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Wei M, Huang Y, Mo C, Wang H, Zeng Q, Yang W, Chen J, Zhang X, Kong Q. Telomere-to-telomere genome assembly of melon ( Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits. HORTICULTURE RESEARCH 2023; 10:uhad189. [PMID: 37915500 PMCID: PMC10615816 DOI: 10.1093/hr/uhad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/12/2023] [Indexed: 11/03/2023]
Abstract
Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.
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Affiliation(s)
- Minghua Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changjuan Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Yang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jihao Chen
- Hainan Sanya Experimental Center for Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya 572014, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Hainan Sanya Experimental Center for Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya 572014, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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Bi YH, Li Z, Zhou ZG. Karyotype analysis of the brown seaweed Saccharina (or Laminaria) japonica. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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She CW, Jiang XH, He CP. Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. COMPARATIVE CYTOGENETICS 2023; 17:31-58. [PMID: 37305810 PMCID: PMC10252140 DOI: 10.3897/compcytogen.v17.i1.99236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/23/2023] [Indexed: 06/13/2023]
Abstract
To have an insight into the karyotype variation of eight Cucurbitaceae crops including Cucumissativus Linnaeus, 1753, Cucumismelo Linnaeus, 1753, Citrulluslanatus (Thunberg, 1794) Matsumura et Nakai, 1916, Benincasahispida (Thunberg, 1784) Cogniaux, 1881, Momordicacharantia Linnaeus, 1753, Luffacylindrica (Linnaeus, 1753) Roemer, 1846, Lagenariasicerariavar.hispida (Thunberg, 1783) Hara, 1948 and Cucurbitamoschata Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the chromosomal distribution of heterochromatin and 18S-5.8S-26S rRNA genes (45S rDNA) was investigated using sequential combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. Detailed karyotypes were established using the dataset of chromosome measurements, fluorochrome bands and rDNA FISH signals. Four karyotype asymmetry indices, CVCI, CVCL, MCA and Stebbins' category, were measured to elucidate the karyological relationships among species. All the species studied had symmetrical karyotypes composed of metacentric and submetacentric or only metacentric chromosomes, but their karyotype structure can be discriminated by the scatter plot of MCA vs. CVCL. The karyological relationships among these species revealed by PCoA based on x, 2n, TCL, MCA, CVCL and CVCI was basically in agreement with the phylogenetic relationships revealed by DNA sequences. CPD staining revealed all 45S rDNA sites in all species, (peri)centromeric GC-rich heterochromatin in C.sativus, C.melo, C.lanatus, M.charantia and L.cylindrica, terminal GC-rich heterochromatin in C.sativus. DAPI counterstaining after FISH revealed pericentromeric DAPI+ heterochromatin in C.moschata. rDNA FISH detected two 45S loci in five species and five 45S loci in three species. Among these 45S loci, most were located at the terminals of chromosome arms, and a few in the proximal regions. In C.sativus, individual chromosomes can be precisely distinguished by the CPD band and 45S rDNA signal patterns, providing an easy method for chromosome identification of cucumber. The genome differentiation among these species was discussed in terms of genome size, heterochromatin, 45S rDNA site, and karyotype asymmetry based on the data of this study and previous reports.
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Affiliation(s)
- Chao-Wen She
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
| | - Xiang-Hui Jiang
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
| | - Chun-Ping He
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
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Santos MC, Souza MM, de Melo CAF, Silva GS. Karyotyping of commercial cultivars of melon (Cucumis melo L.). Mol Biol Rep 2022; 49:10279-10292. [PMID: 36097123 DOI: 10.1007/s11033-022-07520-z] [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: 04/15/2021] [Revised: 04/18/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND This study on cultivars of melon (Cucumis melo L.) marketed in Brazil was conducted to obtain information to be used in breeding programs of this species. Little is known about the karyotype variability among C. melo L. cultivars targeted at the consumer market. The objective of the present study was to verify the karyotype variability in eight commercial melon cultivars used in the Brazilian market. METHODS AND RESULTS Slides were stained with 2% Giemsa and assembled with Neomount to perform chromosomal morphometry. GC-rich heterochromatin was observed by CMA3/DAPI staining. 5 S rDNA, centromeric satellite DNA (SatDNA), and telomeric sites were visualized using fluorescence in situ hybridization. All images were captured on an Olympus BX41 microscope equipped with a 5 M Olympus DP25 digital camera and DP2-BSW software. The cultivars showed symmetrical karyotypes with significant differences in total chromosome length and average chromosome size. Heterochromatic CMA3+ blocks were observed in terminal regions related to satellites (secondary constrictions), as well as in centromeric and pericentromeric regions. A single chromosomal pair of 5 S rDNA sites was observed in all cultivars, but at distinct locations. Centromeric satellite sequences, tested for the first time in melon, revealed only centromeric sites. Telomeric sites were observed in all the chromosomes of the cultivars. CONCLUSIONS Karyotype variation was observed in cultivars of melon, which were analyzed for chromosomal morphology and localization of GC-rich heterochromatin, as well centromeric SatDNA, rDNA, and telomeric chromosomal markers. Hence, these cultivars can be used in future breeding programs.
