Database Authors
Karen Parker, Moss Landing Marine Labs; G. Jason Smith, Moss Landing Marine Labs
Summary Thalassiosira pseudonana is a marine diatom. Thalassiosira pseudonana CCMP1335 was the first diatom genome to be sequenced [Armbrust04]. The annotation was updated in 2012 using the DOE JGI microbial annotation pipeline for eukaryotes.

The Pathway/Genome Database (PGDB) was generated by Karen Parker and Jason Smith of the Moss Landing Marine Labs using the PathoLogic component of the Pathway Tools software [Karp11, Karp19] and the MetaCyc reference database [Caspi20]. Pruning was turned off and the automatic hole filler was not used.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation. The consistency checker and Transport Inference Parser (TIP) were used to refine the PGDB. Manual editing included evaluation of probable enzymes, hole filling, and the addition of pathways. Locus tag synonyms without the prefix of THAPSDRAFT_, THAPS_ or THAPSDRAFT_bd were created so that expression data files that do not use the locus tag prefix can be used without modification.

Citations: [Zhang05a, Bowler08, Mock08, Mavromatis09, May09, Zhang10, Markowitz12, Fabris12]

Genome
Replicon/ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome11,1771,177003,042,585
Chromosome21,0211,021002,707,195
Chromosome3986986002,440,052
Chromosome4913913002,402,323
Chromosome5872872002,305,972
Chromosome6773773002,071,480
Chromosome7710710001,992,434
Chromosome8483483001,267,198
Chromosome9393393001,191,060
Chromosome12349349001,128,382
Chromosome10386386001,105,668
Chromosome22324324001,057,565
Chromosome13376376001,052,196
Chromosome1435135100998,643
Chromosome1530330300931,268
Chromosome1830330300827,053
Chromosome11a27127100806,142
Chromosome2025625600800,234
Chromosome1721821800659,924
Chromosome19a20320300607,239
Chromosome16a16416400459,776
Chromosome2315215200454,954
Chromosome24868600297,349
Chromosome19c868600291,194
Chromosome16b535300169,376
Chromosome19b575700151,677
ThapsContig4323200138,550
Plastid179141380128,814
ThapsContig5363600100,292
ThapsContig630300083,390
Chromosome11b30300082,843
ThapsContig735350079,656
ThapsContig812120070,851
ThapsContig923230066,660
ThapsContig1049490063,870
ThapsContig1118180051,378
Mitochon623527043,827
ThapsContig1215150043,458
ThapsContig1313130037,633
27 Undisplayed Contigs/Replicons11411400399,845
Total:11,91411,84965032,610,006
Ortholog data available?Yes
Database Contents
Genes11,914
Pathways527
Enzymatic Reactions2,620
Transport Reactions68
Polypeptides11,847
Protein Complexes2
Enzymes1,675
Transporters257
Compounds1,594
tRNAs56
Growth Media1
Protein Features8,323
Database Version29.0
Taxonomic Lineage cellular organisms
Eukaryota
Sar
Stramenopiles
Ochrophyta
Bacillariophyta
Coscinodiscophyceae
Thalassiosirophycidae
Thalassiosirales
Thalassiosiraceae
Thalassiosira
Thalassiosira pseudonana
Thalassiosira pseudonana CCMP1335
Genetic Code Number 1 -- Standard
GOLD0000536
NCBI-Taxonomy296543

References

Armbrust04: Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004). "The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism." Science 306(5693);79-86. PMID: 15459382

Bowler08: Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV (2008). "The Phaeodactylum genome reveals the evolutionary history of diatom genomes." Nature 456(7219);239-44. PMID: 18923393

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Fabris12: Fabris M, Matthijs M, Rombauts S, Vyverman W, Goossens A, Baart GJ (2012). "The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway." Plant J. PMID: 22332784

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

Markowitz12: Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC (2012). "IMG: the Integrated Microbial Genomes database and comparative analysis system." Nucleic Acids Res 40(Database issue);D115-22. PMID: 22194640

Mavromatis09: Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC (2009). "The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes." Stand Genomic Sci 1(1);63-7. PMID: 21304638

May09: May P, Christian JO, Kempa S, Walther D (2009). "ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii." BMC Genomics 10;209. PMID: 19409111

Mock08: Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Holtermann K, Durkin C, Bondurant SS, Richmond K, Rodesch M, Kallas T, Huttlin EL, Cerrina F, Sussman MR, Armbrust EV (2008). "Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses." Proc Natl Acad Sci U S A 105(5);1579-84. PMID: 18212125

Zhang05a: Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY (2005). "MetaCyc and AraCyc. Metabolic pathway databases for plant research." Plant Physiol 138(1);27-37. PMID: 15888675

Zhang10: Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (2010). "Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants." Plant Physiol 153(4);1479-91. PMID: 20522724

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.