genomes
Data license: ODbL · Data source: Larue & Roy, 2023
- taxonomy_id
- INTEGER (primary key), unique identifier for each species
- species
- TEXT, binomial name of the species
- family
- TEXT, taxonomic family of the species
- order
- TEXT, taxonomic order of the species
- phylum
- TEXT, taxonomic phylum of the species
- accession
- TEXT, accession number of the genome assembly
- n_minor_introns
- INTEGER, total number of minor introns in the genome
- n_major_introns
- INTEGER, total number of major introns in the genome
- percent_minor_introns
- REAL, percentage of minor introns in the genome
- busco_score
- REAL, BUSCO score assessing the genome assembly completeness (vs. eukaryota_odb10)
- minor_snRNAs
- TEXT, minor snRNAs found in the annotated transcriptome
- genome_version
- TEXT, version of the genome assembly
- source_url
- TEXT, URL for the source genome/annotation files
- source_metadata
- TEXT, additional metadata from the original data source
- minor_intron+
- INTEGER, indicates if the species is inferred to contain real minor introns (1) or not (0)
25 rows where phylum = "Platyhelminthes" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, order, n_minor_introns, busco_score, minor_snRNAs, minor_snRNAs (array)
| taxonomy_id | species | family | order | phylum | accession | n_minor_introns | n_major_introns | percent_minor_introns ▲ | busco_score | minor_snRNAs | genome_version | source_url | source_metadata | minor_intron+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 147828 | Opisthorchis felineus | Opisthorchiidae | Opisthorchiida | Platyhelminthes | GCA_004794785.1 | 110 | 72977 | 0.150505561864627 | 91.4 | ["u11", "u12", "u4atac", "u6atac"] | ICG_Ofel_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/794/785/GCA_004794785.1_ICG_Ofel_1.0 | GCA_004794785.1;PRJNA413383;SAMN07740813;SJOL00000000.1;representative genome;147828;147828;Opisthorchis felineus;;AK-0245;latest;Scaffold;Major;Full;2019/04/15;ICG_Ofel_1.0;Institute of Cytology and Genetics SB RAS;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/794/785/GCA_004794785.1_ICG_Ofel_1.0;;;na | 1 |
| 100268 | Paragonimus heterotremus | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_013368495.1 | 83 | 64664 | 0.1281912675490756 | 74.5 | ["u4atac", "u6atac"] | P_heterotremus_1.0.allpaths.pg.lrna | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/368/495/GCA_013368495.1_P_heterotremus_1.0.allpaths.pg.lrna | GCA_013368495.1;PRJNA284523;SAMN04324906;LUCH00000000.1;representative genome;100268;100268;Paragonimus heterotremus;strain=LC;;latest;Scaffold;Major;Full;2020/06/23;P_heterotremus_1.0.allpaths.pg.lrna;McDonnell Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/368/495/GCA_013368495.1_P_heterotremus_1.0.allpaths.pg.lrna;;;na | 1 |
| 6183 | Schistosoma mansoni | Schistosomatidae | Strigeidida | Platyhelminthes | GCF_000237925.1 | 75 | 58434 | 0.1281854073732246 | 87.5 | ["u11", "u12", "u4atac", "u6atac"] | ASM23792v2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/237/925/GCF_000237925.1_ASM23792v2 | GCF_000237925.1;PRJNA39937;SAMEA2272516;CABG00000000.1;representative genome;6183;6183;Schistosoma mansoni;strain=Puerto Rico;;latest;Chromosome;Major;Full;2011/12/13;ASM23792v2;Schistosoma Genome Network;GCA_000237925.2;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/237/925/GCF_000237925.1_ASM23792v2;;;na | 1 |
