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Baisvar VS, Kushwaha B, Kumar R, Kumar MS, Singh M, Rai A, Sarkar UK. BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning. Int J Mol Sci 2022; 23:ijms232415958. [PMID: 36555603 PMCID: PMC9781557 DOI: 10.3390/ijms232415958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Construction of a physical chromosome map of a species is important for positional cloning, targeted marker development, fine mapping of genes, selection of candidate genes for molecular breeding, as well as understanding the genome organization. The genomic libraries in the form of bacterial artificial chromosome (BAC) clones are also a very useful resource for physical mapping and identification and isolation of full-length genes and the related cis acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of Clarias magur (magur) to understand the genome organization of the species and to establish the relationships with other species in respect to genes' organization and evolution in the past. In the present study, we generated end sequences of the BAC clones and analyzed those end sequences within the scaffolds of the draft genome of magur to identify and map the genes bioinformatically for each clone. A total of 36 clones mostly possessing genes were identified and used in probe construction and their subsequent hybridization on the metaphase chromosomes of magur. This study successfully mapped all 36 specific clones on 16 chromosome pairs, out of 25 pairs of magur chromosomes. These clones are now recognized as chromosome-specific makers, which are an aid in individual chromosome identification and fine assembly of the genome sequence, and will ultimately help in developing anchored genes' map on the chromosomes of C. magur for understanding their organization, inheritance of important fishery traits and evolution of magur with respect to channel catfish, zebrafish and other species.
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Affiliation(s)
- Vishwamitra Singh Baisvar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Basdeo Kushwaha
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Ravindra Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
- Correspondence:
| | - Murali Sanjeev Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Mahender Singh
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR—Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Uttam Kumar Sarkar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
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Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
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Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 PMCID: PMC6944119 DOI: 10.7717/peerj.8344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 01/15/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium.,Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 DOI: 10.7287/peerj.preprints.27806v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 05/23/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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Liu Y, Wang X, Wei Y, Liu Z, Lu Q, Liu F, Zhang T, Peng R. Chromosome Painting Based on Bulked Oligonucleotides in Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:802. [PMID: 32695125 PMCID: PMC7338755 DOI: 10.3389/fpls.2020.00802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 05/06/2023]
Abstract
Chromosome painting is one of the key technologies in cytogenetic research, which can accurately identify chromosomes or chromosome regions. Oligonucleotide (oligo) probes designed based on genome sequences have both flexibility and specificity, which would be ideal probes for fluorescence in situ hybridization (FISH) analysis of genome structure. In this study, the bulked oligos of the two arms of chromosome seven of cotton were developed based on the genome sequence of Gossypium raimondii (DD, 2n = 2× = 26), and each arm contains 12,544 oligos. Chromosome seven was easily identified in both D genome and AD genome cotton species using the bulked chromosome-specific painting probes. Together with 45S ribosomal DNA (rDNA) probe, the chromosome-specific painting probe was also successfully used to correct the chromosomal localization of 45S rDNA in G. raimondii. The study reveals that bulked oligos specific to a chromosome is a useful tool for chromosome painting in cotton.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, China
| | | | | | - Zhen Liu
- Anyang Institute of Technology, Anyang, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang,
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, China
- Renhai Peng,
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6
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Liu Y, Zhang B, Wen X, Zhang S, Wei Y, Lu Q, Liu Z, Wang K, Liu F, Peng R. Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum. PLoS One 2018; 13:e0196847. [PMID: 29771937 PMCID: PMC5957370 DOI: 10.1371/journal.pone.0196847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/20/2018] [Indexed: 11/18/2022] Open
Abstract
A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD4) was constructed. Intact nuclei from G. mustelinum (AD4) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G. mustelinum, the BAC library was estimated to have a total coverage of 10.50 × genome equivalents. The high capacity library of G. mustelinum will serve as a giant gene resource for map-based cloning of quantitative trait loci or genes associated with important agronomic traits or resistance to Verticillium wilt, physical mapping and comparative genome analysis.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States of America
| | - Xinpeng Wen
- Anyang Institute of Technology, Anyang, Henan, China
| | - Shulin Zhang
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
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Montes E, Coriton O, Eber F, Huteau V, Lacape JM, Reinhardt C, Marais D, Hofs JL, Chèvre AM, Pannetier C. Assessment of Gene Flow Between Gossypium hirsutum and G. herbaceum: Evidence of Unreduced Gametes in the Diploid Progenitor. G3 (BETHESDA, MD.) 2017; 7:2185-2193. [PMID: 28546386 PMCID: PMC5499127 DOI: 10.1534/g3.117.041509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/03/2017] [Indexed: 11/30/2022]
Abstract
In the framework of a gene flow assessment, we investigated the natural hybridization rate between Gossypium hirsutum (AADD genome) and G. herbaceum (AA genome). The latter species, a diploid progenitor of G. hirsutum, is spontaneously present in South Africa. Reciprocal crosses were performed without emasculation between G. herbaceum and G. hirsutum Neither examination of the morphological characteristics nor flow cytometry analysis of the 335 plants resulting from the G. hirsutum × G. herbaceum cross showed any hybrid features. Of the 148 plants produced from the G. herbaceum × G. hirsutum cross, three showed a hybrid phenotype, and their hybrid status was confirmed by SSR markers. Analysis of DNA content by flow cytometry and morphological traits clearly showed that two of these plants were triploid (AAD). The third plant had a flow cytometry DNA content slightly higher than G. hirsutum In addition, its morphological characteristics (plant architecture, presence and size of petal spots, leaf shape) led us to conclude that this plant was AAAD thus resulting from fertilization with an unreduced AA gamete of the female G. herbaceum parent. Fluorescent In Situ Hybridization (FISH) and meiotic behavior confirmed this hypothesis. To the best of our knowledge, this is the first description of such gametes in G. herbaceum, and it opens new avenues in breeding programs. Furthermore, this plant material could provide a useful tool for studying the expression of genes duplicated in the A and D cotton genome.
