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Tapia-Pastrana F, Delgado-Salinas A, Caballero J. Patterns of chromosomal variation in Mexican species of Aeschynomene (Fabaceae, Papilionoideae) and their evolutionary and taxonomic implications. COMPARATIVE CYTOGENETICS 2020; 14:157-182. [PMID: 32206208 PMCID: PMC7080853 DOI: 10.3897/compcytogen.v14i1.47264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
A cytogenetic analysis of sixteen taxa of the genus Aeschynomene Linnaeus, 1753, which includes species belonging to both subgenera Aeschynomene (Léonard, 1954) and Ochopodium (Vogel, 1838) J. Léonard, 1954, was performed. All studied species had the same chromosome number (2n = 20) but exhibited karyotype diversity originating in different combinations of metacentric, submetacentric and subtelocentric chromosomes, chromosome size and number of SAT chromosomes. The plasticity of the genomes included the observation in a taxon belonging to the subgenus Aeschynomene of an isolated spherical structure similar in appearance to the extra chromosomal circular DNA observed in other plant genera. By superimposing the karyotypes in a recent phylogenetic tree, a correspondence between morphology, phylogeny and cytogenetic characteristics of the taxa included in the subgenus Aeschynomene is observed. Unlike subgenus Aeschynomene, the species of Ochopodium exhibit notable karyotype heterogeneity. However the limited cytogenetic information recorded prevents us from supporting the proposal of their taxonomic separation and raise it to the genus category. It is shown that karyotype information is useful in the taxonomic delimitation of Aeschynomene and that the diversity in the diploid level preceded the hybridization/polyploidization demonstrated in the genus. The systematic implications of our results and their value can be extended to other Dalbergieae genera as knowledge about the chromosomal structure and its evolution increases.
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Affiliation(s)
- Fernando Tapia-Pastrana
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Laboratorio de Genecología, Batalla 5 de Mayo s/n esquina Fuerte de Loreto, Col. Ejército de Oriente, Iztapalapa, C.P. 09230, Ciudad de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
| | - Alfonso Delgado-Salinas
- Instituto de Biología, Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado Postal 70-233, 04510, Cd. de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
| | - Javier Caballero
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Campos Deportivos, Ciudad Universitaria, Coyoacán 04510, Cd. de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
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Thakar SB, Dhanavade MJ, Sonawane KD. LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves. CURRENT NUTRITION & FOOD SCIENCE 2019. [DOI: 10.2174/1573401314666180223143523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Legume plants are known for their rich medicinal and nutritional values.
Large amount of medicinal information of various legume plants have been dispersed in the form of
text.
Objective:
It is essential to design and construct a legume medicinal plants database, which integrate
respective classes of legumes and include knowledge regarding medicinal applications along with
their protein/enzyme sequences.
Methods:
The design and development of Legume Medicinal Plants Database (LegumeDB) has been
done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and
ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding.
Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used.
Results:
This database includes information of 50 Legume medicinal species, which might be helpful
to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes
and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis
to understand evolutionary lineage between legumes and mangroves. Homology modeling technique
was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata
using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis
results indicate the conserved residues among legume and mangrove species.
Conclusion:
Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and
mangrove species Thespesia populnea to each other, indicating their similarity and origin from common
ancestor. Thus, these studies might be helpful to understand evolutionary relationship between
legumes and mangroves.
