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Supplemental Material for Gonzalez de la Rosa et al., 2020
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posted on 2020-11-17, 19:49 authored by Pablo Manuel Gonzalez de la Rosa, Marian Thomson, Urmi Trivedi, Alan Tracey, Sophie Tandonnet, Mark BlaxterFigures for paper are found in the pptx. Supplementary tables and data underlying tables and figures are found in the xlsx.
File S1: Defining sets of orthologous loci in linkage through Rhabditid evolution
File S2: Nigon element analysis of Meloidogyne hapla
File S3: Protein sequences of Nigon defining loci
File S4: Bibliography cited in File S1, File S2 and Table S2
Figure S1: Raw data QC and read filtering
Figure S2: Distribution of SL and 5S RNA loci in the Oscheius tipulae genome
Figure S3: Clustering with different k values
Figure S4: t-SNE of orthologous loci co-locations in 9 nematode species
Figure S5: nOti 2.0 assembly aligned to nrOscTipu1.3
Figure S6: GC proportion plots of nematode chromosomes
Figure S7: Nigon painting of Caenorhabditis species
Figure S8: Exploring the robustness of definition of Nigon element-defining sets of orthologues
Table S1: Chromosome numbers in Nematoda
Table S2: Software used
Table S3: Raw data for genomic analysis of Oscheius tipulae
Table S4. Sources of nematode assemblies included in the Kraken2 database for contamination assessment
Table S5. Raw sequence allocation by Kraken grouped by Phylum
Table S6. Contiguity and BUSCO metrics of Oscheius tipulae assemblies
Table S7. Base fold coverage of the Oscheius tipulae assembly
Table S8: Sources and metrics of rhabditid nematode genome data
Table S9. BUSCO scores of assemblies and proteomes of rhabditid nematodes
Table S10: Nigon element-defining loci in fifteen nematode genomes
Table S11. KEGG categories enriched among Nigon defining loci
Table S12: Nigon-defining loci in the Meloidogyne hapla genome assembly
File S2: Nigon element analysis of Meloidogyne hapla
File S3: Protein sequences of Nigon defining loci
File S4: Bibliography cited in File S1, File S2 and Table S2
Figure S1: Raw data QC and read filtering
Figure S2: Distribution of SL and 5S RNA loci in the Oscheius tipulae genome
Figure S3: Clustering with different k values
Figure S4: t-SNE of orthologous loci co-locations in 9 nematode species
Figure S5: nOti 2.0 assembly aligned to nrOscTipu1.3
Figure S6: GC proportion plots of nematode chromosomes
Figure S7: Nigon painting of Caenorhabditis species
Figure S8: Exploring the robustness of definition of Nigon element-defining sets of orthologues
Table S1: Chromosome numbers in Nematoda
Table S2: Software used
Table S3: Raw data for genomic analysis of Oscheius tipulae
Table S4. Sources of nematode assemblies included in the Kraken2 database for contamination assessment
Table S5. Raw sequence allocation by Kraken grouped by Phylum
Table S6. Contiguity and BUSCO metrics of Oscheius tipulae assemblies
Table S7. Base fold coverage of the Oscheius tipulae assembly
Table S8: Sources and metrics of rhabditid nematode genome data
Table S9. BUSCO scores of assemblies and proteomes of rhabditid nematodes
Table S10: Nigon element-defining loci in fifteen nematode genomes
Table S11. KEGG categories enriched among Nigon defining loci
Table S12: Nigon-defining loci in the Meloidogyne hapla genome assembly
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