Description
chapter_2_appendix_table_1.xlsx: Supplementary Table 2.1: The Pfam identities of the genes that were not assigned orthogroups established from the twelve legumes.
unassigned.orthogroups.legumes.fa_predictions.tsv: Supplementary Table 2.2: The Pfam identities of the OrthoFinder orthogroups established from the twelve legumes. The number of genes per orthogroup is also included in the table.
chapter_3_appendix_table_1.xlsx: Supplementary Table 3.1: The Gene Ontology terms associated with the gene models that did not align with one of the twelve legumes or the NR dataset.
Supplementary_Table_4.01_Iterative_additive_method_summary.tsv: Supplementary Table 4.1: The number of gene models in legumes calculated by the iterative additive method. 'x' indicates the order of the species 'spec' is added. 'New_genes' indicates how many new gene models are added to the 'core', which indicates how many gene models were added in prior rounds. The iterative additive method was run 100 times, each run indicated by 'round'.
Supplementary_Table_4.02_pea_iterative_rounds.tsv: Supplementary Table 4.2: The number of gene models in legumes calculated by the iterative additive method when pea is the first legume. 'x' indicates the order of the species 'spec' is added. 'New_genes' indicates how many new gene models are added to the 'core', which indicates how many gene models were added in prior rounds. The iterative additive method was run 100 times, each run indicated by 'round'.
Supplementary_Table_4.03_GO_term_rep_legumes.xlsx: Supplementary Table 4.3: Enriched Gene Ontology terms of the representative legume gene set when compared with twelve legume genomes.
Supplementary_Table_4.04_GO_term_strawberry_no_rep.xlsx: Supplementary Table 4.4: Enriched Gene Ontology terms of strawberry genes that are not present in the legume representative gene set.
Supplementary_Table_4.05_GO_term_rep_no_strawberry.xlsx: Supplementary Table 4.5: Enriched Gene Ontology terms of the representative legume gene set that are not present in the strawberry genome.
Supplementary_Table_4.06_GO_term_human_no_rep.xlsx: Supplementary Table 4.6: Enriched Gene Ontology terms of human genes not present in the legume representative gene set.
Supplementary_Table_4.07_GO_term_rep_no_human.xlsx: Supplementary Table 4.7: Enriched Gene Ontology terms of the representative legume gene set that are not present in the human genome.
Supplementary_Table_4.08_cajan.xlsx: Supplementary Table 4.8: The Pfam annotations of all genes in the largest gene cluster of pigeon peas (Cajanus cajan). Gene clusters were determined by aligning the genome of the pigeon pea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.09_cicar.xlsx: Supplementary Table 4.9: The Pfam annotations of all genes in the largest gene cluster of chickpea (Cicer arietinum). Gene clusters were determined by aligning the genome of the chickpea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.10_glyma.xlsx: Supplementary Table 4.10: The Pfam annotations of all genes in the largest gene cluster of soybean (Glycine max). Gene clusters were determined by aligning the genome of the soybean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.11_lotja.xlsx: Supplementary Table 4.11: The Pfam annotations of all genes in the largest gene cluster of Lotus japonicus. Gene clusters were determined by aligning the genome of Lotus japonicus to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.12_lupan.xlsx: Supplementary Table 4.12: The Pfam annotations of all genes in the largest gene cluster of narrow-leaf lupin (Lupinus angustifolius). Gene clusters were determined by aligning the genome of narrow-leaf lupin to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.13_medtr.xlsx: Supplementary Table 4.13: The Pfam annotations of all genes in the largest gene cluster of barrel medic (Medicago truncatula). Gene clusters were determined by aligning the genome of the barrel medic to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.14_phavu.xlsx: Supplementary Table 4.14: The Pfam annotations of all genes in the largest gene cluster of common bean (Phaseolus vulgaris). Gene clusters were determined by aligning the genome of the common bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.15_pissa.xlsx: Supplementary Table 4.15: The Pfam annotations of all genes in the largest gene cluster of pea (Pisum sativum). Gene clusters were determined by aligning the genome of the pea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.16_tripr.xlsx: Supplementary Table 4.16: The Pfam annotations of all genes in the largest gene cluster of red clover (Trifolium pratense). Gene clusters were determined by aligning the genome of red clover to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.17_vigan.xlsx: Supplementary Table 4.17: The Pfam annotations of all genes in the largest gene cluster of adzuki bean (Vigna angularis). Gene clusters were determined by aligning the genome of the adzuki bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.18_vigra.xlsx: Supplementary Table 4.18: The Pfam annotations of all genes in the largest gene cluster of mung bean (Vigna radiata). Gene clusters were determined by aligning the genome of the mung bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.19_vigun.xlsx: Supplementary Table 4.19: The Pfam annotations of all genes in the largest gene cluster of cowpea (Vigna unguiculata). Gene clusters were determined by aligning the genome of the cowpea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.20_rep_set.xlsx: Supplementary Table 4.20: The Pfam annotations of all genes in the largest gene cluster of the representative gene set. Gene clusters were determined by aligning the genome of the representative genes to itself. Pfam annotations were acquired from InterProScan.
unassigned.orthogroups.legumes.fa_predictions.tsv: Supplementary Table 2.2: The Pfam identities of the OrthoFinder orthogroups established from the twelve legumes. The number of genes per orthogroup is also included in the table.
chapter_3_appendix_table_1.xlsx: Supplementary Table 3.1: The Gene Ontology terms associated with the gene models that did not align with one of the twelve legumes or the NR dataset.
