Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs
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We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2). [BMB reports 2011; 44(4): 238-243]
Abstract
We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2). [BMB reports 2011; 44(4): 238-243]
참고문헌 (31)
- Cruz, F, "The legacy of domestication: accumulation of deleterious mutations in the dog genome", Mol. Biol. Evol, 25, pp.2331~2336 (2008)
- Palmer, L. E, "A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface", J. Hered, 94, pp.15~22 (2003)
- Lindblad-Toh, K, "Genome sequence, comparative analysis and haplotype structure of the domestic dog", Nature, 438, pp.803~819 (2005)
- Ostrander, E. A, "The canine genome", Genome Res, 15, pp.1706~1716 (2005)
- Frentiu, F. D, "An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation stu", BMC Genomics, 10, pp.40~ (2009)
- Picoult-Newberg, L, "Mining SNPs from EST databases", Genome Res, 9, pp.167~174 (1999)
- Barbazuk, W. B, "SNP discovery via 454 transcriptome sequencing", Plant J, 51, pp.910~918 (2007)
- Hayes, B. J, "SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates", Bioinformatics, 23, pp.1692~1693 (2007)
- Kwok, P. Y, "Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products", Genomics, 23, pp.138~144 (1994)
- Wang, D. G, "Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome", Science, 280, pp.1077~1082 (1998)
- Hacia, J. G, "Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis", Nat. Genet, 14, pp.441~447 (1996)
- Cadieu, E, "Coat variation in the domestic dog is governed by variants in three genes", Science, 326, pp.150~153 (2009)
- Vage, J, "Single nucleotide polymorphisms (SNPs) in coding regions of canine dopamineand serotonin-related genes", BMC Genet, 9, pp.10~ (2008)
- Spady, T. C, "Canine behavioral genetics: pointing out the phenotypes and herding up the genes", Am. J. Hum. Genet, 82, pp.10~18 (2008)
- Arata, S, "Sequences and polymorphisms of the canine monoamine transporter genes SLC6A2, SLC6A3, and SLC6A4 among five dog breeds", J. Vet. Med. Sci, 70, pp.971~975 (2008)
- Lesniak, A, "Canine olfactory receptor gene polymorphism and its relation to odor detection performance by sniffer dogs", J. Hered, 99, pp.518~527 (2008)
- Huang, X, "CAP3: a DNA sequence assembly program", Genome Res, 9, pp.868~877 (1999)
- Nakaya, H. I, "Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription", Genome Biol, 8, pp.R43~ (2007)
- Werbowetski-Ogilvie, T. E, "Isolation of a natural inhibitor of human malignant glial cell invasion: inter alpha-trypsin inhibitor heavy chain 2", Cancer Res, 66, pp.1461~1472 (2006)
- Walker, K, "Genetic polymorphism in N-Acetyltransferase (NAT): Population distribution of NAT1 and NAT2 activity", J. Toxicol. Environ. Health B. Crit. Rev, 12, pp.440~472 (2009)
- Jung-HwaOh, "An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material", Experimental and Molecular Medicine, 35(6), pp.588~592 (2003), 생화학분자생물학회
- Sasako, M, "Overview of clinical trials on adjuvant chemotherapy for curatively resected gastric cancer", Gan. To. Kagaku. Ryoho, 21(Suppl 3), pp.384~394 (1994)
- Ju Hyun Kim, "cSNP Mining from Full-Length Enriched cDNA Libraries of the Korean Native Pig", Genes & Genomics, 27(4), pp.329~335 (2005), 한국유전학회
- Ewing, B, "Base-calling of automated sequencer traces using phred", I. Accuracy assessment. Genome Res, 8, pp.175~185 (1995)
- Jurka,J, "Repbase update: a database and an electronic journal of repetitive elements", Trends Genet, 16, pp.418~420 (2000)
- Kent, W. J, "BLAT--the BLAST-like alignment tool", Genome Res, 12, pp.656~664 (2002)
- Altschul, S. F, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res, 25, pp.3389~3402 (1997)
- Christoffels, A, "STACK: Sequence Tag Alignment and Consensus Knowledgebase", Nucleic Acids Res, 29, pp.234~238 (2001)
- Useche, F. J, "High-throughput identification, database storage and analysis of SNPs in EST sequences", Genome Inform, 12, pp.194~203 (2001)
- Ramensky, V, "Human non-synonymous SNPs: server and survey", Nucleic Acids Res, 30, pp.3894~3900 (2002)
- Sunyaev, S, "Prediction of deleterious human alleles", Hum. Mol. Genet, 10, pp.591~597 (2001)