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Affiliation(s)
- E Montes
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - O Coriton
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique (INRA), Agrocampus Ouest, Université de Rennes I., BP35327, 35653 Le Rheu, France
| | - F Eber
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique (INRA), Agrocampus Ouest, Université de Rennes I., BP35327, 35653 Le Rheu, France
| | - V Huteau
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique (INRA), Agrocampus Ouest, Université de Rennes I., BP35327, 35653 Le Rheu, France
| | - J M Lacape
- CIRAD, UMR AGAP, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales, 34398 Montpellier, France
| | - C Reinhardt
- Department of Plant and Soil Sciences, University of Pretoria, 0001, South Africa
| | - D Marais
- Department of Plant and Soil Sciences, University of Pretoria, 0001, South Africa
| | - J L Hofs
- CIRAD, UR AIDA, Agro-écologie et Intensification Durable des cultures Annuelles, 34398 Montpellier, France
| | - A M Chèvre
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique (INRA), Agrocampus Ouest, Université de Rennes I., BP35327, 35653 Le Rheu, France
| | - C Pannetier
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
- CIRAD, UMR AGAP, Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales, 34398 Montpellier, France
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Comprehensive cytological characterization of the Gossypium hirsutum genome based on the development of a set of chromosome cytological markers. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Portela-Bens S, Merlo MA, Rodríguez ME, Cross I, Manchado M, Kosyakova N, Liehr T, Rebordinos L. Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis. Chromosoma 2016; 126:261-277. [PMID: 27080536 DOI: 10.1007/s00412-016-0589-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022]
Abstract
The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.
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Affiliation(s)
- Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Manchado
- Centro IFAPA "El Toruño", 11500, Puerto de Santa María, Cádiz, Spain
| | - Nadezda Kosyakova
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
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Liu Y, Peng R, Liu F, Wang X, Cui X, Zhou Z, Wang C, Cai X, Wang Y, Lin Z, Wang K. A Gossypium BAC clone contains key repeat components distinguishing sub-genome of allotetraploidy cottons. Mol Cytogenet 2016; 9:27. [PMID: 27006694 PMCID: PMC4802715 DOI: 10.1186/s13039-016-0235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
Background Dissecting genome organization is indispensable for further functional and applied studies. As genome sequences data shown, cotton genomes contain more than 60 % repetitive sequences, so study on repetitive sequences composition, structure, and distribution is the key step to dissect cotton genome. Results In this study, a bacterial artificial chromosome (BAC) clone enriched in repetitive sequences, was discovered initiatively by fluorescence in situ hybridization (FISH). FISHing with allotetraploidy cotton as target DNA, dispersed signals on most regions of all A sub-genome chromosomes, and only middle regions of all D sub-genome chromosomes were detected. Further FISHing with other cotton species bearing A or D genome as target DNA, specific signals were viewed. After BAC sequencing and bioinformational analysis, 129 repeat elements, size about 57,172 bp were found, accounting for more than 62 % of the BAC sequence (91,238 bp). Among them, a type of long terminal repeat-retrotransposon (LTR-RT), LTR/Gypsy was the key element causing the specific FISH results. Using the fragments of BAC matching with the identified Gypsy-like LTR as probes, the BAC-57I23-like FISH signals were reappeared. Running BLASTN, the fragments had good match with all chromosomes of G. arboreum (A2) genome and A sub-genome of G. hirsutum (AD1), and had relatively inferior match with all chromosomes of D sub-genome of AD1, but had little match with the chromosomes of G. raimondii (D5) genome, which was consistent with the FISH results. Conclusion A repeats-enriched cytogenetic marker to identify A and D sub-genomes of Gossypium was discovered by FISH. Combined sequences analysis with FISH verification, the assembly quality of repetitive sequences in the allotetraploidy cotton draft genome was assessed, and better chromosome belonging was verified. We also found the genomic distribution of the identified Gypsy-LTR-RT was similar to the distribution of heterochromatin. The expansion of this type of Gypsy-LTR-RT in heterochromatic regions may be one of the major reasons for the size gap between A and D genome. The findings showed here will help to understand the composition, structure, and evolution of cotton genome, and contribute to the further perfection of the draft genomes of cotton.
