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Individual chromosome identification in Clarias magur using BAC-FISH and comparative genes analyses

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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 sub-metacentric 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.

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Acknowledgments

Authors are highly grateful to the CABin Scheme of ICAR-Indian Agricultural Statistics Research Institute, New Delhi, for financial support and to the Director, ICAR-National Bureau of Fish Genetic Resources, Lucknow, for providing the laboratory facilities and other supports.

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Correspondence to Ravindra Kumar.

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The authors declare that there is no conflict of interest to publish this manuscript.

Ethical approval

For the present work, live healthy specimens of C. magur (n = 10) were collected from Gomti river near Lucknow, Uttar Pradesh, India. All applicable national and institutional guidelines for the care and use of fishes were followed. The undertaken species is not listed in the endangered/ special category or otherwise enlisted fish species and does not restrict the use of this species for laboratory experiments/research. The experiments with live fish does not come under the CPCSEA (Committee for the Purpose of Control and Supervision on Experiments on Animals) guidelines of the Ministry of Environment, Forest & Climate Change (MoEFCC), Government of India, New Delhi. There are no guidelines available for using live fish for experiments in India as on today.

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13237_2020_344_MOESM1_ESM.tif

Supplementary Fig. 1: Phylogenetic tree at repeat level of the studied species, Clarias magur, zebrafish and channel catfish, using UPGMA method (TIF 94 kb)

Supplementary Table 1: Details of the SSRs present on the BACs (XLSX 42 kb)

13237_2020_344_MOESM3_ESM.xlsx

Supplementary Table 2: (a) Descriptions of genes present on Pool A clones of C. magur, zebrafish and channel catfish, and (b) gene pathway mapping using KEGG Mapper (XLSX 14 kb)

13237_2020_344_MOESM4_ESM.xlsx

Supplementary Table 3: (a) Descriptions of genes present on Pool B clones of C. magur, zebrafish and channel catfish, and (b) gene pathway mapping using KEGG Mapper (XLSX 14 kb)

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Kumar, R., Baisvar, V.S., Kushwaha, B. et al. Individual chromosome identification in Clarias magur using BAC-FISH and comparative genes analyses. Nucleus 64, 203–209 (2021). https://doi.org/10.1007/s13237-020-00344-x

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  • DOI: https://doi.org/10.1007/s13237-020-00344-x

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