1
|
Cao X, Liu Y, Liu Z, Liu F, Wu Y, Zhou Z, Cai X, Wang X, Zhang Z, Wang Y, Luo Z, Peng R, Wang K. Microdissection of the A h01 chromosome in upland cotton and microcloning of resistance gene anologs from the single chromosome. Hereditas 2017; 154:13. [PMID: 28529470 PMCID: PMC5437636 DOI: 10.1186/s41065-017-0035-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome microdissection is one of the most important techniques in molecular cytogenetic research. Cotton (Gossypium Linnaeus, 1753) is the main natural fiber crop in the world. The resistance gene analog (RGA) cloning after its single chromosome microdissection can greatly promote cotton genome research and breeding. RESULTS Using the linker adaptor PCR (LA-PCR) with the primers of rice disease-resistance homologues, three nucleotide sequences PS016 (KU051681), PS054 (KU051682), and PS157 (KU051680) were obtained from the chromosome Ah01 of upland cotton (cv. TM-1). The Blast results showed that the three sequences are the nucleotide binding site-leucine rich repeat (NBS-LRR) type RGAs. Clustering results indicated that they are homologous to these published RGAs. Thus, the three RGAs can definitely be confirmed as NBS-LRR class of RGAs in upland cotton. CONCLUSIONS Using single chromosome microdissection technique, DNA libraries containing cotton RGAs were obtained. This technique can promote cotton gene cloning, marker development and even the improvement of cotton genome research and breeding.
Collapse
Affiliation(s)
- Xinchuan Cao
- Tarium Universty, Alar, Xinjiang 843300 China.,State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Yuling Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China.,Anyang Institute of Technology, Anyang, Henan 455000 China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, Henan 455000 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Yalei Wu
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001 China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| | - Zhimin Luo
- Anyang Institute of Technology, Anyang, Henan 455000 China
| | - Renhai Peng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China.,Anyang Institute of Technology, Anyang, Henan 455000 China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan 455000 China
| |
Collapse
|
2
|
Taguchi T, Kubota S, Mezaki T, Tagami E, Sekida S, Nakachi S, Okuda K, Tominaga A. Identification of homogeneously staining regions by G-banding and chromosome microdissection, and FISH marker selection using human Alu sequence primers in a scleractinian coral Coelastrea aspera Verrill, 1866 (Cnidaria). COMPARATIVE CYTOGENETICS 2016; 10:61-75. [PMID: 27186338 PMCID: PMC4856926 DOI: 10.3897/compcytogen.v10i1.5699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/22/2015] [Indexed: 05/29/2023]
Abstract
Karyotype analysis was performed on the scleractinian coral Coelastrea aspera Verrill, 1866, commonly found along temperate coasts in Japan (30-35°N) and in coastal waters in the Indian and Pacific oceans. G-banding of Coelastrea aspera was successfully performed, although the banding pattern was not as clear as that in mammals. The karyogram clearly revealed that this coral had a homogeneously staining region (hsr) in chromosome 11. This hsr consisted of ribosomal RNA (rRNA) related genes, which was demonstrated by fluorescence in situ hybridization (FISH) with probes generated using 28S ribosomal DNA (rDNA) primers and those generated through chromosome microdissection. In addition, we conducted silver-stained nucleolus organizer region (Ag-NOR) analysis and found Ag depositions in the interphase nuclei but not on rRNA gene loci and hsr(s) in the mitotic stage. The hsr of this coral was observed in approximately 50% of the metaphase spreads analyzed. This may explain the diversity of coral rDNA based on the molecular study of sequence analysis. Furthermore, it was discovered that human telomere and Alu repeated sequences were present in this Coelastrea aspera. Probes derived from human Alu sequences are expected to play an important role in the classification of corals. Overall, our data can be of great value in discriminating among scleractinian coral species and understanding their genetics, including chromosomal evolution.
