Sphingidae Taxonomic Inventory

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Genome-wide in-silico identification of microsatellites in Eri Silkworm, Samia ricini (Lepidoptera: Saturniidae)

Publication Type:Journal Article
Year of Publication:2024
Authors:C. Vanitha, Balakrishnan, I. K., Debnath, R., Lavanya, C., Tulsi_Naik, K. S., Moorthy, S. M., Ramesh, K. V., Dubey, H.
Journal:Ecology, Environment & Conservation
Volume:30
Issue:4
Start Page:1888
Pagination:1888-1898
Keywords:GENE ONTOLOGY, ISSR, MICROSATELLITES, SAMIA, SATURNIIDAE
Abstract:

"Effective utilization of microsatellite or simple sequence repeat (SSR) markers along with ongoing advanced technologies in the field of molecular biology have made great advantages. In the present study, the genome-wide distribution of SSRs in Eri silkworm, Samia ricini Donovan was studied along with the in-silico transferability of SSR primers to the closely related species S. wangi and S. watsoni. We also analyzed and compared the SSRs in two closely related Samia species with the motifs identified in S. ricini genome. The overall abundance of SSR motifs was more in S. watsoni compared to S. ricini and S. wangi. The cross-amplification analysis through in-silico PCR method with the 25,252 SSR primer pairs developed for S. ricini, showed that 2,978 and 1,508 primer sets were amplified in the S. wangi and in S. watsoni, respectively. The distribution of SSR motifs in S. ricini genome showed a higher proportion of SSR motifs in intergenic regions than exonic and intronic regions (41%, 30% and 29%, respectively). The gene ontology analysis of the SSR containing genes showed that a greater number of genes were associated with the biological process (889) followed by molecular function (215) and cellular components (213). The SSRs present in the coding region revealed, Alanine (Ala) as the most abundant amino acid in these loci followed by Tyrosine (Tyr) and Methionine (Met) in the coding region of the Samia ricini. To validate our in-silico analysis, we randomly selected 20 SSR primers and amplified them in different morphotypes of Eri silkworm."

URL:http://doi.org/10.53550/EEC.2024.v30i04.070
DOI:10.53550/EEC.2024.v30i04.070
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith