Bioinformatic analysis and characterization of BAC clones of Clarias magur (Hamilton,1822) using FISH and BAC end sequencing
DOI:
https://doi.org/10.36253/caryologia-3196Keywords:
end sequencing, FISH, PPI, SDG, synteny, BAC clones, Clarias magurAbstract
The clones of BAC library combined with FISH are an excellent tool for mapping and identifying full-length genes. The present study was to sequence, mine and characterize the BAC clones of Clarias magur (magur) genome. The end sequences of the BAC clones were bioinformatically mapped onto the genome scaffolds of magur to identify and locate the genes in each clone and FISH was utilized to locate clones on specific chromosomes of magur. A total of 13 BAC clones could be mapped using BAC end sequences on 12 genome scaffolds of magur. From the 13 clones, 34 genes were mined, annotated and characterized. Physical mapping using BAC-FISH signal was used to localize two clones, 012H23 and 012H7 on 11th and 14th chromosome pairs of magur. The gene enrichment analysis revealed involvement of several genes in growth and regulatory processes, such as protein neddylation and metal ion transport. PPI Network analysis revealed two types of interactions among 11 nodes and between 10 edges; and 4 genes (ash2l, cnot2, lin7c, uba3) were identified to be important. The study reveals the presence of important genes on the 13 undertaken clones, making this a useful genomic resource. The FISH probe could not only be helpful in generation of basic information of gene location for identification of genes on the chromosomes as a chromosome marker, but also in detection of chromosomal defects arisen due to genetic mutation occurred if any on a particular location of reported genes in C. magur.
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Copyright (c) 2025 Rashmi Verma, Basdeo Kushwaha, Uzma Afaq, Vishwamitra Singh Baisvar, Satyamvada Maurya, Murali S Kumar, Tanwy Dasmandal, Akhilesh Kumar Mishra, Ravindra Kumar, Uttam Kumar Sarkar
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