A comparative gene index for the white sturgeon Acipenser transmontanus

Marine Genomics

Volumn 1, Issue 1, 2008, Pages 15-21

  Lazzari, Barbara ^a   Mariani, Valentina ^a   Malinverni, Roberto ^a   Caprera, Andrea ^a   Giuffra, Elisabetta ^a  

^a PARCO TECNOLOGICO PADANO   (Italy)

Author keywords

Database; Expressed sequenced tags; Skin; Spleen

Indexed keywords

ACIPENSER TRANSMONTANUS; ACIPENSERIDAE; ICTALURUS PUNCTATUS; PISCES; SALMO SALAR; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODONTIDAE;

EID: 45449113588     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2008.04.002     Document Type: Article

References (32)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Barker G., Batley J., O' Sullivan H., Edwards K.J., and Edwards D. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19 (2003) 421-422
3. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acid Res. 27 (1999) 573-580
4. Birstein V., and DeSalle R. Molecular phylogeny of Acipenserinae. Mol. Phylogenet. Evol. 9 (1998) 141-155
5. Caprera A., Lazzari B., Stella A., Merelli I., Caetano A.R., and Mariani P. GoSh: a web-based database for goat and sheep EST sequences. Bioinformatics 23 (2007) 1043-1045
6. Chou H.H., and Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 17 (2001) 1093-1104
7. Clark M.S., Edwards Y.J.K., Peterson D., Clifton S.W., Thompson A.J., Sasaki M., Suzuki Y., Kikuchi K., Watabe S., Kawakami K., Sugano S., Elgar G., and Johnson S.L. Fugu ESTs: new resources for transcription analysis and genome annotation. Genome Res. 13 (2003) 2747-2753
8. Devarajan P., Johnston J.J., Ginsberg S.S., Van Wart H.E., and Berliner N. Structure and expression of neutrophil gelatinase cDNA. Identity with type IV collagenase from HT1080 cells. J. Biol. Chem. 267 (1992) 25228-25232
9. dos Santos N.M., Romano N., de Sousa M., Ellis A.E., and Rombout J.H. Ontogeny of B and T cells in sea bass (Dicentrarchus labrax, L.). Fish Shellfish Immunol. 10 (2000) 583-596
10. Ellis A.E. Ontogeny of the immune response in Salmo salar. Histogenesis of the lymphoid organs and appearance of membrane immunoglobulin and mixed leucocyte reactivity. In: Solomon J.B., and Horton J.D. (Eds). Developmental Immunobiology (1977), Elsevier/North-Holland Biomedical Press 225-231
11. Ewing B., Hiller L., Wendl M., and Green P. Truffle.org Basecalling of automated sequence traces using phred. I. Accuracy assessment. Genome Res. 8 (1998) 175-185
12. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., and Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30 (2002) 235-238
13. Gattiker A., Gasteiger E., and Bairoch A. ScanPROSITE: a reference implementation of a PROSITE scanning tool. Appl. Bioinformatics 1 (2002) 107-108
14. Hasty K.A., Pourmotabbed T.F., Goldberg G.I., Thompson J.P., Spinella D.G., Stevens R.M., and Mainardi C.L. Human neutrophil collagenase. A distinct gene product with homology to other matrix metalloproteinases. J. Biol. Chem. 265 (1990) 11421-11424
15. Huan X., and Madan A. CAP3: a DNA sequence assembly program. Genome Res. 9 (1999) 868-877
16. Huttenhuis H.B., Huising M.O., van der Meulen T., van Oosterhoud C.N., Sánchez N.A., Taverne-Thiele A.J., Stroband H.W., and Rombout J.H. Rag expression identifies B and T cell lymphopoietic tissues during the development of common carp (Cyprinus carpio). Dev. Comp. Immunol. 29 (2005) 1033-1047
17. Karsi A., Cao D., Li P., Patterson A., Kocabas A., Feng J., Ju Z., Mickett K., and Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene 285 (2002) 157-168
18. Klomklao S., Benjakul S., Visessanguan W., Kishimura H., Simpson B., and Saeki H. Trypsins from yellowfin tuna (Thunnus albacores) spleen: purification and characterization. Comp. Biochem. Physiol., Part B Biochem. Mol. Biol. 144 (2006) 47-56
19. Klomklao S., Benjakul S., Visessanguan W., Kishimura H., and Simpson B.K. Purification and characterization of trypsin from the spleen of tongol tuna (Thunnus tonggol). J. Agric. Food Chem. 54 (2006) 5617-5622
20. Kocabas A., Li P., Cao D., Karsi A., He C., Patterson A., Ju Z., Dunham R., and Liu Z. Expression profile of the channel catfish spleen: analysis of genes involved in immune functions. Mar. Biotechnol. 4 (2002) 526-536
21. Koshikawa N., Hasegawa S., Nagashima Y., Mitsuhashi K., Tsubota Y., Miyata S., Miyagi Y., Yasumitsu H., and Miyazaki K. Expression of trypsin by epithelial cells of various tissues, leukocytes, and neurons in human and mouse. Am. J. Pathol. 153 (1998) 937-944
22. Krieger J., Fuerst P., and Cavender T. Phylogenetic relationships of the North American sturgeons (order Acipenseriformes) based on mitochondrial DNA sequences. Mol. Phylogenet. Evol. 16 (2000) 64-72
23. Lanfredi M., Congiu L., Garrido-Ramos M.A., dela Herrán R., Leis M., Chicca M., Rossi R., Tagliavini J., Rejón C.R., Rejón M.R., and Fontana F. Chromosomal location and evolution of a satellite DNA family in seven sturgeon species. Chromosom. Res. 9 (2001) 47-52
24. Lazzari B., Caprera A., Cosentino C., Stella A., Milanesi L., and Viotti A. ESTuber db: an online database for Tuber borchii EST sequences. BMC Bioinformatics 8 (2007) S13
25. Lazzari B., Caprera A., Vecchietti A., Stella A., Milanesi L., and Pozzi C. ESTree db: a tool for peach functional genomics. BMC Bioinformatics 6 (2005) S16
26. Lee T.-H.D., Streb J.W., Georger M.A., and Miano J.M. Tissue expression of the novel serine carboxypeptidase Scpep1. J. Histochem. Cytochem. 54 (2006) 701-711
27. Lundqvist M., Strömberg S., and Pilström L. Ig heavy chain of the sturgeon Acipenser baeri: cDNA sequence and diversity. Immunogenetics 48 (1998) 372-382
28. Park K., Osborne J., Tsoi S., Brown L., and Johnson S. Expressed sequence tags analysis of Atlantic halibut (Hippoglossus hippoglossus) liver, kidney and spleen tissues following vaccination against Vibrio anguillarum and Aeromonas salmonicida. Fish Shellfish Immunol. 18 (2005) 393-415
29. Pertea G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., and Quackenbush J. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19 (2003) 651-652
30. Petrie-Hanson L., and Ainsworth A.J. Differential cytochemical staining characteristics of channel catfish leukocytes identify cell populations in lymphoid organs. Vet. Immunol. Immunopathol. 73 (2000) 129-144
31. Robles F., de la Herrán R., Ludwig A., Ruiz R., Ruiz R., and Garrido-Ramos M. Evolution of ancient satellite DNAs in sturgeon genomes. Gene 338 (2004) 133-142
32. Thiel T., Michalek, Michalek W., Varshney, Varshney R., Graner, and Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). TAG Theor. Appl. Genet. 106 (2003) 411-422