본문 바로가기
KERD
논문KCI 등재

Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs

1

조회

0

다운로드

0

인용

0

참고문헌

키워드

주제분류화학

초록

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)

  1. Cruz, F, "The legacy of domestication: accumulation of deleterious mutations in the dog genome", Mol. Biol. Evol, 25, pp.2331~2336 (2008)
  2. 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)
  3. Lindblad-Toh, K, "Genome sequence, comparative analysis and haplotype structure of the domestic dog", Nature, 438, pp.803~819 (2005)
  4. Ostrander, E. A, "The canine genome", Genome Res, 15, pp.1706~1716 (2005)
  5. 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)
  6. Picoult-Newberg, L, "Mining SNPs from EST databases", Genome Res, 9, pp.167~174 (1999)
  7. Barbazuk, W. B, "SNP discovery via 454 transcriptome sequencing", Plant J, 51, pp.910~918 (2007)
  8. Hayes, B. J, "SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates", Bioinformatics, 23, pp.1692~1693 (2007)
  9. Kwok, P. Y, "Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products", Genomics, 23, pp.138~144 (1994)
  10. Wang, D. G, "Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome", Science, 280, pp.1077~1082 (1998)
  11. 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)
  12. Cadieu, E, "Coat variation in the domestic dog is governed by variants in three genes", Science, 326, pp.150~153 (2009)
  13. Vage, J, "Single nucleotide polymorphisms (SNPs) in coding regions of canine dopamineand serotonin-related genes", BMC Genet, 9, pp.10~ (2008)
  14. Spady, T. C, "Canine behavioral genetics: pointing out the phenotypes and herding up the genes", Am. J. Hum. Genet, 82, pp.10~18 (2008)
  15. 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)
  16. Lesniak, A, "Canine olfactory receptor gene polymorphism and its relation to odor detection performance by sniffer dogs", J. Hered, 99, pp.518~527 (2008)
  17. Huang, X, "CAP3: a DNA sequence assembly program", Genome Res, 9, pp.868~877 (1999)
  18. 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)
  19. 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)
  20. 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)
  21. 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
  22. 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)
  23. 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
  24. Ewing, B, "Base-calling of automated sequencer traces using phred", I. Accuracy assessment. Genome Res, 8, pp.175~185 (1995)
  25. Jurka,J, "Repbase update: a database and an electronic journal of repetitive elements", Trends Genet, 16, pp.418~420 (2000)
  26. Kent, W. J, "BLAT--the BLAST-like alignment tool", Genome Res, 12, pp.656~664 (2002)
  27. Altschul, S. F, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res, 25, pp.3389~3402 (1997)
  28. Christoffels, A, "STACK: Sequence Tag Alignment and Consensus Knowledgebase", Nucleic Acids Res, 29, pp.234~238 (2001)
  29. Useche, F. J, "High-throughput identification, database storage and analysis of SNPs in EST sequences", Genome Inform, 12, pp.194~203 (2001)
  30. Ramensky, V, "Human non-synonymous SNPs: server and survey", Nucleic Acids Res, 30, pp.3894~3900 (2002)
  31. Sunyaev, S, "Prediction of deleterious human alleles", Hum. Mol. Genet, 10, pp.591~597 (2001)

관련 논문AI추천

Functional Analysis of Expressed Sequence Tags from Hanwoo (Korean Cattle) cDNA Libraries변미정, 신윤희, 윤두학, 이승환, 임다정, 임석기, 조용민한국축산학회 · 한국축산학회지2009 · 제51권 제1호Transcript profiling of expressed sequence tags from intramuscular fat, longissimus dorsi muscle and liver in Korean cattle (Hanwoo)김규원, 김희발, Dajeong Lim, Duhak Yoon, Hye Sun Park, Seung Hwan Lee, Yong Min Cho, Younhee Shin생화학분자생물학회 · BMB Reports2010 · 제43권 제2호Expressed Sequence Tag Analysis of Olive Flounder (Paralichthys olivaceus): Genes and Expression Profile from the Liver김경길, 김규원, 김영옥, 김우진, 박두원, 박중연, 이정호한국수산과학회 · Fisheries and Aquatic Sciences2003 · 제6권 제3호Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus)김경길, 김정은, 김현철, 노재구, 박종원, 박철지, 이영미, 이정호한국발생생물학회 · 발생과 생식2014 · 제18권 제4호EST-based Identification of Genes Expressed in the Brain of the Olive Flounder Paralichthys olivaceus김경길, 김영옥, 김우진, 김종현, 김현철, 노재구, 명정인, 민병화, 박철지, 이정호한국수산과학회 · Fisheries and Aquatic Sciences2009 · 제12권 제4호Gene Expression Profiling in Hepatic Tissue of two Pig Breeds김경태, 김명직, 김태헌, 김희발, 박종은, 임다정, 장길원, 최봉환한국축산학회 · 한국축산학회지2012 · 제54권 제6호

이 간행물의 다른 논문 (10건)