{"id":"W3125995565","doi":"10.1093/dnares/dsaa029","title":"<i>De novo</i> genome assembly of two tomato ancestors, <i>Solanum pimpinellifolium</i> and <i>Solanum</i> <i>  lycopersicum</i> var. <i>cerasiforme</i>, by long-read sequencing","year":2020,"lang":"en","type":"article","venue":"DNA Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":46,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Bio-oriented Technology Research Advancement Institution; Japan Society for the Promotion of Science; University of California, Davis","keywords":"Biology; Genome; Contig; Sequence assembly; Solanum; Genetics; Gene; Transcriptome; Reference genome; Whole genome sequencing; Chromosome; Botany; Gene expression","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0009533605,0.0003564207,0.000465719,0.00007076737,0.0002766282,0.00009794875,0.0006058133,0.0002050942,0.00002768916],"category_scores_gemma":[0.0001555483,0.0003502997,0.0001332343,0.0003967989,0.00037036,0.000006244068,0.0006074194,0.0003739466,0.00001766323],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007102805,"about_ca_system_score_gemma":0.000336106,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002262703,"about_ca_topic_score_gemma":0.00006401926,"domain_scores_codex":[0.9969613,0.0002362798,0.0004814857,0.0008257019,0.0005207543,0.0009744538],"domain_scores_gemma":[0.9984608,0.00009863752,0.0001379217,0.0005123561,0.0003318162,0.000458469],"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":[0.0001609588,0.00005963412,0.007626568,0.0001552656,0.0001233004,0.00001907196,0.000447077,0.00008105046,0.9822167,0.0000533351,0.008482396,0.0005746807],"study_design_scores_gemma":[0.002141772,0.001219162,0.001083736,0.0000450155,0.00005269239,0.0001061431,0.0007319347,0.0002131091,0.8783246,0.00008816462,0.11531,0.00068368],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9839965,0.009177688,0.0004702132,0.000948897,0.00007858513,0.0004515983,0.000511006,0.00001330371,0.004352215],"genre_scores_gemma":[0.9934525,0.003058742,0.0007168525,0.001622832,0.0004535982,0.00005228572,0.0001858799,0.00007234336,0.0003849252],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1068277,"threshold_uncertainty_score":0.9998949,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04559525211993846,"score_gpt":0.3138022664930277,"score_spread":0.2682070143730892,"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."}}