AmphiEST: Enabling comparative analysis of ESTs from five developmental stages of amphioxus

Marine Genomics

Volumn 3, Issue 3-4, 2010, Pages 151-155

  Jin, Ping ^a   Ji, Xinglai ^b   Wang, Hui ^a   Li Ling, Jesse ^c,d   Ma, Fei ^a  

^a NANJING NORMAL UNIVERSITY   (China)

^b YUNNAN UNIVERSITY   (China)

^c CHINA MEDICAL UNIVERSITY   (China)

^d NORTHEASTERN UNIVERSITY   (China)

Author keywords

AmphiEST database; Amphioxus; Developmental stage; MiRNA; MiRNA target gene

Indexed keywords

BRANCHIOSTOMA LANCEOLATUM; CHORDATA; VERTEBRATA;

EID: 78649528216     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2010.09.003     Document Type: Article

References (38)

1. Arunkumar K.P., Mita K., Nagaraju J. The silkworm Z chromosome is enriched in testis-specific genes. Genetics 2009, 182:493-501.
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25:25-29.
3. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S. The universal protein resource (UniProt). Nucleic Acids Res. 2005, 33:D154-D159.
4. Bourlat S.J., Juliusdottir T., Lowe C.J., Freeman R., Aronowicz J., Kirschner M., Lander E.S., Thorndyke M., Nakano H., Kohn A.B., Heyland A., Moroz L.L., Copley R.R., Telford M.J. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 2006, 444:85-88.
5. Chen Z., Xue C., Zhu S.X., Zhou F., Ling X.B., Liu G., Chen L. GoPipe: streamlined gene ontology annotation for batch anonymous sequences with statistics. Prog. Biochem. Biophys. 2005, 32:187-191.
6. Chen F., Lee Y., Jiang Y., Wang S., Peatman E., Abernathy J., Liu H., Liu S., Kucuktas H., Ke C., Liu Z. Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). PLoS ONE 2010, 5:e11546.
7. D'Aniello S., Irimia M., Maeso I., Pascual-Anaya J., Jiménez-Delgado S., Bertrand S. Massive gene expansion but not loss leads to unprecedented tyrosine kinase diversity and richness in amphioxus. Mol. Biol. Evol. 2008, 25:1841-1854.
8. Dai Z., Chen Z., Ye H., Zhou L., Cao L., Wang Y., Peng S., Chen L. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol. Dev. 2009, 11:41-49.
9. Dawson H.D., Royaee A.R., Nishi S., Kuhar D., Schnitzlein W.M., Zuckermann F., Urban J., Lunney J.K. Identification of key immune mediators regulating T helper 1 responses in swine. Vet. Immunol. Immunopathol. 2004, 100:105-111.
10. Delsuc F., Brinkmann H., Chourrout D., Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006, 439:965-968.
11. Enright A.J., John B., Gaul U., Tuschl T., Sander C., Marks D.S. MicroRNA target detection. Genome Biol. 2003, 5:R1.
12. Garcia-Fernàndez J., Benito-Gutièrrez É. It's a long way from amphioxus: descendants of the earliest chordate. BioEssays 2009, 31:665-675.
13. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36:D154-D158.
14. Heimberg A.M., Sempere L.F., Moy V.N., Donoghue P.C., Peterson K.J. MicroRNAs and the advent of vertebrate morphological complexity. Proc. Natl Acad. Sci. USA 2008, 105:2946-2950.
15. Hendrickson D.G., Hogan D.J., McCullough H.L., Myers J.W., Herschlag D., Ferrell J.E., Brown P.O. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 2009, 7:e1000238.
16. Holland L.Z., Holland N.D. Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate?. J. Anat. 2001, 199:85-98.
17. Holland L.Z., Laudet V., Schubert M. The chordate amphioxus: an emerging model organism for developmental biology. Cell. Mol. Life Sci. 2004, 61:2290-2308.
18. Holland L.Z., Albalat R., Azumi K., Benito-Gutiérrez E., Blow M.J., Bronner-Fraser M., Brunet F., Butts T., Candiani S., Dishaw L.J., Ferrier D.E., Garcia-Fernàndez J., Gibson-Brown J.J., Gissi C., Godzik A., Hallböök F., Hirose D., Hosomichi K., Ikuta T., Inoko H., Kasahara M., Kasamatsu J., Kawashima T., Kimura A., Kobayashi M., Kozmik Z., Kubokawa K., Laudet V., Litman G.W., McHardy A.C., Meulemans D., Nonaka M., Olinski R.P., Pancer Z., Pennacchio L.A., Pestarino M., Rast J.P., Rigoutsos I., Robinson-Rechavi M., Roch G., Saiga H., Sasakura Y., Satake M., Satou Y., Schubert M., Sherwood N., Shiina T., Takatori N., Tello J., Vopalensky P., Wada S., Xu A., Ye Y., Yoshida K., Yoshizaki F., Yu J.K., Zhang Q., Zmasek C.M., de Jong P.J., Osoegawa K., Putnam N.H., Rokhsar D.S., Satoh N., Holland P.W. The amphioxus genome illuminates vertebrate origins and chephalochordate biology. Genome Res. 2008, 18:1100-1111.
