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Genetics Research International
Volume 2015, Article ID 638679, 11 pages
http://dx.doi.org/10.1155/2015/638679
Research Article

De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing

1Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388001, India
2Department of Zoology, Genetic Diagnostic Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat 380009, India
3Datar Genetics Ltd., F-8 D Road, Ambad, Nasik, Maharashtra 422010, India
4Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India
5Department of Pharmaceutical Science, Saurashtra University, Rajkot, Gujarat 360005, India

Received 31 July 2015; Revised 10 November 2015; Accepted 11 November 2015

Academic Editor: Norman A. Doggett

Copyright © 2015 Bhaskar Reddy et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.