PSVIII-20 Identification of functional INDELS responsible for alternative splicing in acute stress responders grazing sheep exposed to gastrointestinal nematode infection
Notice bibliographique
Résumé
Abstract Gastrointestinal nematodes (GINs) are a major constraint to the sheep industry. Infected animals can develop clinical signs, like anemia, hypoproteinemia, diarrhea, and in extreme cases death. The misuse of anthelmintics to treat infected animals has led to the development of GIN resistance making necessary the integration of different approaches to reduce the impact of GINs on the sheep industry. The application of transcriptomics using RNA-Sequencing technology to better understand the underlying genetic mechanisms of resistance to GIN can help accelerate the genetic gain. This study aimed to identify insertion and deletions (INDELs) responsible for alternative splicing in Rideau x Dorset crossbred sheep with different immune profiles under natural exposure to gastrointestinal nematodes using RNA-Sequencing. High (H) and medium (M) acute stress responders with the highest and lowest worm burden, after natural exposure to GIN, were selected for liver RNA extraction (H; n = 5 and M; n = 6). In addition, GIN-unexposed lambs (U; n = 4) were used as immunological controls. Quality control analyses were performed on fastq files using the CLC Bio Genomics workbench software including the guanine-cytosine (GC) content, ambiguous base content, Phred score, base coverage, nucleotide contributions, and over-represented sequence parameters. Pair-end sequence reads were aligned to the annotated Oar_rambouillet_v.2.0 ovine reference genome. After that, variant discovery analysis and functional consequence analysis were performed using CLC Bio Genomics workbench software to identify INDELs leading to amino acid changes and splice site events (SSEs). Genes associated with the list of INDELs leading to SSE were recovered from Ensembl BioMart. Unique INDELs with SSEs for H, M, and U groups (162, 244, and 161, respectively) and shared (372) among groups were identified. Among them, 4 INDELS with SSE uniquely identified in the M group were located within the NLRC5, SIGLEC1, CFD, and STAT6 genes related to the immune system. Significant enriched metabolic pathways (FDR< 0.05) were identified using the list of genes with INDELs that led to SSEs unique for each group and shared among groups using Reactome. Metabolic pathways related to the immune system response such as cross-presentation of soluble exogenous antigens (endosomes) and NIK noncanonical NF-kB signaling pathways were identified in the M group. These results can help to better understand the mechanisms responsible for the immune response of sheep to GIN.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,003 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,001 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
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 tête enseignante, 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 ».