| 79923 | Clonorchis sinensis | Opisthorchiidae | Opisthorchiida | Platyhelminthes | GCA_003604175.2 | 97 | 75791 | 0.127819945182374 | 88.2 | ["u11", "u12", "u4atac", "u6atac"] | CSKR.v2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/604/175/GCA_003604175.2_CSKR.v2 | GCA_003604175.2;PRJNA386618;SAMN07109486;NIRI00000000.2;representative genome;79923;79923;Clonorchis sinensis;;Cs-k2;latest;Chromosome;Major;Full;2021/04/12;CSKR.v2;The University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/604/175/GCA_003604175.2_CSKR.v2;;;na | 1 |
| 59628 | Paragonimus skrjabini miyazakii | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_014338405.1 | 92 | 72182 | 0.1272933558402745 | 79.6 | ["u11", "u4atac", "u6atac"] | P_miyazaki_1.0.pg.lrna | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/338/405/GCA_014338405.1_P_miyazaki_1.0.pg.lrna | GCA_014338405.1;PRJNA245325;SAMN03154469;JTDE00000000.1;representative genome;59628;59628;Paragonimus skrjabini miyazakii;strain=Japan;;latest;Scaffold;Major;Full;2020/08/31;P_miyazaki_1.0.pg.lrna;The Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/338/405/GCA_014338405.1_P_miyazaki_1.0.pg.lrna;;;na | 1 |
| 6182 | Schistosoma japonicum | Schistosomatidae | Strigeidida | Platyhelminthes | GCA_021461655.1 | 81 | 71813 | 0.1126658691963168 | 87.5 | ["u11", "u12", "u4atac", "u6atac"] | ASM2146165v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/461/655/GCA_021461655.1_ASM2146165v1 | GCA_021461655.1;PRJNA739049;SAMN19770425;JAHRBV000000000.1;representative genome;6182;6182;Schistosoma japonicum;;SjaV3_Hu;latest;Chromosome;Major;Full;2022/01/13;ASM2146165v1;Fudan University;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/461/655/GCA_021461655.1_ASM2146165v1;;;na | 1 |
| 64606 | Sparganum proliferum | Diphyllobothriidae | Diphyllobothriidea | Platyhelminthes | GCA_902702955.1 | 92 | 85008 | 0.1081081081081081 | 66.3 | ["u11", "u12", "u6atac"] | SprV_v2_2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/702/955/GCA_902702955.1_SprV_v2_2 | GCA_902702955.1;PRJEB35374;SAMEA6224978;CACRXO000000000.1;representative genome;64606;64606;Sparganum proliferum;;Venezuela;latest;Scaffold;Major;Full;2019/12/05;SprV_v2_2;University of Miyazaki;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/702/955/GCA_902702955.1_SprV_v2_2;;;na | 1 |
| 6211 | Echinococcus multilocularis | Taeniidae | Cyclophyllidea | Platyhelminthes | GCA_000469725.3 | 61 | 60916 | 0.1000377191400036 | 90.2 | ["u11", "u12", "u6atac"] | EMULTI002 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/469/725/GCA_000469725.3_EMULTI002 | GCA_000469725.3;PRJEB122;SAMEA2271939;CBLO000000000.2;representative genome;6211;6211;Echinococcus multilocularis;;;latest;Scaffold;Major;Full;2015/12/10;EMULTI002;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/469/725/GCA_000469725.3_EMULTI002;;;na | 1 |
| 27845 | Fasciolopsis buski | Fasciolidae | Plagiorchiida | Platyhelminthes | GCA_008360955.1 | 47 | 48950 | 0.0959242402596077 | 63.9 | ["u11", "u12", "u4atac", "u6atac"] | F_buski_1.0.allpaths-lg | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/360/955/GCA_008360955.1_F_buski_1.0.allpaths-lg | GCA_008360955.1;PRJNA284521;SAMN11554071;LUCM00000000.1;representative genome;27845;27845;Fasciolopsis buski;;HT;latest;Scaffold;Major;Full;2019/09/09;F_buski_1.0.allpaths-lg;McDonnell Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/360/955/GCA_008360955.1_F_buski_1.0.allpaths-lg;;;na | 1 |
