BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning
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 artifi...
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MDPI AG
2022-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/24/15958 |
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| author | Vishwamitra Singh Baisvar Basdeo Kushwaha Ravindra Kumar Murali Sanjeev Kumar Mahender Singh Anil Rai Uttam Kumar Sarkar |
| author_facet | Vishwamitra Singh Baisvar Basdeo Kushwaha Ravindra Kumar Murali Sanjeev Kumar Mahender Singh Anil Rai Uttam Kumar Sarkar |
| author_sort | Vishwamitra Singh Baisvar |
| collection | DOAJ |
| description | 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 <i>cis</i> acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of <i>Clarias magur</i> (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 <i>C. magur</i> 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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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T16:18:27Z |
| publishDate | 2022-12-01 |
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| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-10bb1672814d4262879cecef4cafed462023-11-24T15:30:30ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-12-0123241595810.3390/ijms232415958BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional CloningVishwamitra Singh Baisvar0Basdeo Kushwaha1Ravindra Kumar2Murali Sanjeev Kumar3Mahender Singh4Anil Rai5Uttam Kumar Sarkar6ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaDivision of Agricultural Bioinformatics, ICAR—Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, IndiaICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, IndiaConstruction 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 <i>cis</i> acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of <i>Clarias magur</i> (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 <i>C. magur</i> for understanding their organization, inheritance of important fishery traits and evolution of magur with respect to channel catfish, zebrafish and other species.https://www.mdpi.com/1422-0067/23/24/15958BAC cloneschromosome<i>Clarias magur</i>DNA probeFISH |
| spellingShingle | Vishwamitra Singh Baisvar Basdeo Kushwaha Ravindra Kumar Murali Sanjeev Kumar Mahender Singh Anil Rai Uttam Kumar Sarkar BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning International Journal of Molecular Sciences BAC clones chromosome <i>Clarias magur</i> DNA probe FISH |
| title | BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning |
| title_full | BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning |
| title_fullStr | BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning |
| title_full_unstemmed | BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning |
| title_short | BAC-FISH Based Physical Map of Endangered Catfish <i>Clarias magur</i> for Chromosome Cataloguing and Gene Isolation through Positional Cloning |
| title_sort | bac fish based physical map of endangered catfish i clarias magur i for chromosome cataloguing and gene isolation through positional cloning |
| topic | BAC clones chromosome <i>Clarias magur</i> DNA probe FISH |
| url | https://www.mdpi.com/1422-0067/23/24/15958 |
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