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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.
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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
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Ding X, Chen J, Dai C, Shi P, Pan H, Lin Y, Chen Y, Gong L, Chen L, Wu W, Qiu X, Xu J, Huang Z, Liao B. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154882. [PMID: 37210961 DOI: 10.1016/j.phymed.2023.154882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Artemisia annua, a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. A. annua is distributed globally, with great diversity of morphological characteristics and artemisinin contents. Diverse traits among A. annua populations impeded the stable production of artemisinin, which needs an efficient tool to identify strains and assess population genetic homogeneity. PURPOSE In this study, ribosomal DNA (rDNA), were characterized for A. annua for strains identification and population genetic homogeneity assessment. METHODS The ribosomal RNA (rRNA) genes were identified using cmscan and assembled using rDNA unit of LQ-9 as a reference. rDNA among Asteraceae species were compared performing with 45S rDNA. The rDNA copy number was calculated based on sequencing depth. The polymorphisms of rDNA sequences were identified with bam-readcount, and confirmed by Sanger sequencing and restriction enzyme experiment. The ITS2 amplicon sequencing was used to verify the stability of ITS2 haplotype analysis. RESULTS Different from other Asteraceae species, 45S and 5S linked-type rDNA was only found in Artemisia genus. Rich polymorphisms of copy number and sequence of rDNA were identified in A. annua population. The haplotype composition of internal transcribed spacer 2 (ITS2) region which had moderate sequence polymorphism and relative short size was significantly different among A. annua strains. A population discrimination method was developed based on ITS2 haplotype analysis with high-throughput sequencing. CONCLUSION This study provides comprehensive characteristics of rDNA and suggests that ITS2 haplotype analysis is ideal tool for A. annua strain identification and population genetic homogeneity assessment.
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Affiliation(s)
- Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yanqi Lin
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yikang Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Linming Chen
- Guangzhou Huibiao Testing Technology Center, Guangzhou 510700, China
| | - Wenguang Wu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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Lukjanová E, Hanulíková A, Řepková J. Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods. PLANTS (BASEL, SWITZERLAND) 2023; 12:235. [PMID: 36678948 PMCID: PMC9866396 DOI: 10.3390/plants12020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin.
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He J, Zhao Y, Zhang S, He Y, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes (Basel) 2022; 13:genes13050894. [PMID: 35627279 PMCID: PMC9141308 DOI: 10.3390/genes13050894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosomal DNA (rDNA) is an excellent cytogenetic marker owing to its tandem arrangement and high copy numbers. However, comparative studies have focused more on the number of rDNA site variations within the Chrysanthemum genus, and studies on the types of rDNA sites with the same experimental procedures at the species levels are lacking. To further explore the number and types of rDNA site variations, we combined related data to draw ideograms of the rDNA sites of Chrysanthemum accessions using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Latent variations (such as polymorphisms of 45S rDNA sites and co-localized 5S-45S rDNA) also occurred among the investigated accessions. Meanwhile, a significant correlation was observed between the number of 5S rDNA sites and chromosome number. Additionally, the clumped and concentrated geographical distribution of different ploidy Chrysanthemum accessions may significantly promote the karyotype evolution. Based on the results above, we identified the formation mechanism of rDNA variations. Furthermore, these findings may provide a reliable method to examine the sites and number of rDNA variations among Chrysanthemum and its related accessions and allow researchers to further understand the evolutionary and phylogenetic relationships of the Chrysanthemum genus.
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Qu M, Zhang L, Li K, Sun J, Li Z, Han Y. Karyotypic stability of Fragaria (strawberry) species revealed by cross-species chromosome painting. Chromosome Res 2021; 29:285-300. [PMID: 34152515 DOI: 10.1007/s10577-021-09666-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Chromosome karyotyping analysis is particularly useful in determining species relationships and the origin of polyploid species. Identification of individual chromosomes is the foundation for karyotype development. For Fragaria (strawberry) species, definitive identification of the individual chromosomes is extremely difficult because of their small size and similar shape. Here, we identified all chromosomes for 11 representative Fragaria species with different ploidy using a set of oligonucleotide-based probes developed in Fragaria vesca. Comprehensive molecular cytogenetic karyotypes were established based on the individually identified chromosomes. In addition, we used oligo probes to assign the 5S and 45S rDNA loci to specific chromosomes in 16 Fragaria species. We found that these Fragaria species maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements at the cytological level were observed in any of the chromosomes among these species. Despite karyotypic stability and similarity, variations in the signal intensity of oligo probes were observed among the homologous chromosomes in several polyploid species. Moreover, most Fragaria species also showed differences in the distribution patterns of 45S and 5S rDNA. These data provide new insights into the origins of several polyploid Fragaria species.
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Affiliation(s)
- Manman Qu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Luyue Zhang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Kunpeng Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jianying Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
| | - Yonghua Han
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
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