Cargando…

BAC-FISH Based Physical Map of Endangered Catfish Clarias magur 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...

Descripción completa

Detalles Bibliográficos
Autores principales: Baisvar, Vishwamitra Singh, Kushwaha, Basdeo, Kumar, Ravindra, Kumar, Murali Sanjeev, Singh, Mahender, Rai, Anil, Sarkar, Uttam Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9781557/
https://www.ncbi.nlm.nih.gov/pubmed/36555603
http://dx.doi.org/10.3390/ijms232415958
_version_ 1784857103560605696
author Baisvar, Vishwamitra Singh
Kushwaha, Basdeo
Kumar, Ravindra
Kumar, Murali Sanjeev
Singh, Mahender
Rai, Anil
Sarkar, Uttam Kumar
author_facet Baisvar, Vishwamitra Singh
Kushwaha, Basdeo
Kumar, Ravindra
Kumar, Murali Sanjeev
Singh, Mahender
Rai, Anil
Sarkar, Uttam Kumar
author_sort Baisvar, Vishwamitra Singh
collection PubMed
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 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.
format Online
Article
Text
id pubmed-9781557
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-97815572022-12-24 BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning Baisvar, Vishwamitra Singh Kushwaha, Basdeo Kumar, Ravindra Kumar, Murali Sanjeev Singh, Mahender Rai, Anil Sarkar, Uttam Kumar Int J Mol Sci Article 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. MDPI 2022-12-15 /pmc/articles/PMC9781557/ /pubmed/36555603 http://dx.doi.org/10.3390/ijms232415958 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Baisvar, Vishwamitra Singh
Kushwaha, Basdeo
Kumar, Ravindra
Kumar, Murali Sanjeev
Singh, Mahender
Rai, Anil
Sarkar, Uttam Kumar
BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title_full BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title_fullStr BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title_full_unstemmed BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title_short BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning
title_sort bac-fish based physical map of endangered catfish clarias magur for chromosome cataloguing and gene isolation through positional cloning
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9781557/
https://www.ncbi.nlm.nih.gov/pubmed/36555603
http://dx.doi.org/10.3390/ijms232415958
work_keys_str_mv AT baisvarvishwamitrasingh bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT kushwahabasdeo bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT kumarravindra bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT kumarmuralisanjeev bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT singhmahender bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT raianil bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning
AT sarkaruttamkumar bacfishbasedphysicalmapofendangeredcatfishclariasmagurforchromosomecataloguingandgeneisolationthroughpositionalcloning