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Affiliation(s)
- Matusalem Campos Santos
- Departamento de Ciências Biológicas, Laboratório de Melhoramento de Plantas, Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, km 16, 45662-900, Ilhéus, Brasil
| | - Margarete Magalhães Souza
- Departamento de Ciências Biológicas, Laboratório de Melhoramento de Plantas, Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, km 16, 45662-900, Ilhéus, Brasil.
| | - Cláusio Antônio Ferreira de Melo
- Departamento de Ciências Biológicas, Laboratório de Melhoramento de Plantas, Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, km 16, 45662-900, Ilhéus, Brasil
| | - Gonçalo Santos Silva
- Departamento de Ciências Biológicas, Laboratório de Melhoramento de Plantas, Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, km 16, 45662-900, Ilhéus, Brasil
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The Divergence of Chromosome Structures and 45S Ribosomal DNA Organization in Cucumis debilis Inferred by Comparative Molecular Cytogenetic Mapping. PLANTS 2022; 11:plants11151960. [PMID: 35956438 PMCID: PMC9370355 DOI: 10.3390/plants11151960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
Cucumis debilis W.J.de Wilde & Duyfjes is an annual and monoecious plant. This species is endemic to Southeast Asia, particularly Vietnam. However, C. debilis is rarely studied, and no detailed information is available regarding its basic chromosome number, 45S ribosomal DNA (rDNA) status, and divergence among other Cucumis species. In this study, we characterized the morphological characters and determined and investigated the basic chromosome number and chromosomal distribution of 45S rDNA of C. debilis using the fluorescent in situ hybridization (FISH) technique. A maximum likelihood tree was constructed by combining the chloroplast and internal transcribed spacer of 45S rDNAs to infer its relationship within Cucumis. C. debilis had an oval fruit shape, green fruit peel, and protrusion-like white spots during the immature fruit stage. FISH analysis using 45S rDNA probe showed three pairs of 45S rDNA loci located at the terminal region in C. debilis, similar to C. hystrix. Meanwhile, two, two, and five pairs of 45S rDNA loci were observed for C. melo, C. metuliferus, and C. sativus, respectively. One melon (P90) and cucumber accessions exhibited different chromosomal localizations compared with other members of Cucumis. The majority of Cucumis species showed the terminal location of 45S rDNA, but melon P90 and cucumber exhibited terminal–interstitial and all interstitial orientations of 45S rDNA loci. Based on molecular cytogenetics and phylogenetic evidence, C. debilis is more closely related to cucumber than melon. Therefore, C. debilis may serve as a potential parental accession for genetic improvement of cucumber through interspecific hybridization.
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Bhowmick BK, Jha S. A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa. COMPARATIVE CYTOGENETICS 2022; 16:93-125. [PMID: 36761811 PMCID: PMC9849056 DOI: 10.3897/compcytogen.v16.i2.79033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/13/2023]
Abstract
The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata-700006, West Bengal, IndiaScottish Church CollegeKolkataIndia
| | - Sumita Jha
- Plant Cytogenetics and Biotechnology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species. Cytogenet Genome Res 2020; 160:554-564. [DOI: 10.1159/000511119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that <i>Menolird18</i>, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in <i>Cucumis melo</i>, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, <i>Menolird18</i> was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of <i>Menolird18</i> were found in centromeric and rDNA regions of mitotic chromosomes suggests that <i>Menolird18</i> is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of <i>Menolird18</i> in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (<i>C. melo</i>) and cucumber (<i>C. sativus</i>) genomes.
