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)
13 rows where phylum = "Oomycota" 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4792 | Phytophthora parasitica | Peronosporaceae | Peronosporales | Oomycota | GCF_000247585.1 | 18 | 26540 | 0.0677761879659612 | 94.1 | ["u11", "u12", "u6atac"] | PP_INRA-310_V2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/247/585/GCF_000247585.1_PP_INRA-310_V2 | GCF_000247585.1;PRJNA259235;SAMN02981373;AGFV00000000.2;representative genome;761204;4792;Phytophthora parasitica INRA-310;strain=INRA-310;;latest;Scaffold;Major;Full;2013/12/19;PP_INRA-310_V2;Broad Institute;GCA_000247585.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/247/585/GCF_000247585.1_PP_INRA-310_V2;;;na | 1 |
| 112098 | Saprolegnia diclina | Saprolegniaceae | Saprolegniales | Oomycota | GCF_000281045.1 | 34 | 54580 | 0.0622550994250558 | 93.3 | ["u11", "u12", "u4atac", "u6atac"] | Sap_diclina_VS20_V1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/281/045/GCF_000281045.1_Sap_diclina_VS20_V1 | GCF_000281045.1;PRJNA255245;SAMN02981407;AIJL00000000.1;representative genome;1156394;112098;Saprolegnia diclina VS20;strain=VS20;;latest;Scaffold;Major;Full;2013/02/22;Sap_diclina_VS20_V1;Broad Institute;GCA_000281045.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/281/045/GCF_000281045.1_Sap_diclina_VS20_V1;;;na | 1 |
| 164328 | Phytophthora ramorum | Peronosporaceae | Peronosporales | Oomycota | GCA_020800215.1 | 13 | 23004 | 0.0564799930486162 | 94.9 | ["u11", "u12", "u6atac"] | PR-102_v3_p | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/800/215/GCA_020800215.1_PR-102_v3_p | GCA_020800215.1;PRJNA738483;SAMN19730089;JAICDV000000000.1;representative genome;164328;164328;Phytophthora ramorum;;Pr-102;latest;Scaffold;Major;Full;2021/11/08;PR-102_v3_p;USDA ARS;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/800/215/GCA_020800215.1_PR-102_v3_p;;;na | 1 |
| 101203 | Saprolegnia parasitica | Saprolegniaceae | Saprolegniales | Oomycota | GCF_000151545.1 | 29 | 59106 | 0.0490403314449987 | 86.7 | ["u11", "u12", "u4atac", "u6atac"] | ASM15154v2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/151/545/GCF_000151545.1_ASM15154v2 | GCF_000151545.1;PRJNA280969;SAMN02981252;ADCG00000000.2;representative genome;695850;101203;Saprolegnia parasitica CBS 223.65;strain=CBS 223.65;;latest;Scaffold;Major;Full;2014/05/29;ASM15154v2;Broad Institute;GCA_000151545.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/151/545/GCF_000151545.1_ASM15154v2;;;na | 1 |
| 4785 | Phytophthora cinnamomi | Peronosporaceae | Peronosporales | Oomycota | GCA_018691715.1 | 9 | 30065 | 0.0299261820841923 | 93.3 | ["u11", "u12", "u6atac"] | ASM1869171v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/691/715/GCA_018691715.1_ASM1869171v1 | GCA_018691715.1;PRJNA675400;SAMN16706909;JAFJYM000000000.1;representative genome;4785;4785;Phytophthora cinnamomi;strain=GKB4;;latest;Scaffold;Major;Full;2021/06/03;ASM1869171v1;University of Pretoria;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/691/715/GCA_018691715.1_ASM1869171v1;genome length too large;;na | 1 |
| 112090 | Aphanomyces astaci | Saprolegniaceae | Saprolegniales | Oomycota | GCF_000520075.1 | 16 | 56082 | 0.028521515918571 | 95.7 | ["u11", "u12", "u4atac", "u6atac"] | Apha_asta_APO3_V1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/520/075/GCF_000520075.1_Apha_asta_APO3_V1 | GCF_000520075.1;PRJNA264335;SAMN01906578;AYTG00000000.1;representative genome;112090;112090;Aphanomyces astaci;strain=APO3;;latest;Scaffold;Major;Full;2014/01/14;Apha_asta_APO3_V1;Broad Institute;GCA_000520075.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/520/075/GCF_000520075.1_Apha_asta_APO3_V1;;;na | 1 |
