Individual chromosome identification in Clarias magur using BAC-FISH and comparative genes analyses
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ORIGINAL ARTICLE
Individual chromosome identification in Clarias magur using BAC‑FISH and comparative genes analyses Ravindra Kumar1 · Vishwamitra Singh Baisvar1 · Basdeo Kushwaha1 · Manmohan Pandey1 · Mahender Singh1 Received: 23 June 2020 / Accepted: 5 November 2020 © Archana Sharma Foundation of Calcutta 2020
Abstract BAC library has always been an important genomic source for preserving the genetic material of an organism for sequencing, developing physical map as well as addressing the novel evolutionary biology questions. Here, the end sequences of BAC clones were generated using a set of primers and mapped on the genome scaffolds of C. magur using bioinformatics tool. Numbers of genes present on the clones were identified using scaffolds’ annotation information. Further, the clone insert DNA was labeled through nick translation using tetra methyl rhodamine-5-dUTP (Pool A contained 6 clones possessing 36 genes mapped on scaffold A) and fluorescein 12-dUTP (Pool B contained 4 clones possessing 15 genes mapped on scaffold B) fluorophores for probe construction and was subsequently hybridized on metaphase chromosomes using FISH. The BAC-FISH revealed the mapping of red color probe on 19th sub-telocentric chromosome and green color on 14th submetacentric chromosome. These findings will be useful in understanding the chromosomes organization and evolution of genomic structure as well as function of the species in comparison to its closely related and well studies species, such as channel catfish and zebrafish. Keywords BAC end sequence · Chromosome · Clarias magur · DNA probe · FISH
Introduction A Bacterial artificial chromosome (BAC) is a foreign DNA construct which are cloned in the transformed bacteria. These bacteria can be replicated quickly and a good amount of quality plasmid DNA can be obtained for various applications. The library of BAC clones has always been a source of good quality DNA useful for high throughput BAC end sequencing, chromosomal mapping and genome sequencing [14]. The BAC clones are always a unique representation of a genome. This is also useful in positional cloning, targeted marker development, physical mapping for understanding Corresponding Editor : Rabindra Nath Chatterjee. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13237-020-00344-x) contains supplementary material, which is available to authorized users. * Ravindra Kumar [email protected]; [email protected] 1
the genome organization and helpful in finding overlapping regions in genome assembly. The undertaken catfish species, Clarias magur (Hamilton 1822), is a high value food fish [16] with wide distribution in Bangladesh and India. It possesses accessory air-breathing organ that allows them to breath in air without water [6]. It is categorized as endangered (A3cde + 4acde) in IUCN Red List Status (2010) due to over exploitation and habitat alterations in its native place. As an important catfish, some molecular works has been reported in this sp
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