morphology of sex chromosomes, ranging from homomorphic to highly heteromorphic. Additionally, the co-existence of genotypic sex determination (GSD) and temperature-dependent sex determination (TSD) within and among sister clades makes this group an attractive model to study and understand the evolution of sex chromosomes. This is particularly so with Lizards (Order Squamata) which, among reptiles, show extraordinary morphological diversity. They also show no particular pattern of sex chromosome degeneration of the kind observed in mammals, birds and or even in snakes. We therefore speculate that sex determination sensu sex chromosome evolution is labile and rapid and largely follows independent trajectories within lizards. Here, we review the current knowledge on the evolution of sex chromosomes in lizards and discuss how sex chromosome evolution within that group differs from other amniote taxa, facilitating unique evolutionary pathways.
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Affiliation(s)
| | - Stephen D Sarre
- Institute for Applied Ecology, University of Canberra, Canberra 2616, Australia.
| | - Dianne Gleeson
- Institute for Applied Ecology, University of Canberra, Canberra 2616, Australia.
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra 2616, Australia.
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra 2616, Australia.
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100
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Gui S, Peng J, Wang X, Wu Z, Cao R, Salse J, Zhang H, Zhu Z, Xia Q, Quan Z, Shu L, Ke W, Ding Y. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:721-734. [PMID: 29575237 DOI: 10.1111/tpj.13894] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 05/11/2023]
Abstract
Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
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Affiliation(s)
- Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihua Wu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Cao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jérôme Salse
- Paleogenomics & Evolution (PaleoEvo) Group, Génétique Diversité & Ecophysiologie des Céréales (GDEC), Institut National de la Recherché Agronomique UMR 1095, Clermont-Ferrand, 63100, France
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiuju Xia
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Zhiwu Quan
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Liping Shu
- Wuhan Ice-Harbor Biological Technology Co. Ltd, Wuhan, 430040, China
| | - Wedong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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