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

Q3 Biochemistry, Genetics and Molecular Biology Genetics Research International Pub Date : 2015-12-16 DOI:10.1155/2015/638679

B. Reddy, Amrutlal K. Patel, Krishna M. Singh, D. Patil, P. Parikh, D. N. Kelawala, P. Koringa, V. Bhatt, M. V. Rao, C. Joshi

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引用次数: 3

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.

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利用高通量测序技术对犬视网膜进行从头组装和转录组表征

我们利用454 GS-FLX和Ion Torrent PGM平台对犬视网膜组织进行转录组测序。CLC Genomics Workbench的RNA-Seq分析绘制了10360个基因的表达图谱。视网膜转录组的基因本体论分析揭示了大量已知参与视觉相关过程的转录本。利用CAP3对序列进行从头组装，得到29,683个contigs，平均长度为560.9,N50为619个碱基。进一步分析预测了3827个全长cdna和29481个(99%)开放阅读框(orf)。此外，3,782个contigs被分配到316个KEGG通路，包括黑色素生成，光导和视黄醇代谢，分别有33个，15个和11个contigs。在所鉴定的微卫星中，二核苷酸重复序列占68.84%，其次是三核苷酸、四核苷酸、五核苷酸和六核苷酸，分别占25.76%、9.40%、2.52%和0.96%。本研究为进一步了解犬视网膜的生物学和功能提供了宝贵的资源。

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来源期刊

Genetics Research International Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

2.90

自引率

0.00%

发文量

期刊介绍： Genetics Research International is a peer-reviewed, Open Access journal that publishes original research articles as well as review articles in all areas of genetics and genomics. The journal focuses on articles bearing on heredity, biochemistry, and molecular biology, as well as clinical findings.