1
|
Dias S, Souza RC, Vasconcelos EV, Vasconcelos S, da Silva Oliveira AR, do Vale Martins L, de Oliveira Bustamante F, da Costa VA, Souza G, da Costa AF, Benko-Iseppon AM, Knytl M, Brasileiro-Vidal AC. Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera. PROTOPLASMA 2024:10.1007/s00709-024-01944-z. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.
Collapse
Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Rosilda Cintra Souza
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | | | - Lívia do Vale Martins
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Campus Amilcar Ferreira Sobral, Universidade Federal Do Piauí, Floriano, PI, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Do Estado de Minas Gerais - Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Victor Alves da Costa
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
| | | |
Collapse
|
2
|
Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M, Kwasniewska J. Phaseolus vulgaris mutants reveal variation in the nuclear genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1308830. [PMID: 38239224 PMCID: PMC10794375 DOI: 10.3389/fpls.2023.1308830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.
Collapse
Affiliation(s)
- Nasya Tomlekova
- Laboratory of Molecular Biology, Department of Breeding, Marisa Vegetable Crops Research Institute, Plovdiv, Agricultural Academy, Sofia, Bulgaria
| | - Dominika Idziak-Helmcke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paula Franke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
de Oliveira Bustamante F, do Nascimento TH, Montenegro C, Dias S, do Vale Martins L, Braz GT, Benko-Iseppon AM, Jiang J, Pedrosa-Harand A, Brasileiro-Vidal AC. Oligo-FISH barcode in beans: a new chromosome identification system. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3675-3686. [PMID: 34368889 DOI: 10.1007/s00122-021-03921-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7-15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.
Collapse
Affiliation(s)
- Fernanda de Oliveira Bustamante
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade do Estado de Minas Gerais, Unidade Divinópolis, Divinópolis, MG, Brazil
| | | | - Claudio Montenegro
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Sibelle Dias
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Lívia do Vale Martins
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Departamento de Biologia, Universidade Federal do Piauí, Teresina, PI, Brazil
| | | | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | | |
Collapse
|
5
|
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.
Collapse
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
| | | |
Collapse
|
6
|
Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. BMC Genomics 2021; 22:194. [PMID: 33736599 PMCID: PMC7977240 DOI: 10.1186/s12864-021-07467-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited. Results The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. lunatus Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found significant variation, the intergenic regions of trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11-rsp19, ndhF-ccsA was found in a high degree of divergence. A phylogenetic analysis showed that P. lunatus appears to be more closely related to P. vulgaris, V.unguiculata and V. radiata. Conclusions The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07467-8.
Collapse
|
7
|
Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck DG, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 2021; 12:702. [PMID: 33514713 PMCID: PMC7846787 DOI: 10.1038/s41467-021-20921-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
Collapse
Affiliation(s)
- Tatiana Garcia
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,grid.17088.360000 0001 2150 1785Present Address: Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI USA
| | - Jorge Duitama
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Stephanie Smolenski Zullo
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Juanita Gil
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia ,grid.411017.20000 0001 2151 0999Present Address: Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR USA
| | - Andrea Ariani
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA ,Present Address: BASF BBCC - Innovation Center, Gent, Belgium
| | - Sarah Dohle
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Antonia Palkovic
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Paola Skeen
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,Present Address: Nunhems USA, Vegetable Seeds BASF, Acampo, CA USA
| | - Clara Isabel Bermudez-Santana
- grid.10689.360000 0001 0286 3748Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel G. Debouck
- grid.418348.20000 0001 0943 556XCentro Internacional de Agricultura Tropical, Cali, Colombia
| | - Jaime Martínez-Castillo
- grid.418270.80000 0004 0428 7635Centro de Investigación Científica de Yucatán, Yucatán, Mexico
| | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Maria Isabel Chacón-Sánchez
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| |
Collapse
|
8
|
Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). Chromosome Res 2020; 28:293-306. [PMID: 32654079 DOI: 10.1007/s10577-020-09635-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced genome, and compared with V. unguiculata (Vu, subgenus Vigna) and Phaseolus vulgaris (Pv) maps. Seventeen Pv BACs, eight Vu BACs, and 5S and 35S rDNA probes were hybridized in situ on the 11 Vac chromosome pairs. Five Vac chromosomes (Vac6, Vac7, Vac9, Vac10, and Vac11) showed conserved macrosynteny and collinearity between V. unguiculata and P. vulgaris. On the other hand, we observed collinearity breaks, identified by pericentric inversions involving Vac2 (Vu2), Vac4 (Vu4), and Vac3 (Pv3). We also detected macrosynteny breaks of translocation type involving chromosomes 1 and 8 of V. aconitifolia and P. vulgaris; 2 and 3 of V. aconitifolia and P. vulgaris; and 1 and 5 of V. aconitifolia and V. unguiculata. Considering our data and previous BAC-FISH studies, six chromosomes (1, 2, 3, 4, 5, and 8) are involved in major karyotype divergences between genera and five (1, 2, 3, 4, and 5) between Vigna subgenera, including mechanisms such as duplications, inversions, and translocations. Macrosynteny breaks between Vigna and Phaseolus suggest that the major chromosomal rearrangements have occurred within the Vigna clade. Our cytogenomic comparisons bring new light on the degree of shared macrosynteny and mechanisms of karyotype diversification during Vigna and Phaseolus evolution.
