Abstract
Next-generation sequencing has allowed us to explore new methods, where comparative and population genomics can be used simultaneously. Keeping this in mind, we surveyed and analyzed the frequency and distribution of microsatellites in the Indian gharial (Gavialis gangeticus) and compared it with American alligator (Alligator mississippiensis) and saltwater crocodile (Crocodylus porosus) to enrich them with genomic resources. The Indian gharial has a low frequency, relative abundance (RA), and relative density (RD) of microsatellites as compared to other crocodilians. RA and RD were positively correlated with the GC content of genomic and transcriptomic sequences. The genomic sequences were dominated by dinucleotide repeats, whereas the transcriptomic sequences had an excess of trinucleotide repeats. Motif conservation studies among the three crocodilians revealed conservation of 69.2% of motifs. Species-specific unique motifs identified in this study could be used as molecular probes for species identification. A total of 67,311 primers were designed in all three species to enrich the crocodilians with genomic resources. The genomic resources developed in this study could accelerate diversity analysis within its individuals to design a proper mating plan to reduce inbreeding stress and further improve the species.
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List of unique motifs identified in the present study (Table S1, Supporting Information).
List of microsatellite primers designed for all the three crocodilians (Table S2, Supporting Information).
List of loci amplified using virtual PCR (Table S3, Supporting Information).
Figure showing PCA plot (Fig. S1, Supporting Information).
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Acknowledgements
Research in YA Lab was supported by the Extramural Grant from the Indian Council of Medical Research (MoFHW, Government of India) and the Department of Biotechnology, (MoS&T, Government of India).
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Mahfooz, S., Singh, P. & Akhter, Y. A comparative study of microsatellites among crocodiles and development of genomic resources for the critically endangered Indian gharial. Genetica 150, 67–75 (2022). https://doi.org/10.1007/s10709-021-00148-0
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DOI: https://doi.org/10.1007/s10709-021-00148-0