Comparative analysis of catfish BAC end sequences with the zebrafish genome

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Liu, Hong ^a,b   Jiang, Yanliang ^a,c   Wang, Shaolin ^a   Ninwichian, Parichart ^a   Somridhivej, Benjaporn ^a   Xu, Peng ^a   Abernathy, Jason ^a   Kucuktas, Huseyin ^a   Liu, Zhanjiang ^a  

^a AUBURN UNIVERSITY   (United States)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c HUNAN NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATFISH; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; FISH GENETICS; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC LINKAGE; GENOME ANALYSIS; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; UNINDEXED SEQUENCE; ZEBRA FISH; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; COMPARATIVE STUDY; CONTIG MAPPING; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; SYNTENY;

DANIO RERIO;

MICROSATELLITE DNA;

ANIMALS; CATFISHES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONTIG MAPPING; GENOME; GENOMICS; LINKAGE (GENETICS); MICROSATELLITE REPEATS; SEQUENCE ANALYSIS, DNA; SYNTENY; ZEBRAFISH;

EID: 73149094080     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-592     Document Type: Article

References (53)

1. Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai S-F, Park H-S, Yaspo M-L, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y, Hattori M, Sakaki Y. Construction and Analysis of a Human-Chimpanzee Comparative Clone Map. Science 2002, 295:131-134. 10.1126/science.1065199, 11778049.
2. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu A-L, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature 2002, 418:743-750. 10.1038/nature00957, 12181558.
3. Larkin DM, Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PJ, Lewin HA. A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res 2003, 13:1966-1972. 403790, 12902387.
4. Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, Bloker H. A human-horse comparative map based on equine BAC end sequences. Genomics 2006, 87:772-776. 10.1016/j.ygeno.2006.03.002, 16603334.
5. Meyers SN, Rogatcheva MB, Larkin DM, Yerle M, Milan D, Hawken RJ, Schook LB, Beever JE. Piggy-BACing the human genome: II. A high-resolution, physically anchored, comparative map of the porcine autosomes. Genomics 2005, 86:739-752. 10.1016/j.ygeno.2005.04.010, 16246521.
6. Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O'Grady M, Nicholas F, Crawford AM, Smith T, de Jong PJ, McEwan J, Oddy VH, Cockett NE. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol 2007, 8:R152. 10.1186/gb-2007-8-7-r152, 2323240, 17663790.
7. Moen T, Hayes B, Baranski M, Berg PR, Kjoglum S, Koop BF, Davidson WS, Omholt SW, Lien S. A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 2008, 9:223. 10.1186/1471-2164-9-223, 2405805, 18482444.
8. Ng SHS, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJM, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 2005, 86:396-404. 10.1016/j.ygeno.2005.06.001, 16026963.
9. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res 2004, 14:478-490. 10.1101/gr.1687304, 353236, 14962987.
10. Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F, Quillet E. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 2006, 7:302. 10.1186/1471-2164-7-302, 1698487, 17137492.
11. Rexroad CE, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res 2003, 102:347-354. 10.1159/000075773, 14970727.
12. Katagiri T, Kidd C, Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD. A BAC-based physical map of the Nile tilapia genome. BMC Genomics 2005, 6:89. 10.1186/1471-2164-6-89, 1180826, 15946383.
13. Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, Hulata G, Slettan A, Stern JE, Terai Y, Kocher TD. A second-generation genetic linkage map of tilapia (Oreochromis spp.). Genetics 2005, 170:237-244. 10.1534/genetics.104.035022, 1449707, 15716505.
