SmedGD 2.0: The Schmidtea mediterranea genome database

Genesis

Volumn 53, Issue 8, 2015, Pages 535-546

  Robb, Sofia M C ^a   Gotting, Kirsten ^a   Ross, Eric ^a   Sánchez Alvarado, Alejandro ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

GBrowse; GMOD; Planaria genome; Schmidtea mediterranea

Indexed keywords

TRANSCRIPTOME; HELMINTH PROTEIN;

ARTICLE; BIOTYPE; CELL FUNCTION; GENE EXPRESSION; GENE ONTOLOGY; GENE SEQUENCE; GENETIC DATABASE; GENOME; GENOMICS; IN SITU HYBRIDIZATION; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PLATYHELMINTH; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA INTERFERENCE; SCHMIDTEA MEDITERRANEA; SEQUENCE HOMOLOGY; TISSUE REGENERATION; TRANSCRIPTOMICS; TURBELLARIA; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; INTERNET; METABOLISM; REGENERATION;

PLANARIA; PLATYHELMINTHES; SCHMIDTEA MEDITERRANEA; TURBELLARIA;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOME; HELMINTH PROTEINS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PLANARIANS; REGENERATION;

EID: 84939469691     PISSN: 1526954X     EISSN: 1526968X     Source Type: Journal    
DOI: 10.1002/dvg.22872     Document Type: Article

References (58)

1. Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sanchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W. 2011. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 21:1193-1200.
2. Adler CE, Seidel CW, McKinney SA, Sánchez Alvarado A. 2014. Selective amputation of the pharynx identifies a FoxA-dependent regeneration program in planaria. Elife 3:e02238.
3. Bender CE, Fitzgerald P, Tait SW, Llambi F, McStay GP, Tupper DO, Pellettieri J, Sánchez Alvarado A, Salvesen GS, Green DR. 2012. Mitochondrial pathway of apoptosis is ancestral in metazoans. Proc Natl Acad Sci U S A 109:4904-4909.
4. Brusca RC, Brusca GJ. 2003. Invertebrates, 2nd ed. Sunderland, MA: Sinauer Associates. pp xix, 936.
5. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10:421.
6. Campbell MS, Holt C, Moore B, Yandell M. 2014. Genome annotation and curation using MAKER and MAKER-P. Curr Protoc Bioinformatics 48:4 11 11-14 11 39.
7. Chen CC, Wang IE, Reddien PW. 2013. pbx is required for pole and eye regeneration in planarians. Development 140:719-729.
8. Chen Y, Yu P, Luo J, Jiang Y. 2003. Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT. Mamm Genome 14:859-865.
9. Collins JJ III, Hou X, Romanova EV, Lambrus BG, Miller CM, Saberi A, Sweedler JV, Newmark PA. 2010. Genome-wide analyses reveal a role for peptide hormones in planarian germline development. PLoS Biol 8:e1000509.
10. Collins JJ III, Newmark PA. 2013. It's no fluke: The planarian as a model for understanding schistosomes. PLoS Pathog 9:e1003396.
11. Collins JJ III, Wang B, Lambrus BG, Tharp ME, Iyer H, Newmark PA. 2013. Adult somatic stem cells in the human parasite Schistosoma mansoni. Nature 494:476-479.
12. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Giron CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kahari AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P. 2015. Ensembl 2015. Nucleic Acids Res 43:D662-D669.
13. Eisenhoffer GT, Kang H, Sánchez Alvarado A. 2008. Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3:327-339.
14. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. 2014. Pfam: The protein families database. Nucleic Acids Res 42:D222-D230.
15. Finn RD, Clements J, Eddy SR. 2011. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res 39:W29-W37.
16. Forsthoefel DJ, James NP, Escobar DJ, Stary JM, Vieira AP, Waters FA, Newmark PA. 2012. An RNAi screen reveals intestinal regulators of branching morphogenesis, differentiation, and stem cell proliferation in planarians. Dev Cell 23:691-704.
17. Forsthoefel DJ, Park AE, Newmark PA. 2011. Stem cell-based growth, regeneration, and remodeling of the planarian intestine. Dev Biol 356:445-459.
18. Friedlander MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Sánchez Alvarado A, Kim JK, Rajewsky N. 2009. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A 106:11546-11551.
19. Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150-3152.
20. Gavino MA, Wenemoser D, Wang IE, Reddien PW. 2013. Tissue absence initiates regeneration through follistatin-mediated inhibition of activin signaling. Elife 2:e00247.
21. Gene OC. 2015. Gene ontology consortium: Going forward. Nucleic Acids Res 43:D1049-D1056.
22. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644-652.
23. Guedelhoefer OC, Sánchez Alvarado A. 2012. Amputation induces stem cell mobilization to sites of injury during planarian regeneration. Development 139:3510-3520.
24. Gurley KA, Elliott SA, Simakov O, Schmidt HA, Holstein TW, Sánchez Alvarado A. 2010. Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response. Dev Biol 347:24-39.
25. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305:567-580.
26. Lapan SW, Reddien PW. 2012. Transcriptome analysis of the planarian eye identifies ovo as a specific regulator of eye regeneration. Cell Rep 2:294-307.
27. Laumer CE, Hejnol A, Giribet G. 2015. Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation. Elife 4.
28. Littlewood TJ, Bray RA. 2001. Interrelationships of the platyhelminthes. London, New York: Taylor and Francis.
29. Liu SY, Selck C, Friedrich B, Lutz R, Vila-Farre M, Dahl A, Brandl H, Lakshmanaperumal N, Henry I, Rink JC. 2013. Reactivating head regrowth in a regeneration-deficient planarian species. Nature 500:81-84.
30. Lupas A. 1996. Prediction and analysis of coiled-coil structures. Methods Enzymol 266:513-525.
31. MySQL. 2015. Available at: http://dev.mysql.com. Last accessed July 13, 2015.
32. Newmark PA, Wang Y, Chong T. 2008. Germ cell specification and regeneration in planarians. Cold Spring Harb Symp Quant Biol 73:573-581.
33. Pearson BJ, Sánchez Alvarado A. 2010. A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages. Development 137:213-221.
34. Pellettieri J, Fitzgerald P, Watanabe S, Mancuso J, Green DR, Sánchez Alvarado A. 2010. Cell death and tissue remodeling in planarian regeneration. Dev Biol 338:76-85.
35. Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nat Methods 8:785-786.
36. Reddien PW, Bermange AL, Murfitt KJ, Jennings JR, Sánchez Alvarado A. 2005. Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. Dev Cell 8:635-649.
37. Robb SM, Ross E, Sánchez Alvarado A. 2008. SmedGD: The Schmidtea mediterranea genome database. Nucleic Acids Res 36:D599-D606.
38. Roberts-Galbraith RH, Newmark PA. 2013. Follistatin antagonizes activin signaling and acts with notum to direct planarian head regeneration. Proc Natl Acad Sci U S A 110:1363-1368.
39. Rossi A, Ross EJ, Jack A, Sánchez Alvarado A. 2014. Molecular cloning and characterization of SL3: A stem cell-specific SL RNA from the planarian Schmidtea mediterranea. Gene 533:156-167.
40. Rouhana L, Vieira AP, Roberts-Galbraith RH, Newmark PA. 2012. PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells. Development 139:1083-1094.
41. Rouhana L, Weiss JA, King RS, Newmark PA. 2014. PIWI homologs mediate histone H4 mRNA localization to planarian chromatoid bodies. Development 141:2592-2601.
42. Sánchez Alvarado A. 2013a. Learning about loss. Elife 2:e00533.
43. Sánchez Alvarado A. 2013b. On the trail of a tropical disease. Elife 2:e0111.
44. Sánchez Alvarado A. 2015. Unravelling a can of worms. Elife 4.
45. seqclean. 2011. Available at: http://sourceforge.net/projects/seqclean/. Last accessed July 13, 2015.
46. Sikes JM, Newmark PA. 2013. Restoration of anterior regeneration in a planarian with limited regenerative ability. Nature 500:77-80.
47. Srivastava M, Mazza-Curll KL, van Wolfswinkel JC, Reddien PW. 2014. Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling. Curr Biol 24:1107-1113.
48. Stajich JE. 2007. An introduction to BioPerl. Methods Mol Biol 406:535-548.
49. Stein LD. 2013. Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform 14:162-171.
50. sydcode. 2014. pubmed-posts Available at: https://wordpress.org/plugins/pubmed-posts/.
51. Umesono Y, Tasaki J, Nishimura Y, Hrouda M, Kawaguchi E, Yazawa S, Nishimura O, Hosoda K, Inoue T, Agata K. 2013. The molecular logic for planarian regeneration along the anterior-posterior axis. Nature 500:73-76.
52. UniProt C. 2015. UniProt: A hub for protein information. Nucleic Acids Res 43:D204-D212.
53. van Wolfswinkel JC, Wagner DE, Reddien PW. 2014. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell 15:326-339.
54. Wang B, Collins JJ III, Newmark PA. 2013. Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni. Elife 2:e00768.
55. Wang Y, Stary JM, Wilhelm JE, Newmark PA. 2010. A functional genomic screen in planarians identifies novel regulators of germ cell development. Genes Dev 24:2081-2092.
56. Wang Y, Zayas RM, Guo T, Newmark PA. 2007. Nanos function is essential for development and regeneration of planarian germ cells. Proc Natl Acad Sci U S A 104:5901-5906.
57. WordPress. 2015. Available at: https://wordpress.org/. Last accessed July 13, 2015.
58. Xiang Y, Miller DE, Ross EJ, Sánchez Alvarado A, Hawley RS. 2014. Synaptonemal complex extension from clustered telomeres mediates full-length chromosome pairing in Schmidtea mediterranea. Proc Natl Acad Sci U S A 111:E5159-E5168.