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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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2
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de Assis R, Gonçalves LSA, Guyot R, Vanzela ALL. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome 2023; 66:269-280. [PMID: 37364373 DOI: 10.1139/gen-2022-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.
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Affiliation(s)
- Rafael de Assis
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina 86097-570, Paraná, Brazil
| | | | - Romain Guyot
- Institute de Recherche pour le Développement, CIRAD, Université de Montpellier, UMR DIADE, Montpellier, France
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3
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Ramos LC, Báez M, Fuchs J, Houben A, Carvalho R, Pedrosa-Harand A. Differential Repeat Accumulation in the Bimodal Karyotype of Agave L. Genes (Basel) 2023; 14:491. [PMID: 36833420 PMCID: PMC9956584 DOI: 10.3390/genes14020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The genus Agave presents a bimodal karyotype with x = 30 (5L, large, +25S, small chromosomes). Bimodality within this genus is generally attributed to allopolyploidy in the ancestral form of Agavoideae. However, alternative mechanisms, such as the preferential accumulation of repetitive elements at the macrochromosomes, could also be important. Aiming to understand the role of repetitive DNA within the bimodal karyotype of Agave, genomic DNA from the commercial hybrid 11648 (2n = 2x = 60, 6.31 Gbp) was sequenced at low coverage, and the repetitive fraction was characterized. In silico analysis showed that ~67.6% of the genome is mainly composed of different LTR retrotransposon lineages and one satellite DNA family (AgSAT171). The satellite DNA localized at the centromeric regions of all chromosomes; however, stronger signals were observed for 20 of the macro- and microchromosomes. All transposable elements showed a dispersed distribution, but not uniform across the length of the chromosomes. Different distribution patterns were observed for different TE lineages, with larger accumulation at the macrochromosomes. The data indicate the differential accumulation of LTR retrotransposon lineages at the macrochromosomes, probably contributing to the bimodality. Nevertheless, the differential accumulation of the satDNA in one group of macro- and microchromosomes possibly reflects the hybrid origin of this Agave accession.
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Affiliation(s)
- Lamonier Chaves Ramos
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115 Bonn, Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Graduate Program in Agronomy, Genetic Plant Breeding—PPGAMGP, Department of Agronomy, Federal Rural University of Pernambuco, Recife 52171-900, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife 50670-420, Brazil
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Anjos A, Milani D, Bardella VB, Paladini A, Cabral-de-Mello DC. Evolution of satDNAs on holocentric chromosomes: insights from hemipteran insects of the genus Mahanarva. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:5. [PMID: 36705735 DOI: 10.1007/s10577-023-09710-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 01/28/2023]
Abstract
Satellite DNAs (satDNAs) constitute one of the main components of eukaryote genomes and are involved in chromosomal organization and diversification. Although largely studied, little information was gathered about their evolution on holocentric species, i.e., diffuse centromeres, which, due to differences in repeat organization, could result in different evolutionary patterns. Here, we combined bioinformatics and cytogenetic approaches to evaluate the evolution of the satellitomes in Mahanarva holocentric insects. In two species, de novo identification revealed a high number of satDNAs, 110 and 113, with an extreme monomer length range of 18-4228 bp. The overall abundance of satDNAs was observed to be 6.67% in M. quadripunctata and 1.98% in M. spectabilis, with different abundances for the shared satDNAs. Chromosomal mapping of the most abundant repeats of M. quadripunctata and M. spectabilis on other Mahanarva reinforced the dynamic nature of satDNAs. Variable patterns of chromosomal distribution for the satDNAs were noticed, with the occurrence of clusters on distinct numbers of chromosomes and at different positions and the occurrence of scattered signals or nonclustered satDNAs. Altogether, our data demonstrated the high dynamism of satDNAs in Mahanarva with the involvement of this genomic fraction in chromosome diversification of the genus. The general characteristics and patterns of evolution of satDNAs are similar to those observed on monocentric chromosomes, suggesting that the differential organization of genome compartments observed on holocentric chromosomes compared with monocentric chromosomes does not have a large impact on the evolution of satDNAs. Analysis of the satellitomes of other holocentric species in a comparative manner will shed light on this issue.