14. Franch R, Louro B, Tsalavouta M, Chatziplis D, Tsigenopoulos CS, Sarropoulou E, Antonello J, Magoulas A, Mylonas CC, Babbucci M, Patarnello T, Power DM, Kotoulas G, Bargelloni L. A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 2006, 174:851-861. 10.1534/genetics.106.059014, 1602104, 16951080.
15. Sarropoulou E, Power DM, Magoulas A, Geisler R, Kotoulas G. Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos. Aquaculture 2005, 243:69-81.
16. Sarropoulou E, Franch R, Louro B, Power DM, Bargelloni L, Magoulas A, Senger F, Tsalavouta M, Patarnello T, Galibert F, Kotoulas G, Geisler R. A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis. BMC Genomics 2007, 8:44. 10.1186/1471-2164-8-44, 1805437, 17286862.
17. Senger F, Priat C, Hitte C, Sarropoulou E, Franch R, Geisler R, Bargelloni L, Power D, Galibert F. The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L). Genomics 2006, 87:793-800. 10.1016/j.ygeno.2005.11.019, 16413167.
18. Chistiakov DA, Hellemans B, Haley CS, Law AS, Tsigenopoulos CS, Kotoulas G, Bertotto D, Libertini A, Volckaert FA. A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Genetics 2005, 170:1821-1826. 10.1534/genetics.104.039719, 1449790, 15937133.
19. Whitaker HA, McAndrew BJ, Taggart JB. Construction and characterization of a BAC library for the European sea bass Dicentrarchus labrax. Anim Genet 2006, 37:526. 10.1111/j.1365-2052.2006.01514.x, 16978191.
20. Liu Z. A review of catfish genomics: progress and perspectives. Comp Funct Genomics 2003, 4:259-265. 10.1002/cfg.265, 2447413, 18629126.
21. Liu Z. Catfish. Genome Mapping and Genomics in Fishes and Aquatic Animals 2008, 2:85-100. Berlin Heidelberg: Springer, Kocher T, Kole C, [Kole C (Series Editor): Genome Mapping and Genomics in Animals, vol. 2].
22. He C, Chen L, Simmons M, Li P, Kim S, Liu ZJ. Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis. Anim Genet 2003, 34:445-448. 10.1046/j.0268-9146.2003.01054.x, 14687075.
23. Serapion J, Kucuktas H, Feng J, Liu Z. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar Biotechnol (NY) 2004, 6:364-377. 10.1007/s10126-003-0039-z, 15136916.
24. Somridhivej B, Wang S, Sha Z, Liu H, Quilang J, Xu P, Li P, Hu Z, Liu Z. Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of channel catfish (Ictalurus punctatus): A resource for integration of linkage and physical maps. Aquaculture 2008, 275:76-80.
25. Xu P, Wang S, Liu L, Peatman E, Somridhivej B, Thimmapuram J, Gong G, Liu Z. Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species. Anim Genet 2006, 37:321-326. 10.1111/j.1365-2052.2006.01453.x, 16879340.
26. Kucuktas H, Wang S, Li P, He C, Xu P, Sha Z, Liu H, Jiang Y, Baoprasertkul P, Somridhivej B, Wang Y, Abernathy J, Guo X, Liu L, Muir W, Liu Z. Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-associated Markers. Genetics 2009, 181:1649-1660. 10.1534/genetics.108.098855, 2666527, 19171943.
27. Liu Z, Karsi A, Li P, Cao D, Dunham R. An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. Genetics 2003, 165:687-694. 1462775, 14573480.
28. Waldbieser GC, Bosworth BG, Nonneman DJ, Wolters WR. A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus. Genetics 2001, 158:727-734. 1461682, 11404336.
29. Cao D, Kocabas A, Ju Z, Karsi A, Li P, Patterson A, Liu Z. Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney. Anim Genet 2001, 32:169-188. 10.1046/j.1365-2052.2001.00753.x, 11531695.
30. Ju Z, Karsi A, Kocabas A, Patterson A, Li P, Cao D, Dunham R, Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain. Gene 2000, 261:373-382. 10.1016/S0378-1119(00)00491-1, 11167026.
31. Karsi A, Cao D, Li P, Patterson A, Kocabas A, Feng J, Ju Z, Mickett KD, Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene 2002, 285:157-168. 10.1016/S0378-1119(02)00414-6, 12039042.