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Li Z, Bi Y, Wang X, Wang Y, Yang S, Zhang Z, Chen J, Lou Q. Chromosome identification in Cucumis anguria revealed by cross-species single-copy gene FISH. Genome 2018; 61:397-404. [DOI: 10.1139/gen-2017-0235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cucumis anguria is a potential genetic resource for improving crops of the genus Cucumis, owing to its broad-spectrum resistance. However, few cytogenetic studies on C. anguria have been reported because of its small metaphase chromosomes and the scarcity of distinguished chromosomal landmarks. In this study, 14 single-copy genes from cucumber and rDNAs were used as probes for FISH to identify the individual chromosomes of C. anguria. The distinctive signal distribution patterns of the probes allowed us to distinguish each chromosome of C. anguria (A01–A12). Further, detailed chromosome characteristics were obtained through pachytene chromosome FISH. The lengths of pachytene chromosomes varied from 54.80 to 143.41 μm. The proportion of heterochromatin regions varied from 13.56% to 63.86%. Finally, the chromosomal homeologous relationship between C. anguria and cucumber (C1–C7) was analyzed. The results showed that A06 + A09, A03 + A12, A02 + A04, and A01 + A11 were homeologs of C1, C2, C3, and C6, respectively. Furthemore, chromosomes A08, A10, and A05 were homeologs of C4, C5, and C7, respectively. Chromosome identification and homeologous relationship analysis between C. anguria and cucumber lay the foundation for further research of genome structure evolution in species of Cucumis.
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Affiliation(s)
- Ziang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunfei Bi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunzhu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhentao Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Koba T. An improved method for inducing prometaphase chromosomes in plants. Mol Cytogenet 2018; 11:32. [PMID: 29760782 PMCID: PMC5946395 DOI: 10.1186/s13039-018-0380-6] [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: 02/20/2018] [Accepted: 04/23/2018] [Indexed: 01/14/2023] Open
Abstract
Background Detailed karyotyping using metaphase chromosomes in melon (Cucumis melo L.) remains a challenge because of their small chromosome sizes and poor stainability. Prometaphase chromosomes, which are two times longer and loosely condensed, provide a significantly better resolution for fluorescence in situ hybridization (FISH) than metaphase chromosomes. However, suitable method for acquiring prometaphase chromosomes in melon have been poorly investigated. Results In this study, a modified Carnoy’s solution II (MC II) [6:3:1 (v/v) ethanol: acetic acid: chloroform] was used as a pretreatment solution to obtain prometaphase chromosomes. We demonstrated that the prometaphase chromosomes obtained using the MC II method are excellent for karyotyping and FISH analysis. We also observed that a combination of MC II and the modified air dry (ADI) method provides a satisfactory meiotic pachytene chromosome preparation with reduced cytoplasmic background and clear chromatin spreads. Moreover, we demonstrated that pachytene and prometaphase chromosomes of melon and Abelia × grandiflora generate significantly better FISH images when prepared using the method described. We confirmed, for the first time, that Abelia × grandiflora has pairs of both strong and weak 45S ribosomal DNA signals on the short arms of their metaphase chromosomes. Conclusion The MC II and ADI method are simple and effective for acquiring prometaphase and pachytene chromosomes with reduced cytoplasm background in plants. Our methods provide high-resolution FISH images that can help accelerate molecular cytogenetic research in plants.
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Affiliation(s)
- Agus Budi Setiawan
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Chee How Teo
- 2Center for Research in Biotechnology for Agriculture, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shinji Kikuchi
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Hidenori Sassa
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
| | - Takato Koba
- 1Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510 Japan
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Tan J, Wang J, Luo L, Yu C, Xu T, Wu Y, Cheng T, Wang J, Pan H, Zhang Q. Genetic relationships and evolution of old Chinese garden roses based on SSRs and chromosome diversity. Sci Rep 2017; 7:15437. [PMID: 29133839 PMCID: PMC5684293 DOI: 10.1038/s41598-017-15815-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/02/2017] [Indexed: 11/09/2022] Open
Abstract
Old Chinese garden roses are the foundation of the modern rose, which is one of the best-selling ornamental plants. However, the horticultural grouping and evolution of old Chinese garden roses are unclear. Simple sequence repeat (SSR) markers were employed to survey genetic diversity in old Chinese garden roses and genetic differentiation was estimated among different rose groups. Fluorescence in situ hybridization was used to study the physical localization of 5 S rDNA genes and a karyotype analysis was performed. The SSR data suggest that old Chinese garden roses could be divided into Old Blush group, Odorata group and Ancient hybrid China group. The Old Blush group had the most primitive karyotype. The Ancient hybrid China group and modern rose had the most evolved karyotypes and the highest genetic diversity. During the evolution of rose cultivars, 5 S rDNA increased in number, partially weakened in signal intensity and exhibited variation in distance from the centromere. In conclusion, rose cultivars evolved from the Old Blush Group to the Odorata group, the Ancient Hybrid China group and the modern rose. This work provides a basis for the collection, identification, conservation and innovation of rose germplasm resources.