| 99802 | Spirometra erinaceieuropaei | Diphyllobothriidae | Diphyllobothriidea | Platyhelminthes | GCA_902702965.1 | 95 | 99098 | 0.0957728871997015 | 74.5 | ["u11", "u12", "u6atac"] | SerJ_v2_0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/702/965/GCA_902702965.1_SerJ_v2_0 | GCA_902702965.1;PRJEB35375;SAMEA6224979;CACRXP000000000.1;representative genome;99802;99802;Spirometra erinaceieuropaei;;SerJ.yamaguchi;latest;Scaffold;Major;Full;2020/09/02;SerJ_v2_0;University of Miyazaki;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/702/965/GCA_902702965.1_SerJ_v2_0;;;na | 1 |
| 6185 | Schistosoma haematobium | Schistosomatidae | Strigeidida | Platyhelminthes | GCF_000699445.2 | 59 | 62370 | 0.0945073603613705 | 76.1 | ["u12", "u4atac", "u6atac"] | SchHae_2.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/445/GCF_000699445.2_SchHae_2.0 | GCF_000699445.2;PRJNA273970;SAMN11431408;AMPZ00000000.2;representative genome;6185;6185;Schistosoma haematobium;;;latest;Scaffold;Major;Full;2020/01/28;SchHae_2.0;The University of Melbourne;GCA_000699445.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/445/GCF_000699445.2_SchHae_2.0;;;na | 1 |
| 100269 | Paragonimus kellicotti | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_014220965.1 | 51 | 54311 | 0.0938155329090173 | 63.1 | ["u4atac", "u6atac"] | P_kellicotti_1.0.allpaths.nc.pg.lrna | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/220/965/GCA_014220965.1_P_kellicotti_1.0.allpaths.nc.pg.lrna | GCA_014220965.1;PRJNA179523;SAMN03863379;LOND00000000.1;representative genome;100269;100269;Paragonimus kellicotti;;Missouri;latest;Scaffold;Major;Full;2020/08/17;P_kellicotti_1.0.allpaths.nc.pg.lrna;The Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/220/965/GCA_014220965.1_P_kellicotti_1.0.allpaths.nc.pg.lrna;;;na | 1 |
| 6198 | Opisthorchis viverrini | Opisthorchiidae | Opisthorchiida | Platyhelminthes | GCF_000715545.1 | 62 | 75914 | 0.0816047172791407 | 74.1 | ["u11", "u12", "u4atac", "u6atac"] | OpiViv1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/715/545/GCF_000715545.1_OpiViv1.0 | GCF_000715545.1;PRJNA259756;SAMN00996407;JACJ00000000.1;representative genome;6198;6198;Opisthorchis viverrini;;;latest;Scaffold;Major;Full;2014/07/09;OpiViv1.0;The University of Melbourne;GCA_000715545.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/715/545/GCF_000715545.1_OpiViv1.0;;;na | 1 |
| 48269 | Schistosoma margrebowiei | Schistosomatidae | Strigeidida | Platyhelminthes | GCA_900618395.1 | 36 | 52589 | 0.0684085510688836 | 59.6 | ["u11", "u12", "u4atac", "u6atac"] | S_margrebowiei_Zambia_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/395/GCA_900618395.1_S_margrebowiei_Zambia_0011_upd | GCA_900618395.1;PRJEB522;SAMEA1984307;UZAI00000000.1;representative genome;48269;48269;Schistosoma margrebowiei;strain=Zambia;;latest;Scaffold;Major;Full;2018/12/05;S_margrebowiei_Zambia_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/395/GCA_900618395.1_S_margrebowiei_Zambia_0011_upd;;;na | 1 |
| 34504 | Paragonimus westermani | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_008508345.1 | 36 | 53189 | 0.0676373884452794 | 71.8 | ["u11", "u6atac"] | ASM850834v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/508/345/GCA_008508345.1_ASM850834v1 | GCA_008508345.1;PRJNA454344;SAMN09005564;QNGE00000000.1;representative genome;34504;34504;Paragonimus westermani;strain=IND2009;;latest;Scaffold;Major;Full;2019/09/18;ASM850834v1;University of Queensland;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/508/345/GCA_008508345.1_ASM850834v1;;;na | 1 |