19. Huang X., Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999, 9:868-877.
20. Huang S., Yuan S., Guo L., Yu Y., Li J., Wu T., Liu T., Yang M., Wu K., Liu H., Ge J., Yu Y., Huang H., Dong M., Yu C., Chen S., Xu A. Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity. Genome Res. 2008, 18:1112-1126.
21. Irimia M., Maeso I., Garcia-Fernàndez J. Convergent evolution of clustering of Iroquois homebox genes across metazoans. Mol. Biol. Evol. 2008, 25:1521-1525.
22. Min X.J., Butler G., Storms R., Tsang A. OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. 2005, 33:W677-W680.
23. Min X.J., Butler G., Storms R., Tsang A. TargetIdentifier: a web server for identifying full-length cDNAs from EST sequences. Nucleic Acids Res. 2005, 33:W669-W672.
24. Mita K., Morimyo M., Okano K., Koike Y., Nohata J., Kawasaki H., Kadono-Okuda K., Yamamoto K., Suzuki M.G., Shimada T., Goldsmith M.R., Maeda S. The construction of an EST database for Bombyx mori and its application. Proc. Natl Acad. Sci. USA 2003, 100:14121-14126.
25. Mrinal N., Nagaraju J. Intron loss is associated with gain of function in the evolution of the gloverin family of antibacterial genes in Bombyx mori. J. Biol. Chem. 2008, 283:23376-23387.
26. Pertea G., Huang X., Liang F., Antonescu V., Sultana R., Karamycheva S., Lee Y., White J., Cheung F., Parvizi B., Tsai J., Quackenbush J. TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19:651-652.
27. Prasad M.D., Muthulakshmi M., Arunkumar K.P., Madhu M., Sreenu V.B., Pavithra V., Bose B., Nagarajaram H.A., Mita K., Shimada T., Nagaraju J. SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. Nucleic Acids Res. 2005, 33:D403-D406.
28. Putnam N.H., Butts T., Ferrier D.E., Furlong R.F., Hellsten U., Kawashima T., Robinson-Rechavi M., Shoguchi E., Terry A., Yu J.K., Benito-Gutiérrez E.L., Dubchak I., Garcia-Fernàndez J., Gibson-Brown J.J., Grigoriev I.V., Horton A.C., de Jong P.J., Jurka J., Kapitonov V.V., Kohara Y., Kuroki Y., Lindquist E., Lucas S., Osoegawa K., Pennacchio L.A., Salamov A.A., Satou Y., Sauka-Spengler T., Schmutz J., Shin-I T., Toyoda A., Bronner-Fraser M., Fujiyama A., Holland L.Z., Holland P.W., Satoh N., Rokhsar D.S. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008, 453:1064-1071.
29. Satou Y., Yamada L., Mochizuki Y., Takatori N., Kawashima T., Sasaki A., Hamaguchi M., Awazu S., Yagi K., Sasakura Y., Nakayama A., Ishikawa H., Inaba K., Satoh N. A cDNA resource from the basal chordate Ciona intestinalis. Genesis 2002, 33:153-154.
30. Satou Y., Kawashima T., Kohara Y., Satoh N. Large scale EST analyses in Ciona intestinalis: its application as Northern blot analyses. Dev. Genes Evol. 2003, 213:314-318.
31. Satou Y., Kawashima T., Shoguchi E., Nakayama A., Satoh N. An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zool. Sci. 2005, 22:723-734.
32. Schubert M., Escriva H., Xavier-Neto J., Laudet V. Amphioxus and tunicates as evolutionary model systems. Trends Ecol. Evol. 2006, 21:269-277.
33. Sempere L.F., Cole C.N., McPeek M.A., Peterson K.J. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. 2006, 306:575-588.
34. Uenishi H., Eguchi T., Suzuki K., Sawazaki T., Toki D., Shinkai H., Okumura N., Hamasima N., Awata T. PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Nucleic Acids Res. 2004, 32:D484-D488.
35. Wang S., Peatman E., Abernathy J., Waldbieser G., Lindquist E., Richardson P., Lucas S., Wang M., Li P., Thimmapuram J., Liu L., Vullaganti D., Kucuktas H., Murdock C., Small B.C., Wilson M., Liu H., Jiang Y., Lee Y., Chen F., Lu J., Wang W., Xu P., Somridhivej B., Baoprasertkul P., Quilang J., Sha Z., Bao B., Wang Y., Wang Q., Takano T., Nandi S., Liu S., Wong L., Kaltenboeck L., Quiniou S., Bengten E., Miller N., Trant J., Rokhsar D., Liu Z. Assembly of 500, 000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010, 11:R8.
36. Yu J.K., Meulemans D., McKeown S.J., Bronner-Fraser M. Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Res. 2008, 18:1127-1132.
37. Yu J.K., Wang M.C., Shin-I T., Kohara Y., Holland L.Z., Satoh N., Satou Y. A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae. Dev. Genes Evol. 2008, 218:723-727.
38. Zhang Q., Zmasek C.M., Dishaw L.J., Mueller M.G., Ye Y., Litman G.W., Godzik A. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol. 2008, 9:R123.