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Affiliation(s)
- Jiongrui Tan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jing Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Le Luo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Chao Yu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tingliang Xu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yuying Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
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Zhang L, Yang X, Tian L, Chen L, Yu W. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. THE NEW PHYTOLOGIST 2016; 211:1424-39. [PMID: 27176118 DOI: 10.1111/nph.13999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/31/2016] [Indexed: 05/17/2023]
Abstract
The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
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Affiliation(s)
- Laining Zhang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Xiaoyu Yang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - Lei Chen
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Weichang Yu
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
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12
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Zhang ZT, Yang SQ, Li ZA, Zhang YX, Wang YZ, Cheng CY, Li J, Chen JF, Lou QF. Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis. Genome 2016; 59:449-57. [PMID: 27334092 DOI: 10.1139/gen-2015-0207] [Citation(s) in RCA: 20] [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
Ribosomal DNAs are useful cytogenetic markers for chromosome analysis. Studies investigating site numbers and distributions of rDNAs have provided important information for elucidating genome organization and chromosomal relationships of many species by fluorescence in situ hybridization. But relevant studies are scarce for species of the genus Cucumis, especially in wild species. In the present study, FISH was conducted to investigate the organization of 45S and 5S rDNA among 20 Cucumis accessions, including cultivars and wild accessions. Our results showed that the number of 45S rDNA sites varied from one to five pairs in different accessions, and most of these sites are located at the terminal regions of chromosomes. Interestingly, up to five pairs of 45S rDNA sites were observed in C. sativus var. sativus, the species which has the lowest chromosome number, i.e., 2n = 14. Only one pair of 5S rDNA sites was detected in all accessions, except for C. heptadactylus, C. sp, and C. spp that had two pairs of 5S rDNA sites. The distributions of 5S rDNA sites showed more variation than 45S rDNA sites. The phylogenetic analysis in this study showed that 45S and 5S rDNA have contrasting evolutionary patterns. We find that 5S rDNA has a polyploidization-related tendency towards the terminal location from an interstitial location but maintains a conserved site number, whereas the 45S rDNA showed a trend of increasing site number but a relatively conserved location.
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Affiliation(s)
- Zhen-Tao Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Shu-Qiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Zi-Ang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Yun-Xia Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Yun-Zhu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Chun-Yan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Jin-Feng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
| | - Qun-Feng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing 210095, China
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13
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Competitive Expression of Endogenous Wheat CENH3 May Lead to Suppression of Alien ZmCENH3 in Transgenic Wheat × Maize Hybrids. J Genet Genomics 2015; 42:639-649. [DOI: 10.1016/j.jgg.2015.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/15/2015] [Accepted: 05/06/2015] [Indexed: 01/26/2023]
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14
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Zhang Y, Cheng C, Li J, Yang S, Wang Y, Li Z, Chen J, Lou Q. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping. BMC Genomics 2015; 16:730. [PMID: 26407707 PMCID: PMC4583154 DOI: 10.1186/s12864-015-1877-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/24/2015] [Indexed: 12/23/2022] Open
Abstract
Background Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Results Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo. Conclusions In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1877-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxia Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yunzhu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ziang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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15
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Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 2015; 16:4. [PMID: 25612459 PMCID: PMC4316794 DOI: 10.1186/s12864-014-1196-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 12/22/2014] [Indexed: 01/01/2023] Open
Abstract
Background The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds. Results A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed. Conclusions By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1196-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason M Argyris
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain.
| | - Pablo Madriz-Masis
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain. .,Present Address: Sequentia Biotech, Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, 08193, Barcelona, Spain.
| | - Jordi Morata
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Marta Pujol
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | | | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
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16
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Cai Z, Liu H, He Q, Pu M, Chen J, Lai J, Li X, Jin W. Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping. BMC Genomics 2014; 15:1025. [PMID: 25425126 PMCID: PMC4256728 DOI: 10.1186/1471-2164-15-1025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/19/2014] [Indexed: 02/07/2023] Open
Abstract
Abstract Background Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9–11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. Results About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. Conclusions The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1025) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Weiwei Jin
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing 100193, China.