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Affiliation(s)
- Yuling Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Renhai Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China ; 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 Science, Anyang, Henan 455000 China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Xinglei Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Chunying Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan 455000 China
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Construction of cytogenetic map of Gossypium herbaceum chromosome 1 and its integration with genetic maps. Mol Cytogenet 2015; 8:2. [PMID: 25628758 PMCID: PMC4307992 DOI: 10.1186/s13039-015-0106-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/08/2015] [Indexed: 12/14/2022] Open
Abstract
Background Cytogenetic map can provide not only information of the genome structure, but also can build a solid foundation for genetic research. With the developments of molecular and cytogenetic studies in cotton (Gossypium), the construction of cytogenetic map is becoming more and more imperative. Results A cytogenetic map of chromosome 1 (A101) of Gossypium herbaceum (A1) which includes 10 bacterial artificial chromosome (BAC) clones was constructed by using fluorescent in situ hybridization (FISH). Meanwhile, comparison and analysis were made for the cytogenetic map of chromosome 1 (A101) of G. herbaceum with four genetic linkage maps of chromosome 1 (Ah01) of G. hirsutum ((AD)1) and one genetic linkage map of chromosome 1 of (A101) G. arboreum (A2). The 10 BAC clones were also used to be localized on G. raimondii (D5) chromosome 1 (D501), and 2 of them showed clear unique hybridized signals. Furthermore, these 2 BAC clones were also shown localized on chromosome 1 of both A sub-genome and D sub-genome of G. hirsutum. Conclusion The comparison of the cytogenetic map with genetic linkage maps showed that most of the identified marker-tagged BAC clones appearing same orders in different maps except three markers showing different positions, which might indicate chromosomal segmental rearrangements. The positions of the 2 BAC clones which were localized on Ah01 and Dh01 chromosomes were almost the same as that on A101 and D501 chromosomes. The corresponding anchored SSR markers of these 2 BAC clones were firstly found to be localized on chromosome D501 (Dh01) as they were not seen mapped like this in any genetic map reported.
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Gan Y, Liu F, Chen D, Wu Q, Qin Q, Wang C, Li S, Zhang X, Wang Y, Wang K. Chromosomal Locations of 5S and 45S rDNA in Gossypium Genus and Its Phylogenetic Implications Revealed by FISH. PLoS One 2013; 8:e68207. [PMID: 23826377 PMCID: PMC3695094 DOI: 10.1371/journal.pone.0068207] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 05/27/2013] [Indexed: 11/26/2022] Open
Abstract
We investigated the locations of 5S and 45S rDNA in Gossypium diploid A, B, D, E, F, G genomes and tetraploid genome (AD) using multi-probe fluorescent in situ hybridization (FISH) for evolution analysis in Gossypium genus. The rDNA numbers and sizes, and synteny relationships between 5S and 45S were revealed using 5S and 45S as double-probe for all species, and the rDNA-bearing chromosomes were identified for A, D and AD genomes with one more probe that is single-chromosome-specific BAC clone from G. hirsutum (A1D1). Two to four 45S and one 5S loci were found in diploid-species except two 5S loci in G. incanum (E4), the same as that in tetraploid species. The 45S on the 7th and 9th chromosomes and the 5S on the 9th chromosomes seemed to be conserved in A, D and AD genomes. In the species of B, E, F and G genomes, the rDNA numbers, sizes, and synteny relationships were first reported in this paper. The rDNA pattern agrees with previously reported phylogenetic history with some disagreements. Combined with the whole-genome sequencing data from G. raimondii (D5) and the conserved cotton karyotype, it is suggested that the expansion, decrease and transposition of rDNA other than chromosome rearrangements might occur during the Gossypium evolution.
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Affiliation(s)
- Yimei Gan
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture (China), Haikou, Hainan, P. R. China
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