Statistics of the DB-AT

Available tables:
 Summary
Data sources
Statistics for new RNA-Seq tags of apicomplexa parasites
Population diversities in Plasmodium falciparum
Statistics for assembled transcriptomes of four Apicomplexa species
Statistics for transcription start sites (TSS) Seq tags for Toxoplasma gondii
Dynamic RNA-Seq tags for Toxoplasma gondii infection/bradyzoite induction

Summary

SpeciesGenome size [Mb]No. of transcripts
(FPKM>1)		Total sequence tagscompletely sequenced
cDNAs
Plasmodium falciparum23.3......348
Plasmodium vivax27.0......2,041
Plasmodium berghei18.63,108142,359,734329
Plasmodium yoelii22.8......311
Theileria equi11.64,018117,015,108n.d.
Theileria parva8.4......n.d.
Theileria orientalis9.0......n.d.
Babesia bigeminaNA......n.d.
Babesia bovis8.2......n.d.
Babesia caballiNA...80,656,968n.d.
Babesia divergensNA...89,996,032n.d.
Babesia gibsoniNA...73,740,894n.d.
Toxoplasma gondii63.7......1,830
Neospora caninum59.18,160117,043,870n.d.
Eimeria tenella51.9......n.d.
Eimeria maxima46.08,619^68,834,980*
100,289,968**		n.d.
Cryptosporidium parvum9.1......1,066

NA: not available

n.d.: not determined

* immature oocyst

** sporozoite

^ number is for combined immature oocyst and sporozoite

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Data sources (Genomes and Gene models of our database are based on EuPathDB)

Organism ID Project Strain ncbi_tax_id Data Source Reference Genome Version All Genes Organism Reference genome sequence (FASTA) Reference gene model (GFF)
bbovT2Bo PiroplasmaDB T2Bo 484906 GenBank Babesia bovis: genome size, number of chromosomes and telomeric probe hybridisation. Jones et al. Int. J. Parasitol. 1997;27(12):1569-73, Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. Brayton et al. PLoS Pathog. 2007 Oct 19;3(10):1401-13 PiroplasmaDB Version 5.0 3781 Babesia bovis T2Bo PiroplasmaDB PiroplasmaDB
cparIowaII CryptoDB Iowa II 353152 GenBank Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Bankier et al. Genome Res. 2003;13(8):1787-99 CryptoDB Version 6.0 3886 Cryptosporidium parvum Iowa II CryptoDB CryptoDB
emaxWeybridge ToxoDB Weybridge null GenBank Genome sequence and annotation for Eimeria maxima Weybridge. The Eimeria maxima Weybridge nuclear genome comprises 14 chromosomes and is estimated to be around 55Mb in size. The GC content is ~54%. The genome assembly consists of 3564 scaffolds with an N50 of 27kb. Arnab Pain (King Abdullah University of Science and Technology). Adam Reid (Wellcome Trust Sanger Institute). ToxoDB Version 11.0 6369 Eimeria maxima Weybridge ToxoDB ToxoDB
etenHoughton ToxoDB strain Houghton 413949 GenBank Genome sequence and annotation for Eimeria tenella Houghton. The Eimeria tenella nuclear genome comprises 14 chromosomes and is estimated to be around 55Mb in size. The GC content is ~58%. The genome assembly consists of 4664 scaffolds with an N50 of 204kb. Funding: BBSRC, Wellcome Trust Sanger Institute ToxoDB Version 11.0 8634 Eimeria tenella strain Houghton ToxoDB ToxoDB
ncanLIV ToxoDB Liverpool 572307 GenBank Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. Reid et al. PLoS Pathog. 2012;8(3):e1002567 ToxoDB Version 11.0 7266 Neospora caninum Liverpool ToxoDB ToxoDB
pberANKA PlasmoDB ANKA 5823 GeneDB Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. Watanabe et al. Nucleic Acids Res. 2007;35(Database issue):D431-8 PlasmoDB Version 11.0 5164 Plasmodium berghei ANKA PlasmoDB PlasmoDB
pfal3D7 PlasmoDB 3D7 36329 GeneDB Genome sequence of the human malaria parasite Plasmodium falciparum. Gardner et al. Nature. 2002 Oct 3;419(6906):498-511. PlasmoDB Version 11.0 5777 Plasmodium falciparum 3D7 PlasmoDB PlasmoDB
pvivSal1 PlasmoDB Sal-1 126793 GeneDB Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Carlton et al. Nature 2008 Oct 9;455(7214):757-63 PlasmoDB Version 11.0 5626 Plasmodium vivax Sal-1 PlasmoDB PlasmoDB
pyoeyoelii17X PlasmoDB yoelii 17X null GeneDB Congenicity and genetic polymorphism in cloned lines derived from a single isolate of a rodent malaria parasite. Pattaradilokrat et al. Mol. Biochem. Parasitol. 2008;157(2):244-7 PlasmoDB Version 11.0 6103 Plasmodium yoelii yoelii 17X PlasmoDB PlasmoDB
tequWA PiroplasmaDB strain WA null GenBank Comparative genomic analysis and phylogenetic position of Theileria equi. Kappmeyer et al. BMC Genomics 2012;13( ):603 PiroplasmaDB Version 5.0 5397 Theileria equi strain WA PiroplasmaDB PiroplasmaDB
tgonME49 ToxoDB ME49 508771 JCVI Toxoplasma gondii ME49 sequence and annotation from Lis Caler at the J. Craig Venter Institute ToxoDB Version 10.0 8920 Toxoplasma gondii ME49 ToxoDB ToxoDB
toriShintoku PiroplasmaDB strain Shintoku 869250 GenBank Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. Hayashida et al. MBio 2012;3(5):e00204-12 PiroplasmaDB Version 5.0 4058 Theileria orientalis strain Shintoku PiroplasmaDB PiroplasmaDB
tparMuguga PiroplasmaDB strain Muguga 333668 GenBank Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Gardner et al. Science 2005 Jul 1;309(5731):134-7 PiroplasmaDB Version 5.0 4167 Theileria parva strain Muguga PiroplasmaDB PiroplasmaDB