Collapse
Affiliation(s)
- Takahiro Taguchi
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Satoshi Kubota
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Takuma Mezaki
- Kuroshio Biological Research Foundation, Otsuki, Hata County, Kochi 788-0333, Japan
| | - Erika Tagami
- Department of Molecular & Cellular Biology, Kochi Medical School, Kochi University
| | - Satoko Sekida
- Division of Marine Bioresources, Graduate School of Kuroshio Science, Kochi University, 2-5-1 Akebono-cho, Kochi 780-8520, Japan
| | - Shu Nakachi
- Kuroshio Biological Research Foundation, Otsuki, Hata County, Kochi 788-0333, Japan
| | - Kazuo Okuda
- Division of Marine Bioresources, Graduate School of Kuroshio Science, Kochi University, 2-5-1 Akebono-cho, Kochi 780-8520, Japan
| | - Akira Tominaga
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8505, Japan
- Department of Molecular & Cellular Biology, Kochi Medical School, Kochi University
| |
Collapse
|
3
|
Taguchi T, Mezaki T, Iwase F, Sekida S, Kubota S, Fukami H, Okuda K, Shinbo T, Oshima SI, Iiguni Y, Testa JR, Tominaga A. Molecular cytogenetic analysis of the scleractinian coral Acropora solitaryensis Veron & Wallace 1984. Zoolog Sci 2014; 31:89-94. [PMID: 24521318 DOI: 10.2108/zsj.31.89] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We performed a molecular cytogenetic investigation of the scleractinian coral Acropora solitaryensis, which is dominant in the temperate region of Japan (30-35°N). Molecular cytogenetic analysis, using fluorescence in situ hybridization (FISH), was carried out for karyotyping and gene mapping. We propose the karyotype of this coral (2n = 30) based on C-banding and FISH analyses. FISH mapping of the rRNA gene was carried out with a probe generated by PCR amplification using rRNA gene primers. Furthermore, the telomeres and centromeres of all chromosomes were visualized using FISH. By comparative genomic hybridization using DNA from sperm and unfertilized eggs of this coral, we offer evidence suggesting the existence of sex chromosomes in this species. Collectively, these data advance our understanding of coral genetics.
Collapse
Affiliation(s)
- Takahiro Taguchi
- 1 Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8505, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Pazian MF, Shimabukuro-Dias CK, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosome painting of Z and W sex chromosomes in Characidium (Characiformes, Crenuchidae). Genetica 2013; 141:1-9. [PMID: 23344657 DOI: 10.1007/s10709-013-9701-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 01/17/2013] [Indexed: 01/23/2023]
Abstract
Some species of the genus Characidium have heteromorphic ZZ/ZW sex chromosomes with a totally heterochromatic W chromosome. Methods for chromosome microdissection associated with chromosome painting have become important tools for cytogenetic studies in Neotropical fish. In Characidium cf. fasciatum, the Z chromosome contains a pericentromeric heterochromatin block, whereas the W chromosome is completely heterochromatic. Therefore, a probe was produced from the W chromosome through microdissection and degenerate oligonucleotide-primed polymerase chain reaction amplification. FISH was performed using the W probe on the chromosomes of specimens of this species. This revealed expressive marks in the pericentromeric region of the Z chromosome as well as a completely painted W chromosome. When applying the same probe on chromosome preparations of C. cf. gomesi and Characidium sp., a pattern similar to C. cf. fasciatum was found, while C. cf. zebra, C. cf. lagosantense and Crenuchus spilurus species showed no hybridization signals. Structural changes in the chromosomes of an ancestral sexual system in the group that includes the species C. cf. gomesi, C. cf. fasciatum and Characidium sp., could have contributed to the process of speciation and could represent a causal mechanism of chromosomal diversification in this group. The heterochromatinization process possibly began in homomorphic and homologous chromosomes of an ancestral form, and this process could have given rise to the current patterns found in the species with sex chromosome heteromorphism.
Collapse
Affiliation(s)
- Marlon F Pazian
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior S/N, Rubião Júnior, Botucatu, SP, Brazil.
| | | | | | | | | |
Collapse
|
5
|
Nieves M, De Oliveira EHC, Amaral PJS, Nagamachi CY, Pieczarka JC, Mühlmann MC, Mudry MD. Analysis of the heterochromatin of Cebus (Primates, Platyrrhini) by micro-FISH and banding pattern comparisons. J Genet 2011; 90:111-7. [PMID: 21677395 DOI: 10.1007/s12041-011-0047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The karyotype of the neotropical primate genus Cebus (Platyrrhini: Cebidae), considered the most ancestral one, shows the greatest amount of heterochromatin described among Platyrrhini genera. Banding techniques and restriction enzyme digestion have previously revealed great variability of quantity and composition of heterochromatin in this genus. In this context, we use fluorescence in situ hybridization (FISH) to analyse this genomic region and discuss its possible role in the diversification of Cebus.We used a heterochromatin probe for chromosome 11 of Cebus libidinosus (11qHe+ CLI probe), obtained by chromosome microdissection. Twenty-six specimens belonging to the families Atelidae, Cebidae, Callitrichidae and Pithecidae (Platyrrhini) were studied. Fourteen out of 26 specimens were Cebus (Cebidae) individuals of C. libidinosus, C. xanthosternos, C. apella, C. nigritus, C. albifrons, C. kaapori and C. olivaceus. In Cebus specimens, we found 6 to 22 positive signals located in interstitial and telomeric positions along the different species. No hybridization signal was observed among the remaining Ceboidea species, thus reinforcing the idea of a Cebus-specific heterochromatin composed of a complex system of repetitive sequences.
Collapse
Affiliation(s)
- Mariela Nieves
- Grupo de Investigación en Biología Evolutiva, Laboratorio 46, 4° piso, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II - Ciudad Universitaria, Intendente Güiraldes 2160 - C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.
| | | | | | | | | | | | | |
Collapse
|
6
|
Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M, Kuroiwa A, Hirai H, Hirai Y, Matsuda Y, Okada N. B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes. PLoS Genet 2011; 7:e1002203. [PMID: 21876673 PMCID: PMC3158035 DOI: 10.1371/journal.pgen.1002203] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/08/2011] [Indexed: 11/19/2022] Open
Abstract
The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation. Although the evolution of the sex-determination system may also play a role in speciation, little is known about the sex-determination system of Lake Victoria cichlids. To understand the evolution of the sex-determination system in these fish, we performed cytogenetic analysis in 11 cichlid species from Lake Victoria. B chromosomes, which are present in addition to standard chromosomes, were found at a high prevalence rate (85%) in these cichlids. In one species, B chromosomes were female-specific. Cross-breeding using females with and without the B chromosomes demonstrated that the presence of the B chromosomes leads to a female-biased sex ratio in this species. Although B chromosomes were believed to be selfish genetic elements with little effect on phenotype and to lack protein-coding genes, the present study provides evidence that B chromosomes have a functional effect on female sex determination. FISH analysis using a BAC clone containing B chromosome DNA suggested that the B chromosomes are derived from sex chromosomes. Determination of the nucleotide sequences of this clone (104.5 kb) revealed the presence of several protein-coding genes in the B chromosome, suggesting that B chromosomes have the potential to contain functional genes. Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes.
Collapse
Affiliation(s)
- Kohta Yoshida
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yohey Terai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masakatsu Watanabe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Asato Kuroiwa
- Laboratory of Animal Cytogenetics, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
7
|
Kume M, Taguchi T, Okada H, Anayama T, Tominaga A, Shuin T, Sasaguri S. Establishment and molecular cytogenetic characterization of non-small cell lung cancer cell line KU-T1 by multicolor fluorescence in situ hybridization, comparative genomic hybridization, and chromosome microdissection. ACTA ACUST UNITED AC 2007; 179:93-101. [PMID: 18036395 DOI: 10.1016/j.cancergencyto.2007.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 07/21/2007] [Accepted: 07/31/2007] [Indexed: 10/22/2022]
Abstract
A human lung adenocarcinoma cell line, designated KU-T1, was established from a Japanese man in Kochi Medical School. Conventional banding and multicolor fluorescence in situ hybridization (M-FISH) analyses of KU-T1 cells revealed a hyperdiploid chromosomal constitution and complex karyotypes. Comparative genomic hybridization showed several chromosomal copy number changes, and five regions that were highly amplified. Two of the five highly amplified regions, 1q and 3q, were identified from distributions of DNA sequences on a metaphase cell by FISH using chromosome microdissection-generated probes hybridized to 1q32 approximately q34 and 3q26 approximately q28, respectively. The 3q probe depicted a homogeneously staining region (hsr) in a derivative chromosome 3 of KU-T1. An hsr probe was regenerated by chromosome microdissection and was hybridized back to KU-T1 and normal metaphases. This hybridization experiment confirmed the probe derived from an hsr and indicated original locations of DNA sequences of hsr on normal chromosome 3. Intense hybridized signals shown at three loci (3p12, 3q26.3, and 3q28) suggests that oncogenes may be involved in the hsr formation. The present study provides a comprehensive analysis of the chromosomal abnormalities, including hsr formation and related oncogenes, in the KU-T1 cell line.
Collapse
Affiliation(s)
- Motohiko Kume
- Department of Surgery II, Kochi Medical School, Nankoku, Kochi 783-8505, Japan
| | | | | | | | | | | | | |
Collapse
|
8
|
Taguchi T, Hirai Y, LoVerde PT, Tominaga A, Hirai H. DNA probes for identifying chromosomes 5, 6, and 7 of Schistosoma mansoni. J Parasitol 2007; 93:724-6. [PMID: 17626377 DOI: 10.1645/ge-1099r.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Schistosoma mansoni has a genome of 270 Mb contained on 8 pairs of chromosomes. C-banding has been a useful technique in identifying the 7 autosomal and sex chromosomes. However, even with C-banding, S. mansoni chromosomes 5, 6, and 7 are difficult to discriminate from each other, because of their small sizes, morphological similarity, and poor banding patterns. We have identified probes that specifically paint chromosomes 5, 6, and 7 of S. mansoni with the use of chromosome microdissection and the degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). Exact chromosome identification is required for accurate chromosome mapping of genomic clones and genetic elements, which is an essential component of the schistosome genome project.
Collapse
Affiliation(s)
- T Taguchi
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Kochi 783-8505, Japan.
| | | | | | | | | |
Collapse
|
9
|
Xia X, Rasmussen T, Alvarez X, Taguchi T, Li M, La Russa VF. Fluorescence in situ hybridization using an old world monkey Y chromosome specific probe combined with immunofluorescence staining on rhesus monkey tissues. J Histochem Cytochem 2007; 55:1115-21. [PMID: 17595337 PMCID: PMC3957529 DOI: 10.1369/jhc.7a7216.2007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To date, there is no commercially available Y chromosome probe that can be used for fluorescence in situ hybridization (FISH) for the male rhesus monkey. We have recently generated a probe for FISH with high specificity to the short arm of the rhesus monkey Y chromosome. In this study, we further describe a method that keeps the integrity of tissue-specific antigenic structures for immunofluorescence staining subsequent to FISH on paraffin-embedded rhesus monkey tissues. We have examined this technique in combination with an epithelial cell-specific marker, cytokeratin 8/18 (CK8/18), on various tissues, including jejunum, liver, kidney, and pancreas. CK8/18 and Y chromosome signals were distinctly seen simultaneously on epithelial cells from the same tissue section from male but not female monkeys. These studies indicate that our FISH immunofluorescence technique can be reliably used to identify and phenotype male cells in paraffin-embedded rhesus monkey tissues.
Collapse
Affiliation(s)
- Xiujin Xia
- Department of Pharmacology, Tulane University Health Sciences Center, New Orleans, Louisiana
- Division of Gene Therapy, Tulane National Primate Research Center, Covington, Louisiana
| | - Terri Rasmussen
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana
| | - Xavier Alvarez
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana
| | - Takahiro Taguchi
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Kochi, Japan
| | - Marilyn Li
- Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, Louisiana
| | - Vincent F. La Russa
- Department of Pharmacology, Tulane University Health Sciences Center, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, Louisiana
- Division of Gene Therapy, Tulane National Primate Research Center, Covington, Louisiana
- Correspondence to: Vincent F. La Russa, PhD, Tulane University Health Sciences Center, Cancer Center, 1415 Tulane Avenue, SL-34, New Orleans, LA. E-mail:
| |
Collapse
|