Additional file 2 of Insights into genomic evolution from the chromosomal and mitochondrial genomes of Ustilaginoidea virens
Notice bibliographique
Résumé
Additional file 2: Figure S1. SNP frequencies in coding, intronic and intergenic sequences in different U. virens strains relative to UV8b genome. The strains are indicated by different colors. Genomic sequences of these strains were aligned to the reference genome with nucmer, and SNPs were called with “show-snps”, a tool in Mummer package. The genes exhibiting full-length gene sequences in the assemblies of all these strains were subjected to SNP calculation. For each strain, lineage-specific regions were excluded from the intergenic regions to avoid the potential miscalculation. Figure S2. Potential inter-chromosomal translocation events illustrated by alignments of DNA sequences between UV8b and UVP1 genomes. Syntenic alignments are indicated by blue stripes. The inter-chromosomal translocation region is indicated by red box. Alignment analysis between these two genomes was conducted with nucmer. The structure variations were identified with the thresholds of the alignment length of ≥200 bp and the identity of ≥95%. Figure S3. The nucleotide diversities in long terminal repeats (LTRs) at flanking regions of LTR-retrotransposons in SVs, LSRs and other regions of UVP1 genome. The LTRs at both flanking regions of LTR-retrotransposons were aligned to each other and the nucleotide diversities were calculated. LTR-RTs, LTR-retrotransposons. Figure S4. The distribution of the lineage-specific regions (LSRs) of UV8b relative to multiple U. virens strains. The lines from top to bottom indicate the genes (orange), transposable elements (TEs) (blue), heatmap of SNPs compared with multiple strains (red), UV8b-specific LSRs that are absent in all other strains (green), and LSRs compared with the indicated strains (grey). LSRs relative to a specific strain were identified by aligning the sequencing reads of this strain to UV8b genome. For IPU010 and GVT without publicly available sequencing reads, the Illumina reads with 100× coverage were simulated based on their assemblies. The other three chromosomes (2, 3, 6) were displayed in Fig. 4. UV8b-LSR, UV8b-specific LSRs. Figure S5. The phylogenetic relationship among U. virens and the related fungal species based on mitochondrial protein sequences. Homologous mitochondrial protein sequences in these indicated fungal species were aligned using ClustalW, and the tree was constructed using the Neighbor-Joining method in MEGA X with 1000 bootstraps. Figure S6. Certain candidate effector genes are located at the lineage-specific regions of UV8b relative to UVP1. Syntenic alignments are indicated by blue stripes. The effector genes are indicated by red boxes, while other genes are indicated by grey boxes. Alignment analysis was performed as described in Figure S2.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,013 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,001 |
| Méta-épidémiologie (sens large) | 0,003 | 0,001 |
| Bibliométrie | 0,004 | 0,007 |
| Études des sciences et des technologies | 0,002 | 0,001 |
| Communication savante | 0,003 | 0,003 |
| Science ouverte | 0,003 | 0,002 |
| Intégrité de la recherche | 0,002 | 0,002 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,793 | 0,145 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».