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Statistics for new RNA-Seq tags of apicomplexa parasites

SpeciesStrainStageReference genomeTotal sequence tagsMapped tags, %Represented
transcripts
(FPKM>1)
Plasmodium bergheiANKAerythrocyticPlasmoDB-11.0142,359,73491.2*3,108
Theileria equiUSDAmerozoitePiroplasmaDB-5.0117,015,10823.0*4,018
Neospora caninumNc-1tachyzoite?ToxoDB-11.0117,043,87083.1*8,160
Eimeria maximaNIAHimmature oocystToxoDB-11.068,834,98085.2*8,619^
Eimeria maximaNIAHsporozoite ToxoDB-11.0100,289,96884.0*
Babesia caballiUSDAerythrocyticNA80,656,96895.6**(NA)
Babesia divergensundeterminederythrocyticNA89,996,03294.0**(NA)
Babesia gibsoniOitaerythrocyticNA73,740,89498.0**(NA)

^ number is for combined immature oocyst and sporozoite

* mapped to reference genome

** mapped back to assembled transcripts (FPKM>1)

NA: not available

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Population diversities in Plasmodium falciparum

Single-cell datasets of P. falciparum in five time courses

Hours after chloroquine
treatment		No. of cell
samples		No. of mapped
tags
0h (replicate 1)3827,623,157
0h (replicate 2)3827,700,140
6h4526,080,027
12h376,130,583
24h411,541,863
48h47458,113

Datasets of Indonesian patients clinical samples

Species ReferenceData setsTotal mapped tagsAverage frequency of
parasite tags,%		Mapped tagsNo. of represented
genes (RPKM>0)		No. of represented
genes (RPKM>1)
Plasmodium falciparum1163,066,215,4219.1244,993,5363,6333,569
Homo sapiens2,846,381,17713,1618,844

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Statistics for assembled transcriptomes of four Apicomplexa species

SpeciesReference genomeNo. of reference
transcripts		No. of assembled
transcript		No. of
reference loci
(missed)		No. of loci for
assembled transcripts
(novel)		No. of represented
transcripts (FPKM>0)		No. of represented
transcripts (FPKM>1)
Plasmodium bergheiPlasmoDB-11.05,1645,2915,145 (1,004)3,968 (189)3,5083,108
Theileria equiPlasmoDB-5.05,3076,0455,395 (328)5,183 (325)4,2974,018
Neospora caninumToxoDB-11.07,26512,9047,265 (8)7,986 (1,128)9,6028,160
Eimeria maximaToxoDB-11.06,36915,6886,364 (70)10,177 (4,398)11,9138,619
SpeciesFragment length
mean		Fragment length
st. dev.		No. of nucleotides
in transcripts		the shortest
transcript [nt]		the longest
transcript [nt]		Median sequence
length		Mean sequence
length		No. of discovered
ORFs
Plasmodium berghei201.4472.1913,329,6062234,6661,6052,519.306,313
Theileria equi170.9554.378,849,2376914,4031,1461,463.896,490
Neospora caninum187.1259.1150,781,0062252,1102,7783,935.2920,669
Eimeria maxima187.4967.335,337,5502732,0571,3822,252.5216,980

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Statistics for transcription start sites (TSS) Seq tags for Toxoplasma gondii

Species Strain Stage Total tags Mapped TSS tags TSS positions
Toxosplasma gondii RH Tachyzoite 6,801,945 2,591,387 85,750
Toxosplasma gondii ME49 Tachyzoite 12,101,228 2,484,257 242,889
Toxosplasma gondii ME49 Bradyzoite 8,418,271 357,792 67,091
Plasmodium falciparum 3D7 Erythrocyte 4,870,527 673,313 239,284

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Dynamic RNA-Seq tags for Toxoplasma gondii infection/bradyzoite induction

Parasite side

Tg infection / bradyzoite induction+/++/--/+-/-
TimeTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genes
0 hr2200411210046105980 ND ND ND14087442633913NDNDND
6 hr242962181315033617417654434 22882461491479602868447 32109298378620 1
24 hr239155151408048657924600426523229459651560482563651681855763580918 2
72 hr2225582815379446850137986551571252668718776986687183256590101091183
144 hr2440247421580256911 ND ND ND15329576611584NDNDND

Host side

Tg infection / bradyzoite induction+/++/--/+-/-
TimeTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genesTotal number of reads
(Parasite + Host)		Number of mapped readsNumber of represented genes
0 hr22004112199024849849 ND ND ND14087442124764139639NDNDND
6 hr24296218219702319907176544341568988198461479602813384068976521092983188738749846
24 hr23915515216122756579246004262332854794641560482513831497976718557635165463879851
72 hr222558281975843097771379865510837233976318776986170827579775256590102330791710001
144 hr24402474216239029770 ND ND ND15329576139492589779 ND ND ND

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