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Affiliation(s)
- Allison Anjos
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Andressa Paladini
- Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
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Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae. Chromosome Res 2022; 30:477-492. [PMID: 35715657 DOI: 10.1007/s10577-022-09702-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 01/25/2023]
Abstract
The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae (P. lunatus) and Glycininae (Amphicarpaea edgeworthii) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus. We also reconstructed the chromosome number reduction in S. suberectus. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.
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Samoluk SS, Vaio M, Ortíz AM, Chalup LMI, Robledo G, Bertioli DJ, Seijo G. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PLANTA 2022; 256:50. [PMID: 35895167 DOI: 10.1007/s00425-022-03961-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Affiliation(s)
- Sergio S Samoluk
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Alejandra M Ortíz
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Laura M I Chalup
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Germán Robledo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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Ribeiro T, Vaio M, Félix LP, Guerra M. Satellite DNA probes of Alstroemeria longistaminea (Alstroemeriaceae) paint the heterochromatin and the B chromosome, reveal a G-like banding pattern, and point to a strong structural karyotype conservation. PROTOPLASMA 2022; 259:413-426. [PMID: 34148192 DOI: 10.1007/s00709-021-01681-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
Alstroemeria species present a well-conserved and asymmetric karyotype. The genus is divided into a Chilean clade, rich in heterochromatin, and a Brazilian clade, poor in heterochromatin. We investigated the distribution of the main repetitive sequences in the chromosomes of the Brazilian species A. longistaminea (2n = 16 + 0-6B) aiming to evaluate the role played by these sequences on the structural organization of the karyotype. In situ hybridization of the three most abundant retrotransposons, corresponding to ~ 45% of the genome, was uniformly distributed. Three satellite DNA sequences, representing near half of the whole satellite fraction (1.93% of the genome), were mainly concentrated on the heterochromatin and one of them painted the whole B chromosome. Noteworthy, some satellites were located on euchromatin, either dispersed or concentrated in clusters along the chromosomes, revealing a G-band-like pattern. The two satellites that presented more C-band- and G-band-like labeling were also hybridized in situ in two other Alstroemeria species. They revealed astonishing similar patterns of distribution, indicating an unusually structural karyotype conservation among Brazilian species.
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Affiliation(s)
- Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil.
- Integrative Plant Research Lab, Department of Botany and Ecology, Federal University of Mato Grosso, Av. Fernando Corrêa da Costa, 2367, Boa Esperança, Cuiabá, 78060-900, MT, Brazil.
| | - Magdalena Vaio
- Laboratorio de Evolución y Domesticación de las Plantas, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Leonardo P Félix
- Laboratory of Plant Cytogenetics, Department of Biosciences, Federal University of Paraíba, Areia, PB, Brazil
| | - Marcelo Guerra
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil
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Costa L, Marques A, Buddenhagen C, Thomas WW, Huettel B, Schubert V, Dodsworth S, Houben A, Souza G, Pedrosa-Harand A. Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA. ANNALS OF BOTANY 2021; 128:835-848. [PMID: 34050647 PMCID: PMC8577205 DOI: 10.1093/aob/mcab063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS With the advance of high-throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data. METHODS Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-alignment-based phylogenetic tree. KEY RESULTS All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 % in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree. CONCLUSIONS Our results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
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Heitkam T, Schulte L, Weber B, Liedtke S, Breitenbach S, Kögler A, Morgenstern K, Brückner M, Tröber U, Wolf H, Krabel D, Schmidt T. Comparative Repeat Profiling of Two Closely Related Conifers ( Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. Front Genet 2021; 12:683668. [PMID: 34322154 PMCID: PMC8312256 DOI: 10.3389/fgene.2021.683668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Luise Schulte
- Institute of Botany, Technische Universität Dresden, Dresden, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Sarah Breitenbach
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kristin Morgenstern
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | | | - Ute Tröber
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Heino Wolf
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Doris Krabel
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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10
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do Vale Martins L, de Oliveira Bustamante F, da Silva Oliveira AR, da Costa AF, de Lima Feitoza L, Liang Q, Zhao H, Benko-Iseppon AM, Muñoz-Amatriaín M, Pedrosa-Harand A, Jiang J, Brasileiro-Vidal AC. BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris. Chromosoma 2021; 130:133-147. [PMID: 33909141 DOI: 10.1007/s00412-021-00758-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/17/2021] [Accepted: 04/05/2021] [Indexed: 01/29/2023]
Abstract
Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.