| 157072 | Aphanomyces invadans | Saprolegniaceae | Saprolegniales | Oomycota | GCF_000520115.1 | 13 | 49726 | 0.0261364321759585 | 94.9 | ["u11", "u12", "u4atac", "u6atac"] | Apha_inva_NJM9701_V1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/520/115/GCF_000520115.1_Apha_inva_NJM9701_V1 | GCF_000520115.1;PRJNA258292;SAMN01907307;AYTH00000000.1;representative genome;157072;157072;Aphanomyces invadans;strain=NJM9701;;latest;Scaffold;Major;Full;2014/01/15;Apha_inva_NJM9701_V1;Broad Institute;GCA_000520115.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/520/115/GCF_000520115.1_Apha_inva_NJM9701_V1;;;na | 1 |
| 112091 | Aphanomyces cochlioides | Saprolegniaceae | Saprolegniales | Oomycota | GCA_019828595.1 | 9 | 42390 | 0.0212269157291445 | 68.6 | ["u11", "u12", "u4atac", "u6atac"] | UMN_Aphcoc_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/828/595/GCA_019828595.1_UMN_Aphcoc_1.0 | GCA_019828595.1;PRJNA719397;SAMN18617838;JAHQRK000000000.1;representative genome;112091;112091;Aphanomyces cochlioides;;103-1;latest;Contig;Major;Full;2021/08/31;UMN_Aphcoc_1.0;University of Minnesota;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/828/595/GCA_019828595.1_UMN_Aphcoc_1.0;;;na | 1 |
| 114742 | Pythium insidiosum | Pythiaceae | Pythiales | Oomycota | GCA_001029375.1 | 4 | 30975 | 0.012911972626618 | 87.1 | ["u12", "u4atac", "u6atac"] | Pythium_insidiosum_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/029/375/GCA_001029375.1_Pythium_insidiosum_1.0 | GCA_001029375.1;PRJDB3817;SAMD00028776;BBXB00000000.1;representative genome;114742;114742;Pythium insidiosum;strain=Pi-s;;latest;Scaffold;Major;Full;2015/05/08;Pythium_insidiosum_1.0;King Mongkut's University of Technology Thonburi;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/029/375/GCA_001029375.1_Pythium_insidiosum_1.0;;;na | 1 |
| 1202772 | Achlya hypogyna | Saprolegniaceae | Saprolegniales | Oomycota | GCA_002081595.1 | 6 | 48280 | 0.0124259619765563 | 94.1 | ["u11", "u12", "u4atac", "u6atac"] | ACH_lane_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/081/595/GCA_002081595.1_ACH_lane_v1 | GCA_002081595.1;PRJNA169234;SAMN02690054;JNBR00000000.1;representative genome;1202772;1202772;Achlya hypogyna;strain=ATCC 48635;;latest;Scaffold;Major;Full;2017/04/06;ACH_lane_v1;University of Rhode Island;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/081/595/GCA_002081595.1_ACH_lane_v1;;;na | 1 |
| 67593 | Phytophthora sojae | Peronosporaceae | Peronosporales | Oomycota | GCF_000149755.1 | 3 | 35271 | 0.008504847763225 | 86.7 | ["u11", "u12", "u6atac"] | P.sojae V3.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/149/755/GCF_000149755.1_P.sojae_V3.0 | GCF_000149755.1;PRJNA262907;SAMN02953656;AAQY00000000.2;representative genome;67593;67593;Phytophthora sojae;strain=P6497;;latest;Scaffold;Major;Full;2011/10/03;P.sojae V3.0;US DOE Joint Genome Institute, USA, Walnut Creek;GCA_000149755.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/149/755/GCF_000149755.1_P.sojae_V3.0;;;na | 1 |
| 74557 | Thraustotheca clavata | Saprolegniaceae | Saprolegniales | Oomycota | GCA_002081575.1 | 4 | 48340 | 0.0082740360747972 | 88.6 | ["u11", "u12", "u4atac", "u6atac"] | Thrcla_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/081/575/GCA_002081575.1_Thrcla_v1 | GCA_002081575.1;PRJNA169235;SAMN02690055;JNBS00000000.1;representative genome;74557;74557;Thraustotheca clavata;strain=ATCC 34112;;latest;Scaffold;Major;Full;2017/04/06;Thrcla_v1;University of Rhode Island;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/081/575/GCA_002081575.1_Thrcla_v1;;;na | 1 |
| 120398 | Aphanomyces stellatus | Saprolegniaceae | Saprolegniales | Oomycota | GCA_009835185.1 | 4 | 57800 | 0.0069199363365857 | 92.9 | ["u11", "u12", "u4atac", "u6atac"] | As_578.67_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/835/185/GCA_009835185.1_As_578.67_v1 | GCA_009835185.1;PRJNA551386;SAMN12145847;VJMH00000000.1;representative genome;120398;120398;Aphanomyces stellatus;strain=CBS 578.67;;latest;Scaffold;Major;Full;2020/01/09;As_578.67_v1;Laboratoire de Recherche en Sciences Vegetales;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/835/185/GCA_009835185.1_As_578.67_v1;;;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]);