{"id":"W4307581779","doi":"10.1094/mpmi-06-22-0133-r","title":"Comparative Genomic Analysis of 31 <i>Phytophthora</i> Genomes Reveals Genome Plasticity and Horizontal Gene Transfer","year":2022,"lang":"en","type":"article","venue":"Molecular Plant-Microbe Interactions","topic":"Plant Pathogens and Resistance","field":"Agricultural and Biological Sciences","cited_by":34,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval; FPInnovations; University of British Columbia","funders":"China National Funds for Distinguished Young Scientists; Biotechnology and Biological Sciences Research Council; National Institute of Food and Agriculture; Forest Growers Levy Trust; Agricultural Research Service; Ministry of Business, Innovation and Employment; Directorate for Biological Sciences; California Walnut Board; U.S. Department of Agriculture","keywords":"Phytophthora; Biology; Genome; Oomycete; Horizontal gene transfer; Phylogenetic tree; Genetics; Effector; Genome size; Genus; Gene; Host (biology); Phylogenetics; Evolutionary biology; Botany","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009968608,0.0001742169,0.0004293884,0.00008917786,0.0003739518,0.00003459766,0.0002040893,0.00003347107,0.0005870249],"category_scores_gemma":[0.000002798813,0.00009539845,0.000218088,0.0005679365,0.0000611932,0.00005750642,0.0001030279,0.0002060495,0.000003335654],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005118616,"about_ca_system_score_gemma":0.00001166426,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001488718,"about_ca_topic_score_gemma":0.000411098,"domain_scores_codex":[0.9988064,0.0001304716,0.0003176217,0.000355494,0.0001565051,0.0002335152],"domain_scores_gemma":[0.99957,0.0001411886,0.0000993471,0.00006384015,0.00004041612,0.00008520645],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00007989757,0.0001168931,0.001422802,0.0000041694,0.0005270033,0.00004825161,0.0001185507,0.0007253204,0.9966629,0.00007479618,0.00009115109,0.0001283037],"study_design_scores_gemma":[0.0005244995,0.0006821276,0.466985,0.00002559893,0.002145608,0.0006004301,0.001994021,0.001341266,0.4873515,0.0001050971,0.03714428,0.001100618],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.986675,0.0007424266,0.0002536828,0.0000781473,0.00009130505,0.0001899127,0.01148266,0.00002080154,0.0004661149],"genre_scores_gemma":[0.9983537,0.00006421447,0.0001598802,0.00010068,0.00003202118,0.00002962854,0.001102824,0.000001630062,0.0001554345],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5093114,"threshold_uncertainty_score":0.6427511,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01556770894577349,"score_gpt":0.2198243691492778,"score_spread":0.2042566602035043,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}