:
LegumeDB availability: http://legumedatabase.co.in
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Affiliation(s)
- Sambhaji B. Thakar
- Department of Biotechnology, Shivaji University, Kolhapur-416 004, (M.S.), India
| | - Maruti J. Dhanavade
- Department of Microbiology, Shivaji University, Kolhapur-416 004, (M.S.), India
| | - Kailas D. Sonawane
- Department of Microbiology, Shivaji University, Kolhapur-416 004, (M.S.), India
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Rodrigues PS, Souza MM, Melo CAF, Pereira TNS, Corrêa RX. Karyotype diversity and 2C DNA content in species of the Caesalpinia group. BMC Genet 2018; 19:25. [PMID: 29642872 PMCID: PMC5896153 DOI: 10.1186/s12863-018-0610-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within this subfamily; together with these species' phenotypic plasticity and the similarities in their morphological descriptors, make this a complex group for taxonomic and phylogenetic studies. The objective of the present work was to evaluate the karyotypic diversity and the 2C DNA content variation in 10 species of the Caesalpinia group, representing six genera: Paubrasilia, Caesalpinia, Cenostigma, Poincianella, Erythrostemon and Libidibia. The GC-rich heterochromatin and 45S rDNA sites (which are used as chromosome markers) were located to evaluate the karyotype diversity in the clade. The variation in the 2C DNA content was determined through flow cytometry. RESULTS The fluorochrome banding indicated that the chromomycin A3+/4',6-diamidino-2-phenylindole- blocks were exclusively in the terminal regions of the chromosomes, coinciding with 45S rDNA sites in all analyzed species. Physical mapping of the species (through fluorescence in situ hybridization) revealed variation in the size of the hybridization signals and in the number and distribution of the 45S rDNA sites. All hybridization sites were in the terminal regions of the chromosomes. In addition, all species had a hybridization site in the fourth chromosome pair. The 2C DNA content ranged from 1.54 pg in Erythrostemon calycina to 2.82 pg in the Paubrasilia echinata large-leaf variant. The Pa. echinata small-leaf variant was isolated from the other leaf variants through Scoot-Knott clustering. CONCLUSIONS The chromosome diversity and the variation in the 2C DNA content reinforce that the actual taxonomy and clustering of the analyzed taxa requires more genera that were previously proposed. This fact indicates that taxonomy, phylogeny and cytoevolutionary inference related to the complex Caesalpinia group have to be done through integrative evaluation.
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Affiliation(s)
- Polliana Silva Rodrigues
- Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP, Ilhéus, BA, 45662-900, Brazil
| | - Margarete Magalhães Souza
- Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP, Ilhéus, BA, 45662-900, Brazil
| | - Cláusio Antônio Ferreira Melo
- Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP, Ilhéus, BA, 45662-900, Brazil
| | - Telma Nair Santana Pereira
- Centro de Ciências e Tecnologias Agropecuárias, Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP, Ilhéus, BA, 45662-900, Brazil.
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Rai KM, Singh SK, Bhardwaj A, Kumar V, Lakhwani D, Srivastava A, Jena SN, Yadav HK, Bag SK, Sawant SV. Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:953-963. [PMID: 23782852 DOI: 10.1111/pbi.12088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/19/2013] [Accepted: 05/04/2013] [Indexed: 06/02/2023]
Abstract
The sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93,363 gene models (21,399 full length) and identified 35,923 gene models which were validated against already sequenced plant genomes. A total of 1,093 transcription factor-encoding genes, 3,135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47,093 novel simple sequence repeats and 66,364 novel single nucleotide polymorphisms. In addition, we developed NBRI-Comprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.
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Affiliation(s)
- Krishan Mohan Rai
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
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Genetic variation and the conservation of isolated populations of Derris trifoliata (Leguminosae), a mangrove-associated vine, in southern China. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jena SN, Srivastava A, Rai KM, Ranjan A, Singh SK, Nisar T, Srivastava M, Bag SK, Mantri S, Asif MH, Yadav HK, Tuli R, Sawant SV. Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011. [PMID: 22038488 DOI: 10.1007/s00122‐011‐1729‐y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.
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Affiliation(s)
- Satya Narayan Jena
- Plant Molecular Biology and Genetic Engineering Laboratory, National Botanical Research Institute, Rana Pratap Marg, Lucknow, India
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Genetic variability among male populations of a minor mangrove Excoecaria agallocha L. as evident by chromosome morphology and DNA markers. THE NUCLEUS 2011. [DOI: 10.1007/s13237-011-0027-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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