Collapse
|
9
|
Franco AL, Figueredo A, Pereira LDM, de Sousa SM, Souza G, Carvalho MA, Simon MF, Viccini LF. Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae). Genet Mol Biol 2020; 43:e20180250. [PMID: 31429856 PMCID: PMC7197990 DOI: 10.1590/1678-4685-gmb-2018-0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
Stylosanthes (Papilionoideae, Leguminosae) is a predominantly Neotropical genus with ~48 species that include worldwide important forage species. This study presents the chromosome number and morphology of eight species of the genus Stylosanthes (S. acuminata, S. gracilis, S. grandifolia, S. guianensis, S. hippocampoides, S. pilosa, S. macrocephala, and S. ruellioides). In addition, staining with CMA and DAPI, in situ hybridization with 5S and 35S rDNA probes, and estimation of DNA content were performed. The interpretation of Stylosanthes chromosome diversification was anchored by a comparison with the sister genus Arachis and a dated molecular phylogeny based on nuclear and plastid loci. Stylosanthes species showed 2n = 20, with low cytomolecular diversification regarding 5S rDNA, 35S rDNA, and genome size. Arachis has a more ancient diversification (~7 Mya in the Pliocene) than the relatively recent Stylosanthes (~2 Mya in the Pleistocene), and it seems more diverse than its sister lineage. Our data support the idea that the cytomolecular stability of Stylosanthes in relation to Arachis could be a result of its recent origin. The recent diversification of Stylosanthes could also be related to the low morphological differentiation among species, and to the recurrent formation of allopolyploid complexes.
Collapse
Affiliation(s)
- Ana Luiza Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Amanda Figueredo
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Lívia de Moraes Pereira
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Saulo Marçal de Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | | | - Marcelo F. Simon
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Brasília, DF, Brazil
| | - Lyderson Facio Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| |
Collapse
|
10
|
Cheng A, Raai MN, Zain NAM, Massawe F, Singh A, Wan-Mohtar WAAQI. In search of alternative proteins: unlocking the potential of underutilized tropical legumes. Food Secur 2019. [DOI: 10.1007/s12571-019-00977-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
11
|
Gujaria-Verma N, Ramsay L, Sharpe AG, Sanderson LA, Debouck DG, Tar'an B, Bett KE. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping. BMC Genomics 2016; 17:239. [PMID: 26979462 PMCID: PMC4793507 DOI: 10.1186/s12864-016-2499-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly. Results Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements. Conclusions The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Lacey-Anne Sanderson
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Daniel G Debouck
- Genetic Resources Program, International Center for Tropical Agriculture, Km 17 recta a Palmira, AA6713, Cali, Colombia
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
| |
Collapse
|
12
|
Fonsêca A, Ferraz ME, Pedrosa-Harand A. Speeding up chromosome evolution in Phaseolus: multiple rearrangements associated with a one-step descending dysploidy. Chromosoma 2015; 125:413-21. [PMID: 26490170 DOI: 10.1007/s00412-015-0548-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022]
Abstract
The genus Phaseolus L. has been subject of extensive cytogenetic studies due to its global economic importance. It is considered karyotypically stable, with most of its ca. 75 species having 2n = 22 chromosomes, and only three species (Phaseolus leptostachyus, Phaseolus macvaughii, and Phaseolus micranthus), which form the Leptostachyus clade, having 2n = 20. To test whether a simple chromosomal fusion was the cause of this descending dysploidy, mitotic chromosomes of P. leptostachyus (2n = 20) were comparatively mapped by fluorescent in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and ribosomal DNA (rDNA) probes. Our results corroborated the conservation of the 5S and 45S rDNA sites on ancestral chromosomes 10 and 6, respectively. The reduction from x = 11 to x = 10 was the result of the insertion of chromosome 10 into the centromeric region of chromosome 11, supporting a nested chromosome fusion (NCF) as the main cause of this dysploidy. Additionally, the terminal region of the long arm of chromosome 6 was translocated to this larger chromosome. Surprisingly, the NCF was accompanied by several additional translocations and inversions previously unknown for the genus, suggesting that the dysploidy may have been associated to a burst of genome reorganization in this otherwise stable, diploid plant genus.
Collapse
Affiliation(s)
- Artur Fonsêca
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves s/n, Recife, PE, 50670-420, Brazil.
| |
Collapse
|
13
|
Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosome Res 2015; 23:253-66. [PMID: 25634499 DOI: 10.1007/s10577-014-9464-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022]
Abstract
Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.
Collapse
|
14
|
Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting. PLoS One 2014; 9:e115108. [PMID: 25493646 PMCID: PMC4262448 DOI: 10.1371/journal.pone.0115108] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n = 10, B. sylvaticum 2n = 18, B. pinnatum 2n = 16; 2n = 18, B. arbuscula 2n = 18 and B. stacei 2n = 20) three allotetraploids (B. pinnatum 2n = 28, B. phoenicoides 2n = 28 and B. hybridum 2n = 30), and two species of unknown ploidy (B. retusum 2n = 38 and B. mexicanum 2n = 40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n = 18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon.
Collapse
|
15
|
Fonsêca A, Richard MM, Geffroy V, Pedrosa-Harand A. Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean ( Phaseolus vulgaris L., Fabaceae) Heterochromatin. Cytogenet Genome Res 2014; 143:168-78. [DOI: 10.1159/000360572] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|