32. Kocabas AM, Li P, Cao D, Karsi A, He C, Patterson A, Ju Z, Dunham RA, Liu Z. Expression profile of the channel catfish spleen: analysis of genes involved in immune functions. Mar Biotechnol (NY) 2002, 4:526-536. 10.1007/s10126-002-0067-0, 14961227.
33. Li P, Peatman E, Wang S, Feng J, He C, Baoprasertkul P, Xu P, Kucuktas H, Nandi S, Somridhivej B, Serapion J, Simmons M, Turan C, Liu L, Muir W, Dunham R, Brady Y, Grizzle J, Liu Z. Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs. BMC Genomics 2007, 8:177. 10.1186/1471-2164-8-177, 1906771, 17577415.
34. Ju Z, Dunham RA, Liu Z. Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Mol Genet Genomics 2002, 268:87-95. 10.1007/s00438-002-0727-9, 12242503.
35. Li RW, Waldbieser GC. Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus. BMC Genomics 2006, 7:134. 10.1186/1471-2164-7-134, 1501020, 16740160.
36. Liu Z, Li RW, Waldbieser GC. Utilization of microarray technology for functional genomics in ictalurid catfish. J Fish Biol 2008, 72:2377-2390.
37. Peatman E, Baoprasertkul P, Terhune J, Xu P, Nandi S, Kucuktas H, Li P, Wang S, Somridhivej B, Dunham R, Liu Z. Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium. Dev Comp Immunol 2007, 31:1183-1196. 10.1016/j.dci.2007.03.003, 17449095.
38. Peatman E, Terhune J, Baoprasertkul P, Xu P, Nandi S, Wang S, Somridhivej B, Kucuktas H, Li P, Dunham R, Liu Z. Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri. Mol Immunol 2008, 45:553-566. 10.1016/j.molimm.2007.05.012, 17599411.
39. Quiniou SM, Katagiri T, Miller NW, Wilson M, Wolters WR, Waldbieser GC. Construction and characterization of a BAC library from a gynogenetic channel catfish Ictalurus punctatus. Genet Sel Evol 2003, 35:673-683. 10.1186/1297-9686-35-7-673, 2698005, 14604514.
40. Wang S, Xu P, Thorsen J, Zhu B, de Jong PJ, Waldbieser G, Kucuktas H, Liu Z. Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. Mar Biotechnol (NY) 2007, 9:701-711. 10.1007/s10126-007-9021-5, 17671813.
41. Quiniou SM, Waldbieser GC, Duke MV. A first generation BAC-based physical map of the channel catfish genome. BMC Genomics 2007, 8:40. 10.1186/1471-2164-8-40, 1800894, 17284319.
42. Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z. A BAC-based physical map of the channel catfish genome. Genomics 2007, 90:380-388. 10.1016/j.ygeno.2007.05.008, 17582737.
43. Nandi S, Peatman E, Xu P, Wang S, Li P, Liu Z. Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus). Genetica 2007, 131:81-90. 10.1007/s10709-006-9115-4, 17091335.
44. Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G. Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol (NY) 2008, 10:227-233. 10.1007/s10126-007-9066-5, 18297360.
45. Sha Z, Abernathy WJ, Wang S, Li P, Kucuktas H, Liu H, Peatman E, Liu Z. NOD-like subfamily of the nucleotide-binding domain and leucine-rich repeat containing family receptors and their expression in channel catfish. Dev Comp Immunol 2009, 31:991-999.
46. Steinke D, Salzburger W, Meyer A. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol 2006, 62:772-784. 10.1007/s00239-005-0170-8, 16752215.
47. CHORI-212: Channel Catfish (Ictalurus punctatus) BAC Library. , http://bacpac.chori.org/library.php?id=103
48. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
49. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
50. Chou HH, Holmes MH. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104. 10.1093/bioinformatics/17.12.1093, 11751217.
51. RepeatMasker Open-3.0. , http://www.repeatmasker.org
52. Msatfinder: detection and characterisation of microsatellites. , http://www.genomics.ceh.ac.uk/msatfinder/
53. Sekino M, Kobayashi T, Hara M. Segregation and linkage analysis of 75 novel microsatellite DNA markers in pair crosses of Japanese abalone (Haliotis discus hannai) using the 5'-tailed primer method. Mar Biotechnol (NY) 2006, 8:453-466. 10.1007/s10126-005-6179-6, 16874445.