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Affiliation(s)
| | | | | | | | | | - Qihua Liang
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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11
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Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PLANTA 2021; 253:86. [PMID: 33792791 DOI: 10.1007/s00425-021-03598-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/18/2021] [Indexed: 05/22/2023]
Abstract
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
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Affiliation(s)
- Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Luiz Augusto Cauz-Santos
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Maria Lucia Carneiro Vieira
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semiarid, Petrolina, Pernambuco, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Mata-Sucre Y, Sader M, Van-Lume B, Gagnon E, Pedrosa-Harand A, Leitch IJ, Lewis GP, Souza G. How diverse is heterochromatin in the Caesalpinia group? Cytogenomic characterization of Erythrostemon hughesii Gagnon & G.P. Lewis (Leguminosae: Caesalpinioideae). PLANTA 2020; 252:49. [PMID: 32918627 DOI: 10.1007/s00425-020-03453-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/27/2020] [Indexed: 05/25/2023]
Abstract
Cytogenomic characterization of Erythrostemon hughesii reveals a heterogeneity of repeats in its subtelomeric heterochromatin. Comparative analyses with other Caesalpinia group species reveal a significant reduction in the abundance of Ty3-gypsy/Chromovirus Tekay retrotransposons during its evolution. In numerically stable karyotypes, repetitive DNA variability is one of the main causes of genome and chromosome variation and evolution. Species from the Caesalpinia group (Leguminosae) are karyotypically characterized by 2n = 24, with small chromosomes and highly variable CMA+ heterochromatin banding patterns that correlate with environmental variables. Erythrostemon hughesii differs from other species of the group examined to date for having subtelomeric CMA+ bands; this contrasts with most species in the group which have proximal bands. Here we analyse the repeatome of E. hughesii using genome skimming and chromosomal mapping approaches to characterize the identity of the most abundant repetitive elements and their physical location. The repetitive fraction of E. hughesii comprises 28.73% of the genome. The most abundant elements were retrotransposons (RT) with long terminal repeats (LTR-RT; 9.76%) and satellite DNAs (7.83%). Within the LTR-RTs, the most abundant lineages were: Ty1/copia-Ale (1%), Ty3/gypsy CRM (0.88%) and Ty3/gypsy Athila (0.75%). Using fluorescent in situ hybridization four satellite DNAs and several LTR-RT elements were shown to be present in most subtelomeric CMA+ bands. These results highlight how the repeatome in E. hughesii, a species from Oaxaca state in Mexico, is clearly distinct from Northeast Brazilian species of the Caesalpinia group, mainly due to its high diversity of repeats in its subtelomeric heterochromatic bands and low amount of LTR-RT Ty3/gypsy-Tekay elements. Comparative sequence analysis of Tekay elements from different species is congruent with a clade-specific origin of this LTR-RT after the divergence of the Caesalpinia group. We hypothesize that repeat-rich heterochromatin may play a role in leading to faster genomic divergence between individuals, increasing speciation and diversification.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil.
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