PSVII-10 Genome-wide discovery and characterization of short interspersed nuclear elements (SINEs) in the bovine genome
Notice bibliographique
Résumé
Abstract Short interspersed nuclear elements (SINEs) constitute a class of nonautonomous retrotransposons endowed with the capability to multiply and spread within a genome. SINEs serve as reliable indicators for assessing genetic variability in dairy populations, aiding in precise determination of breed composition. However, SINEs within the bovine genome remain insufficiently characterized, hindering the understanding of their impact on dairy production and health. This study aimed to systematically identify, classify and unveil the characteristics of SINEs within the bovine reference genome (ARS-UCD1.3). Multiple de novo identification tools, including RepeatModeler, SINE_scan, LongRepMarker, and SINE-finder, were employed for SINE identification and characterization. A total of 1.6 million copies of SINEs were identified, constituting approximately 10.8% of the genome. The SINEs were stratified into seven distinct families based on their structural attributes, denoted as BosSINEL, BosSINE1, BosSINE2, BosSINE3, BosSINE4, BosSINE5 and BosSINE6. BosSINE1 represents a novel family, whereas the remaining six families were previously documented in Repbase. Among these families, BosSINE3 emerges as the most prolific, boasting 254,586 complete copies (over 80% of the length of the consensus sequence), followed by BosSINEL (164,538 copies), BosSINE2 (162,207 copies) and BosSINE1 (150,799 copies). Conversely, the remaining families exhibit lower abundance, each harboring no more than 100,000 copies within the genome. Structural comparisons among SINE families elucidate distinctive features. Notably, BosSINEL lacks a tRNA-related region, including boxA and boxB, which is the hallmark element of the classic SINE structure according to SINEBase. Conversely, all other families exhibit tRNA-related regions. BosSINE1, the lengthiest at 328 bp (excluding Poly-A), possesses two tRNA-related regions, distinguishing it from other families. BosSINEL, BosSINE1, BosSINE2 and BosSINE3 exhibit long interspersed nuclear elements (LINE)-related regions, suggesting their retrotransposition by engaging with the enzymatic machinery encoded by LINEs. In contrast, BosSINE6, the shortest at 109 bp, features a GC-rich region resulting in a high GC content of 67%. Additionally, BosSINE4 contains an AT-rich region. Evolutionary analysis disclosed that BosSINEL is the youngest SINE family in the bovine genome, potentially still harboring active roles and contributing to the genetic diversity related to different dairy production and health performance. Conversely, BosSINE1 to BosSINE6 are comparatively aged in terms of evolution, likely fixed in the bovine genome with diminished or lost activities. In summary, this investigation unveils the comprehensive profile of SINE in the bovine genome, delineating both structural and evolutionary characteristics. Particularly noteworthy is the emergence of BosSINEL as the youngest SINE family, suggesting active roles in the bovine genome. Since lineage-specific TEs (such as Bov-A2 elements) have been reported to regulate interferon-inducible gene expression in bovine, our data warrants further investigations to reveal the potential of SINEs as markers for improving dairy production and health.
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 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 | 0,001 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| 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 ».