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International Journal of Current Microbiology and Applied Sciences (IJCMAS)
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National Academy of Agricultural Sciences (NAAS)
NAAS Score: *5.38 (2019)
[Effective from January 1, 2019]
For more details click here

ICV 2017: 100.00
Index Copernicus ICI Journals Master List 2017 - IJCMAS--ICV 2017: 100.00
For more details click here

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Original Research Articles

PRINT ISSN : 2319-7692
Online ISSN : 2319-7706
Issues : 12 per year
Publisher : Excellent Publishers
Email : editorijcmas@gmail.com / submit@ijcmas.com
Editor-in-chief: Dr.M.Prakash
Index Copernicus ICV 2017: 100.00
NAAS RATING 2018: 5.38

Int.J.Curr.Microbiol.App.Sci.2017.6(11): 2244-2252
DOI: https://doi.org/10.20546/ijcmas.2017.611.266


In Silico Characterization of Selected Microsatellite Loci Reported in Zebrafish Genome
Mujahidkhan A. Pathan*, E. A. Nesnas, Aditya Pratap Acharya, Rameez Roshan, Thushar P. Kumar, P. Gireesh-Babu, Shrinivas Jahageerdar, Aparna Chaudhari and Gopal Krishna
Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai-400061, India
*Corresponding author
Abstract:

Microsatellite loci of zebrafish are an important genetic resource owing to widespread use of microsatellites for a number of applications and the vertebrate model status of zebrafish. Data available in the public domain was mined for microsatellites present in and near transcribed regions. Two thousand loci reported earlier were individually traced to their genome coordinates in order to record type and structure of repeats, location with respect to exonic, intronic and noncoding regions and distribution of each type across linkage groups. Location of 1781 loci could be ascertained using Ensembl BLAT against the zebrafish (GRCz10) genome database or Zv9 (Ensembl release 79), of which a total of 981 loci (55%) were located in the genic regions and 800 (45%) were mapped in the noncoding regions of the zebrafish genome. Within the genes, 700 (39%), 36 (2%) and 245 (14%) were in introns, exons and exon-intron junctions, respectively. None of the microsatellites present in the noncoding region were within +/- 300 bp of the open reading frames, implying lack of STR loci in the 5' and 3' regulatory regions in the available data. Analysis with online Microsatellite Repeat Finder tool revealed 1597 loci with well-defined repeat structures, of which 1524, 19, and 54 were di, tri and tetra repeats, respectively. The genes spanning the loci were recorded and more than ninety percent had biological roles assigned. New PCR primers were designed for selected loci and robust primers are reported for 42 tri, tetra, non-coding and exonic loci. The information generated in this work will facilitate further investigations related to role elucidation of STRs and enable other applications like genotyping of zebrafish strains and cross-species amplification of loci.


Keywords: Danio rerio, SSR, Genome distribution, Repeats, Genome coordinates.
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How to cite this article:

Mujahidkhan A. Pathan, E.A. Nesnas, Aditya Pratap Acharya, Rameez Roshan, Thushar P. Kumar, P. Gireesh-Babu, Shrinivas Jahageerdar, Aparna Chaudhari and Gopal Krishna. 2017. In Silico Characterisation of Selected Microsatellite Loci Reported in Zebrafish Genome.Int.J.Curr.Microbiol.App.Sci. 6(11): 2244-2252. doi: https://doi.org/10.20546/ijcmas.2017.611.266