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Braz GT, Van-Lume B, de Resende KFM, Cardoso FP, Oliveira L, de Andrade MJG, Souza G, Torres GA. Cytomolecular trends in Chamaecrista Moench (Caesalpinioideae, Leguminosae) diversification. Genetica 2024; 152:51-61. [PMID: 38381186 DOI: 10.1007/s10709-024-00205-4] [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: 06/01/2023] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Chamaecrista is a Pantropical legume genus of the tribe Cassieae, which includes six other genera. In contrast to most of the other Cassieae genera, Chamaecrista shows significant variability in chromosome number (from 2n = 14 to 2n = 56), with small and morphologically similar chromosomes. Here, we performed a new cytomolecular analysis on chromosome number, genome size, and rDNA site distribution in a molecular phylogenetic perspective to interpret the karyotype trends of Chamaecrista and other two genera of Cassieae, seeking to understand their systematics and evolution. Our phylogenetic analysis revealed that Chamaecrista is monophyletic and can be divided into four major clades corresponding to the four sections of the genus. Chromosome numbers ranged from 2n = 14, 16 (section Chamaecrista) to 2n = 28 (sections Absus, Apoucouita, and Baseophyllum). The number of 5S and 35S rDNA sites varied between one and three pairs per karyotype, distributed on different chromosomes or in synteny, with no obvious phylogenetic significance. Our data allowed us to propose x = 7 as the basic chromosome number of Cassieae, which was changed by polyploidy generating x = 14 (sections Absus, Apoucouita, and Baseophyllum) and by ascending dysploidy to x = 8 (section Chamaecrista). The DNA content values supported this hypothesis, with the genomes of the putative tetraploids being larger than those of the putative diploids. We hypothesized that ascending dysploidy, polyploidy, and rDNA amplification/deamplification are the major events in the karyotypic diversification of Chamaecrista. The chromosomal marks characterized here may have cytotaxonomic potential in future studies.
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Affiliation(s)
- Guilherme Tomaz Braz
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
| | - Brena Van-Lume
- Programa de Pós-graduação em Biologia Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brasil
| | | | - Felipe Pereira Cardoso
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Ludmila Oliveira
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maria José Gomes de Andrade
- Programa de Pós-graduação em Biodiversidade Vegetal, Departamento de Educação, Campus VIII, Universidade do Estado da Bahia, Bahia, Paulo Afonso, Brasil
| | - Gustavo Souza
- Programa de Pós-graduação em Biologia Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brasil
| | - Giovana Augusta Torres
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
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Mata-Sucre Y, Matzenauer W, Castro N, Huettel B, Pedrosa-Harand A, Marques A, Souza G. Repeat-based phylogenomics shed light on unclear relationships in the monocentric genus Juncus L. (Juncaceae). Mol Phylogenet Evol 2023; 189:107930. [PMID: 37717642 DOI: 10.1016/j.ympev.2023.107930] [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] [Received: 07/04/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
The repetitive fraction (repeatome) of eukaryotic genomes is diverse and usually fast evolving, being an important tool for clarify plant systematics. The genus Juncus L. comprises 332 species, karyotypically recognized by having holocentric chromosomes. However, four species were recently described as monocentric, yet our understanding of their genome evolution is largely masked by unclear phylogenetic relationships. Here, we reassess the current Juncus systematics using low-coverage genome skimming data of 33 taxa to construct repeats, nuclear rDNA and plastome-based phylogenetic hypothesis. Furthermore, we characterize the repeatome and chromosomal distribution of Juncus-specific centromeric repeats/CENH3 protein to test the monocentricity reach in the genus. Repeat-base phylogenies revealed topologies congruent with the rDNA tree, but not with the plastome tree. The incongruence between nuclear and plastome chloroplast dataset suggest an ancient hybridization in the divergence of Juncotypus and Tenageia sections 40 Myr ago. The phylogenetic resolution at section level was better fitted with the rDNA/repeat-based approaches, with the recognition of two monophyletic sections (Stygiopsis and Tenageia). We found specific repeatome trends for the main lineages, such as the higher abundances of TEs in the Caespitosi and Iridifolii + Ozophyllum clades. CENH3 immunostaining confirmed the monocentricity of Juncus, which can be a generic synapomorphy for the genus. The heterogeneity of the repeatomes, with high phylogenetic informativeness, identified here may be correlated with their ancient origin (56 Mya) and reveals the potential of comparative genomic analyses for understanding plant systematics and evolution.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - William Matzenauer
- Laboratório de Morfo-Taxonomia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife PE 50670-901, Brasil
| | - Natália Castro
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - Bruno Huettel
- Max Planck Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gustavo Souza
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco. Recife PE 50670-901, Brasil.
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3
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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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Yurkevich OY, Samatadze TE, Selyutina IY, Suprun NA, Suslina SN, Zoshchuk SA, Amosova AV, Muravenko OV. Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the Genus Hedysarum L. (Fabaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:865958. [PMID: 35574118 PMCID: PMC9101955 DOI: 10.3389/fpls.2022.865958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The section Multicaulia is the largest clade in the genus Hedysarum L. (Fabaceae). Representatives of the sect. Multicaulia are valuable plants used for medicinal and fodder purposes. The taxonomy and phylogeny of the sect. Multicaulia are still ambiguous. To clarify the species relationships within sect. Multicaulia, we, for the first time, explored repeatomes of H. grandiflorum Pall., H. zundukii Peschkova, and H. dahuricum Turcz. using next-generation sequencing technologies and a subsequent bioinformatic analysis by RepeatExplorer/TAREAN pipelines. The comparative repeatome analysis showed that mobile elements made up 20-24% (Class I) and about 2-2.5% (Class II) of their repetitive DNAs. The amount of ribosomal DNA varied from 1 to 2.6%, and the content of satellite DNA ranged from 2.7 to 5.1%. For each species, five high confident putative tandem DNA repeats and 5-10 low confident putative DNA repeats were identified. According to BLAST, these repeats demonstrated high sequence similarity within the studied species. FISH-based mapping of 35S rDNA, 5S rDNA, and satDNAs made it possible to detect new effective molecular chromosome markers for Hedysarum species and construct the species karyograms. Comparison of the patterns of satDNA localization on chromosomes of the studied species allowed us to assess genome diversity within the sect. Multicaulia. In all studied species, we revealed intra- and interspecific variabilities in patterns of the chromosomal distribution of molecular chromosome markers. In H. gmelinii Ledeb. and H. setigerum Turcz. ex Fisch. et Meyer, similar subgenomes were detected, which confirmed the polyploid status of their genomes. Our findings demonstrated a close genomic relationship among six studied species indicating their common origin and confirmed the taxonomic status of H. setigerum as a subspecies of H. gmelinii as well as the validity of combining the sect. Multicaulia and Subacaulia into one sect. Multicaulia.
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Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Peoples’ Friendship University of Russia, Moscow, Russia
| | - Inessa Yu. Selyutina
- Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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5
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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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Cintra LA, Souza TBD, Parteka LM, Barreto LM, Pereira LFP, Gaeta ML, Guyot R, Vanzela ALL. An 82 bp tandem repeat family typical of 3' non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres. Genome 2021; 65:137-151. [PMID: 34727516 DOI: 10.1139/gen-2021-0045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around the centromeres. However, the proximal regions of Coffea chromosomes remain poorly understood, especially regarding the nature and organisation of the sequences. Taking advantage of the genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extends from the pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improves our understanding of the role of the Gypsy/TAT LTR retrotransposon lineage in the organisation of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships between fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated. Highlights: A scattered short tandem repeat, typical of Gypsy/TAT LTR retrotransposons, associated with several fragments of other transposable elements, accumulates in the pericentromeres of Coffea chromosomes. This arrangement is preserved in all clades of the genus and appears to have a strong regulatory role in the organisation of chromatin around centromeres.
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Affiliation(s)
- Leonardo Adabo Cintra
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Letícia Maria Parteka
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | - Lucas Mesquita Barreto
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil.,Programa de Pós-graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
| | | | - Marcos Letaif Gaeta
- 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
- Institut de Recherche pour le Développement, CIRAD, Université Montpellier, 34394, Montpellier, France.,Department of Electronics and Automation, Universidad Autónoma de Manizales, 170002, Manizales, Caldas, Colombia
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, 86097-570, Paraná, Brazil
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7
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Pellicer J, Fernández P, Fay MF, Michálková E, Leitch IJ. Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae). Front Genet 2021; 12:726211. [PMID: 34552621 PMCID: PMC8450539 DOI: 10.3389/fgene.2021.726211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain.,Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom.,School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Aecyo P, Marques A, Huettel B, Silva A, Esposito T, Ribeiro E, Leal IR, Gagnon E, Souza G, Pedrosa-Harand A. Plastome evolution in the Caesalpinia group (Leguminosae) and its application in phylogenomics and populations genetics. PLANTA 2021; 254:27. [PMID: 34236509 DOI: 10.1007/s00425-021-03655-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses. Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
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Affiliation(s)
- Paulo Aecyo
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana Silva
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Tiago Esposito
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Elâine Ribeiro
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
- Laboratory of Biodiversity and Evolutionary Genetics, University of Pernambuco - Campus Petrolina, Petrolina, Brazil
| | - Inara R Leal
- Laboratory of Plant-Animal Interaction, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden of Edinburgh, University of Edinburgh, Edinburgh, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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9
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Vangelisti A, Simoni S, Usai G, Ventimiglia M, Natali L, Cavallini A, Mascagni F, Giordani T. LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome. BMC PLANT BIOLOGY 2021; 21:221. [PMID: 34000996 PMCID: PMC8127270 DOI: 10.1186/s12870-021-02991-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/15/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences. RESULTS In this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established. CONCLUSIONS The data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.
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Affiliation(s)
- Alberto Vangelisti
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Samuel Simoni
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gabriele Usai
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Maria Ventimiglia
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Natali
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Flavia Mascagni
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Tommaso Giordani
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
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