Supplementary_Table_4.01_Iterative_additive_method_summary.tsv: Supplementary Table 4.1: The number of gene models in legumes calculated by the iterative additive method. 'x' indicates the order of the species 'spec' is added. 'New_genes' indicates how many new gene models are added to the 'core', which indicates how many gene models were added in prior rounds. The iterative additive method was run 100 times, each run indicated by 'round'.
Supplementary_Table_4.02_pea_iterative_rounds.tsv: Supplementary Table 4.2: The number of gene models in legumes calculated by the iterative additive method when pea is the first legume. 'x' indicates the order of the species 'spec' is added. 'New_genes' indicates how many new gene models are added to the 'core', which indicates how many gene models were added in prior rounds. The iterative additive method was run 100 times, each run indicated by 'round'.
Supplementary_Table_4.03_GO_term_rep_legumes.xlsx: Supplementary Table 4.3: Enriched Gene Ontology terms of the representative legume gene set when compared with twelve legume genomes.
Supplementary_Table_4.04_GO_term_strawberry_no_rep.xlsx: Supplementary Table 4.4: Enriched Gene Ontology terms of strawberry genes that are not present in the legume representative gene set.
Supplementary_Table_4.05_GO_term_rep_no_strawberry.xlsx: Supplementary Table 4.5: Enriched Gene Ontology terms of the representative legume gene set that are not present in the strawberry genome.
Supplementary_Table_4.06_GO_term_human_no_rep.xlsx: Supplementary Table 4.6: Enriched Gene Ontology terms of human genes not present in the legume representative gene set.
Supplementary_Table_4.07_GO_term_rep_no_human.xlsx: Supplementary Table 4.7: Enriched Gene Ontology terms of the representative legume gene set that are not present in the human genome.
Supplementary_Table_4.08_cajan.xlsx: Supplementary Table 4.8: The Pfam annotations of all genes in the largest gene cluster of pigeon peas (Cajanus cajan). Gene clusters were determined by aligning the genome of the pigeon pea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.09_cicar.xlsx: Supplementary Table 4.9: The Pfam annotations of all genes in the largest gene cluster of chickpea (Cicer arietinum). Gene clusters were determined by aligning the genome of the chickpea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.10_glyma.xlsx: Supplementary Table 4.10: The Pfam annotations of all genes in the largest gene cluster of soybean (Glycine max). Gene clusters were determined by aligning the genome of the soybean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.11_lotja.xlsx: Supplementary Table 4.11: The Pfam annotations of all genes in the largest gene cluster of Lotus japonicus. Gene clusters were determined by aligning the genome of Lotus japonicus to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.12_lupan.xlsx: Supplementary Table 4.12: The Pfam annotations of all genes in the largest gene cluster of narrow-leaf lupin (Lupinus angustifolius). Gene clusters were determined by aligning the genome of narrow-leaf lupin to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.13_medtr.xlsx: Supplementary Table 4.13: The Pfam annotations of all genes in the largest gene cluster of barrel medic (Medicago truncatula). Gene clusters were determined by aligning the genome of the barrel medic to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.14_phavu.xlsx: Supplementary Table 4.14: The Pfam annotations of all genes in the largest gene cluster of common bean (Phaseolus vulgaris). Gene clusters were determined by aligning the genome of the common bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.15_pissa.xlsx: Supplementary Table 4.15: The Pfam annotations of all genes in the largest gene cluster of pea (Pisum sativum). Gene clusters were determined by aligning the genome of the pea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.16_tripr.xlsx: Supplementary Table 4.16: The Pfam annotations of all genes in the largest gene cluster of red clover (Trifolium pratense). Gene clusters were determined by aligning the genome of red clover to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.17_vigan.xlsx: Supplementary Table 4.17: The Pfam annotations of all genes in the largest gene cluster of adzuki bean (Vigna angularis). Gene clusters were determined by aligning the genome of the adzuki bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.18_vigra.xlsx: Supplementary Table 4.18: The Pfam annotations of all genes in the largest gene cluster of mung bean (Vigna radiata). Gene clusters were determined by aligning the genome of the mung bean to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.19_vigun.xlsx: Supplementary Table 4.19: The Pfam annotations of all genes in the largest gene cluster of cowpea (Vigna unguiculata). Gene clusters were determined by aligning the genome of the cowpea to itself. Pfam annotations were acquired from InterProScan.
Supplementary_Table_4.20_rep_set.xlsx: Supplementary Table 4.20: The Pfam annotations of all genes in the largest gene cluster of the representative gene set. Gene clusters were determined by aligning the genome of the representative genes to itself. Pfam annotations were acquired from InterProScan.
| Date made available | 2020 |
|---|---|
| Publisher | The University of Western Australia |
Keywords
- Legumes
- orthogroups
- thesis