Comparative genomics analysis reveals high levels of differential DNA transposition among primates
Notice bibliographique
Résumé
ABSTRACT Mobile elements generated via DNA transposition constitute ∼50% of the primate genomes. As a result of past and ongoing activity, DNA transposition is responsible for generating inter- and intra-species genomic variations, and it plays important roles in shaping genome evolution and impacting gene function. While limited analysis of mobile elements has been performed in many primate genomes, a large-scale comparative genomic analysis examining the impact of DNA transposition on primate evolution is still missing. Using a bioinformatics comparative genomics approach, we performed analysis of species-specific mobile elements (SS-MEs) in eight primate genomes, which include human, chimpanzee, gorilla, orangutan, green monkey, crab-eating macaque, rhesus monkey, and baboon. These species have good representations for the top two primate families, Hominidae (great apes) and the Cercopithecidae (old world monkeys), for which draft genome sequences are available. Our analysis identified a total of 230,855 SS-MEs from the eight primate genomes, which collectively contribute to ∼82 Mbp genome sequences, ranging from 14 to 25 Mbp for individual genomes. Several new interesting observations were made based on these SS-MEs. First, the DNA transposition activity level reflected by the numbers of SS-MEs was shown to be drastically different across species with the highest (baboon genome) being more than 30 times higher than the lowest (crab-eating macaque genome). Second, the compositions of SS-MEs, as well as the top active ME subfamilies, also differ significantly across genomes. By the copy numbers of SS-MEs divided into major ME classes, SINE represents the dominant class in all genomes, but more so in the Cercopithecidae genomes than in the Hominidae genomes in general with the orangutan genome being the outliner of this trend by having LINE as the dominant class. While AluY represents the major SINE groups in the Hominidae genomes, AluYRa1 is the dominant SINE in the Cercopithecidae genomes. For LINEs, each Hominidae genome seems to have a unique most active L1 subfamily, but all Cercopithecidae genomes have L1RS2 as the most active LINEs. While genomes with a high number of SS-MEs all have one or more very active ME subfamilies, the crab-eating macaque genome, being the one with an extremely low level of DNA transposition, has no single ME class being very active, suggesting the existence of a genome-wide mechanism suppressing DNA transposition. Third, DNA transposons, despite being considered dead in primate genomes, were in fact shown to have a certain level of activity in all genomes examined with a total of ∼2,400 entries as SS-MEs. Among these SS-MEs, at least 23% locate to genic regions, including exons and regulatory elements, presenting significant potentials for their impact on gene function. Very interestingly, our data demonstrate that, among the eight primates included in this study, the human genome is shown to be the most actively evolving genome via DNA transposition as having the highest most recent activity of many ME subfamilies, notably the AluYa5/Yb8/Yb9, L1HS, and SVA-D subfamilies. Representing the first of its kind, our large-scale comparative genomics study has shown that mobile elements evolved quite differently among different groups and species of primates, indicating that differential DNA transposition has served as an important mechanism in primate evolution.
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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 | 0,000 | 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 | 0,001 | 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) | 0,001 | 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 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 ».