| 282301 | Macrostomum lignano | Macrostomidae | Macrostomida | Platyhelminthes | GCA_002269645.1 | 120 | 182762 | 0.0656160803140823 | 91.8 | ["u11", "u12", "u4atac", "u6atac"] | Mlig_3_7 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/269/645/GCA_002269645.1_Mlig_3_7 | GCA_002269645.1;PRJNA371498;SAMN07173960;NIVC00000000.1;representative genome;282301;282301;Macrostomum lignano;;DV1;latest;Scaffold;Major;Full;2017/08/24;Mlig_3_7;University Medical Center Groningen;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/269/645/GCA_002269645.1_Mlig_3_7;;;na | 1 |
| 6210 | Echinococcus granulosus | Taeniidae | Cyclophyllidea | Platyhelminthes | GCF_000524195.1 | 36 | 63121 | 0.0570008075114397 | 85.9 | ["u11", "u12", "u4atac", "u6atac"] | ASM52419v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/524/195/GCF_000524195.1_ASM52419v1 | GCF_000524195.1;PRJNA182977;SAMN01914755;APAU00000000.2;representative genome;6210;6210;Echinococcus granulosus;;;latest;Scaffold;Major;Full;2014/01/28;ASM52419v1;Chinese National Human Genome Center at Shanghai;GCA_000524195.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/524/195/GCF_000524195.1_ASM52419v1;;;na | 1 |
| 6184 | Schistosoma bovis | Schistosomatidae | Strigeidida | Platyhelminthes | GCA_003958945.1 | 29 | 53517 | 0.0541590408247114 | 69.0 | ["u11", "u12", "u4atac", "u6atac"] | ASM395894v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/958/945/GCA_003958945.1_ASM395894v1 | GCA_003958945.1;PRJNA451066;SAMN08957538;QMKO00000000.1;representative genome;6184;6184;Schistosoma bovis;strain=TAN1997;;latest;Scaffold;Major;Full;2019/02/15;ASM395894v1;University of Queensland;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/958/945/GCA_003958945.1_ASM395894v1;;;na | 1 |
| 53468 | Mesocestoides corti | Mesocestoididae | Cyclophyllidea | Platyhelminthes | GCA_900604375.1 | 26 | 51693 | 0.0502716603182582 | 80.4 | ["u11", "u12", "u4atac", "u6atac"] | M_corti_Specht_Voge_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/604/375/GCA_900604375.1_M_corti_Specht_Voge_0011_upd | GCA_900604375.1;PRJEB510;SAMEA1484839;UXSR00000000.1;representative genome;53468;53468;Mesocestoides corti;;;latest;Scaffold;Major;Full;2018/12/05;M_corti_Specht_Voge_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/604/375/GCA_900604375.1_M_corti_Specht_Voge_0011_upd;;;na | 1 |
| 27848 | Echinostoma caproni | Echinostomatidae | Plagiorchiida | Platyhelminthes | GCA_900618425.1 | 22 | 45858 | 0.047951176983435 | 40.4 | ["u11", "u12", "u4atac", "u6atac"] | E_caproni_Egypt_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/425/GCA_900618425.1_E_caproni_Egypt_0011_upd | GCA_900618425.1;PRJEB1207;SAMEA1034762;UZAN00000000.1;representative genome;27848;27848;Echinostoma caproni;strain=Egypt;;latest;Scaffold;Major;Full;2018/12/13;E_caproni_Egypt_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/425/GCA_900618425.1_E_caproni_Egypt_0011_upd;;;na | 1 |