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17
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Zhao X, Lu J, Zhang Z, Hu J, Huang S, Jin W. Comparison of the distribution of the repetitive DNA sequences in three variants of Cucumis sativus reveals their phylogenetic relationships. J Genet Genomics 2011; 38:39-45. [PMID: 21338951 DOI: 10.1016/j.jcg.2010.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/20/2010] [Accepted: 12/24/2010] [Indexed: 01/08/2023]
Abstract
Repetitive DNA sequences with variability in copy number or/and sequence polymorphism can be employed as useful molecular markers to study phylogenetics and identify species/chromosomes when combined with fluorescence in situ hybridization (FISH). Cucumis sativus has three variants, Cucumis sativus L. var. sativus, Cucumis sativus L. var. hardwickii and Cucumis sativus L. var. xishuangbannesis. The phylogenetics among these three variants has not been well explored using cytological landmarks. Here, we concentrate on the organization and distribution of highly repetitive DNA sequences in cucumbers, with emphasis on the differences between cultivar and wild cucumber. The diversity of chromosomal karyotypes in cucumber and its relatives was detected in our study. Thereby, sequential FISH with three sets of multi-probe cocktails (combined repetitive DNA with chromosome-specific fosmid clones as probes) were conducted on the same metaphase cell, which helped us to simultaneously identify each of the 7 metaphase chromosomes of wild cucumber C. sativus var. hardwickii. A standardized karyotype of somatic metaphase chromosomes was constructed. Our data also indicated that the relationship between cultivar cucumber and C. s. var. xishuangbannesis was closer than that of C. s. var. xishuangbannesis and C. s. var. hardwickii.
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Affiliation(s)
- Xin Zhao
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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18
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Li D, Cuevas HE, Yang L, Li Y, Garcia-Mas J, Zalapa J, Staub JE, Luan F, Reddy U, He X, Gong Z, Weng Y. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics 2011; 12:396. [PMID: 21816110 PMCID: PMC3199783 DOI: 10.1186/1471-2164-12-396] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/05/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes. RESULTS Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F(2)- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber. CONCLUSIONS Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.
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Affiliation(s)
- Dawei Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Hugo E Cuevas
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Tropical Agriculture Research Station, Mayaguez, P.R. 00680, Puerto Rico
| | - Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Juan Zalapa
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jack E Staub
- USDA-ARS, Forage & Range Research Laboratory, Utah State University, Logan, UT 84322 USA
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University, Harbin, 150030, China
| | - Umesh Reddy
- Department of Biology, West Virginia State University Institute, WV 25112, USA
| | - Xiaoming He
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhenhui Gong
- Horticulture College, Northwest A & F University, Yangling 712100, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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Yoshido A, Yasukochi Y, Sahara K. Samia cynthia versus Bombyx mori: comparative gene mapping between a species with a low-number karyotype and the model species of Lepidoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 41:370-7. [PMID: 21396446 DOI: 10.1016/j.ibmb.2011.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/21/2011] [Accepted: 02/22/2011] [Indexed: 05/08/2023]
Abstract
We performed gene-based comparative FISH mapping between a wild silkmoth, Samia cynthia ssp. with a low number of chromosomes (2n=25-28) and the model species, Bombyx mori (2n=56), in order to identify the genomic components that make up the chromosomes in a low-number karyotype. Mapping of 64 fosmid probes containing orthologs of B. mori genes revealed that the homologues of either two or four B. mori chromosomes constitute the S. c. ricini (Vietnam population, 2n=27♀/28♂, Z0/ZZ) autosomes. Where tested, even the gene order was conserved between S. c. ricini and B. mori. This was also true for the originally autosomal parts of the neo-sex chromosomes in S. c. walkeri (Sapporo population, 2n=26♀/26♂, neo-Wneo-Z/neo-Zneo-Z) and S. cynthia subsp. indet. (Nagano population, 2n=25♀/26♂, neo-WZ₁Z₂/Z₁Z₁Z₂Z₂). The results are evidence for an internal stability of lepidopteran chromosomes even when all autosomes had undergone fusion processes to form a low-number karyotype.
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Affiliation(s)
- Atsuo Yoshido
- Laboratory of Applied Molecular Entomology, Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo 060-8589, Japan.
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