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Zhou W, Li B, Li L, Ma W, Liu Y, Feng S, Wang Z. Genome survey sequencing of Dioscorea zingiberensis. Genome 2018; 61:567-574. [PMID: 29883551 DOI: 10.1139/gen-2018-0011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dioscorea zingiberensis (Dioscoreceae) is the main plant source of diosgenin (steroidal sapogenins), the precursor for the production of steroid hormones in the pharmaceutical industry. Despite its large economic value, genomic information of the genus Dioscorea is currently unavailable. Here, we present an initial survey of the D. zingiberensis genome performed by next-generation sequencing technology together with a genome size investigation inferred by flow cytometry. The whole genome survey of D. zingiberensis generated 31.48 Gb of sequence data with approximately 78.70× coverage. The estimated genome size is 800 Mb, with a high level of heterozygosity based on K-mer analysis. These reads were assembled into 334 288 contigs with a N50 length of 1079 bp, which were further assembled into 92 163 scaffolds with a total length of 173.46 Mb. A total of 4935 genes, 81 tRNAs, 69 rRNAs, and 661 miRNAs were predicted by the genome analysis, and 263 484 repeated sequences were obtained with 419 372 simple sequence repeats (SSRs). Among these SSRs, the mononucleotide repeat type was the most abundant (up to 54.60% of the total SSRs), followed by the dinucleotide (29.60%), trinucleotide (11.37%), tetranucleotide (3.53%), pentanucleotide (0.65%), and hexanucleotide (0.25%) repeat types. The 1C-value of D. zingiberensis was calibrated against Salvia miltiorrhiza and calculated as 0.87 pg (851 Mb) by flow cytometry, which was very close to the result of the genome survey. This is the first report of genome-wide characterization within this taxon.
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Affiliation(s)
- Wen Zhou
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Bin Li
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Lin Li
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Wen Ma
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Yuanchu Liu
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shuchao Feng
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Zhezhi Wang
- a Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China.,b National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
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Sosa MM, Angulo MB, Greppi JA, Bugallo V. Chromosome numbers and DNA content in some species of Mecardonia (Gratiolae, Plantaginaceae). COMPARATIVE CYTOGENETICS 2016; 10:769-780. [PMID: 28123693 PMCID: PMC5240523 DOI: 10.3897/compcytogen.v10i4.10362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Cytogenetic characterization and determination of DNA content by flow cytometry of five species of Mecardonia Ruiz et Pavon, 1798 (Gratiolae, Plantaginaceae) was performed. This is the first study of nuclear DNA content carried out in the genus. Mitotic analysis revealed a base chromosome number x = 11 for all entities and different ploidy levels, ranging from diploid (2n = 2x = 22) to hexaploid (2n = 6x = 66). The results include the first report of the chromosome numbers for Mecardonia flagellaris (Chamisso & Schlechtendal, 1827) (2n = 22), Mecardonia grandiflora (Bentham) Pennell, 1946 (2n = 22), Mecardonia kamogawae Greppi & Hagiwara, 2011 (2n = 66), and Mecardonia sp. (2n = 44). The three ploidy levels here reported suggest that polyploidy is common in Mecardonia and appear to be an important factor in the evolution of this genus. The 2C- and 1Cx-values were also estimated in all the species. The 2C-values ranged from 1.91 to 5.29 pg. The 1Cx-values ranged from 0.88 to 1.03 pg. The general tendency indicated a decrease in the 1Cx-value with increasing ploidy level. The significance of the results is discussed in relation to taxonomy of the genus.
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Affiliation(s)
- María M. Sosa
- Instituto de Botánica del Nordeste (UNNE-CONICET). Sargento Cabral 2131. Facultad de Ciencias Exactas, Naturales y Agrimensura (UNNE). Av. Libertad 5460. 3400. Corrientes, Argentina
| | - María B. Angulo
- Instituto de Botánica del Nordeste (UNNE-CONICET). Sargento Cabral 2131. Facultad de Ciencias Exactas, Naturales y Agrimensura (UNNE). Av. Libertad 5460. 3400. Corrientes, Argentina
| | - Julián A. Greppi
- Instituto de Floricultura, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Buenos Aires, Argentina
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Wolf DE, Steets JA, Houliston GJ, Takebayashi N. Genome size variation and evolution in allotetraploid Arabidopsis kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. AOB PLANTS 2014; 6:plu025. [PMID: 24887004 PMCID: PMC4076644 DOI: 10.1093/aobpla/plu025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Polyploidization and subsequent changes in genome size are fundamental processes in evolution and diversification. Little is currently known about the extent of genome size variation within taxa and the evolutionary forces acting on this variation. Arabidopsis kamchatica has been reported to contain both diploid and tetraploid individuals. The aim of this study was to determine the genome size of A. kamchatica, whether there is variation in ploidy and/or genome size in A. kamchatica and to study how genome size has evolved. We used propidium iodide flow cytometry to measure 2C DNA content of 73 plants from 25 geographically diverse populations of the putative allotetraploid A. kamchatica and its parents, Arabidopsis lyrata and Arabidopsis halleri. All A. kamchatica plants appear to be tetraploids. The mean 2C DNA content of A. kamchatica was 1.034 pg (1011 Mbp), which is slightly smaller than the sum of its diploid parents (A. lyrata: 0.502 pg; A. halleri: 0.571 pg). Arabidopsis kamchatica appears to have lost ∼37.594 Mbp (3.6 %) of DNA from its 2C genome. Tetraploid A. lyrata from Germany and Austria appears to have lost ∼70.366 Mbp (7.2 %) of DNA from the 2C genome, possibly due to hybridization with A. arenosa, which has a smaller genome than A. lyrata. We did find genome size differences among A. kamchatica populations, which varied up to 7 %. Arabidopsis kamchatica ssp. kawasakiana from Japan appears to have a slightly larger genome than A. kamchatica ssp. kamchatica from North America, perhaps due to multiple allopolyploid origins or hybridization with A. halleri. However, the among-population coefficient of variation in 2C DNA content is lower in A. kamchatica than in other Arabidopsis taxa. Due to its close relationship to A. thaliana, A. kamchatica has the potential to be very useful in the study of polyploidy and genome evolution.
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Affiliation(s)
- Diana E Wolf
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
| | - Janette A Steets
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Department of Botany, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078-3013, USA
| | - Gary J Houliston
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA Present Address: Landcare Research, Gerald St, Lincoln 7608, New Zealand
| | - Naoki Takebayashi
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775-7000, USA
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