| 6205 | Hydatigera taeniaeformis | Taeniidae | Cyclophyllidea | Platyhelminthes | GCA_900622495.1 | 17 | 45226 | 0.0375748734610879 | 72.5 | ["u11", "u12", "u4atac", "u6atac"] | H_taeniaeformis_Canary_Islands_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/622/495/GCA_900622495.1_H_taeniaeformis_Canary_Islands_0011_upd | GCA_900622495.1;PRJEB534;SAMEA2034687;UYWX00000000.1;representative genome;6205;6205;Hydatigera taeniaeformis;;;latest;Scaffold;Major;Full;2018/12/05;H_taeniaeformis_Canary_Islands_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/622/495/GCA_900622495.1_H_taeniaeformis_Canary_Islands_0011_upd;;;na | 1 |
| 60516 | Dibothriocephalus latus | Diphyllobothriidae | Diphyllobothriidea | Platyhelminthes | GCA_900617775.1 | 13 | 34585 | 0.0375744262674143 | 34.5 | ["u11", "u12", "u6atac"] | D_latum_Geneva_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/775/GCA_900617775.1_D_latum_Geneva_0011_upd | GCA_900617775.1;PRJEB1206;SAMEA1463519;UYRU00000000.1;representative genome;60516;60516;Dibothriocephalus latus;;;latest;Scaffold;Major;Full;2018/12/05;D_latum_Geneva_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/775/GCA_900617775.1_D_latum_Geneva_0011_upd;;;na | 1 |
| 117903 | Protopolystoma xenopodis | Polystomatidae | Polystomatidea | Platyhelminthes | GCA_900617795.1 | 11 | 31275 | 0.0351594962603081 | 20.0 | ["u11", "u12", "u6atac"] | P_xenopodis_South_Africa_001_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/795/GCA_900617795.1_P_xenopodis_South_Africa_001_upd | GCA_900617795.1;PRJEB1201;SAMEA1034761;CAAALY000000000.1;representative genome;117903;117903;Protopolystoma xenopodis;;;latest;Scaffold;Major;Full;2019/02/12;P_xenopodis_South_Africa_001_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/795/GCA_900617795.1_P_xenopodis_South_Africa_001_upd;;;na | 1 |
| 102285 | Rodentolepis nana | Hymenolepididae | Cyclophyllidea | Platyhelminthes | GCA_900617975.1 | 10 | 52206 | 0.0191512180174659 | 77.6 | ["u11", "u12", "u4atac", "u6atac"] | H_nana_Japan_0011_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/975/GCA_900617975.1_H_nana_Japan_0011_upd | GCA_900617975.1;PRJEB508;SAMEA1034746;UZAE00000000.1;representative genome;102285;102285;Rodentolepis nana;;;latest;Scaffold;Major;Full;2018/12/05;H_nana_Japan_0011_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/617/975/GCA_900617975.1_H_nana_Japan_0011_upd;;;na | 1 |
| 157069 | Trichobilharzia regenti | Schistosomatidae | Strigeidida | Platyhelminthes | GCA_900618515.1 | 3 | 30439 | 0.0098548058603245 | 26.7 | ["u11", "u12", "u4atac", "u6atac"] | T_regenti_v1_0_4_001_upd | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/515/GCA_900618515.1_T_regenti_v1_0_4_001_upd | GCA_900618515.1;PRJEB4662;SAMEA1876470;UZAO00000000.1;representative genome;157069;157069;Trichobilharzia regenti;;;latest;Scaffold;Major;Full;2018/12/13;T_regenti_v1_0_4_001_upd;WTSI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/618/515/GCA_900618515.1_T_regenti_v1_0_4_001_upd;;;na | 1 |
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CREATE TABLE "genomes" (
"taxonomy_id" INTEGER,
"species" TEXT,
"family" TEXT,
"order" TEXT,
"phylum" TEXT,
"accession" TEXT,
"n_minor_introns" INTEGER,
"n_major_introns" INTEGER,
"percent_minor_introns" REAL,
"busco_score" REAL,
"minor_snRNAs" TEXT,
"genome_version" TEXT,
"source_url" TEXT,
"source_metadata" TEXT,
"minor_intron+" INTEGER
,PRIMARY KEY ([taxonomy_id])
);
CREATE INDEX [idx_genomes_phylum]
ON [genomes] ([phylum]);
CREATE INDEX [idx_genomes_order]
ON [genomes] ([order]);
CREATE INDEX [idx_genomes_family]
ON [genomes] ([family]);