Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics
Notice bibliographique
Résumé
Abstract In the study of genetic diversity in non-model species there is a notable lack of the low-cost, high resolution tools that are readily available for model organisms. Genotyping microarray technology for model organisms is well-developed, affordable, and potentially adaptable for cross-species hybridization. The Mouse Diversity Genotyping Array (MDGA), a single nucleotide polymorphism (SNP) genotyping tool designed for Mus musculus , was tested as a tool to survey genomic diversity of wild species for inter-order, inter-genus, and intra-genus comparisons. Application of the MDGA cross-species provides genetic distance information that reflects known taxonomic relationships reported previously between non-model species, but there is an underestimation of genetic diversity for non-Mus samples, indicated by a plateau in loci genotyped beginning 10-15 millions of years divergence from the house mouse. The number and types of samples included in datasets genotyped together must be considered in cross-species hybridization studies. The number of loci with heterozygous genotypes mapped to published genome sequences indicates potential for cross-species MDGA utility. A case study of seven deer mice yielded 159,797 loci (32% of loci queried by the MDGA) that were genotyped in these rodents. For one species, Peromyscus maniculatus , 6,075 potential polymorphic loci were identified. Cross-species utility of the MDGA provides needed genetic information for non-model species that are lacking genomic resources. Genotyping arrays are widely available, developed tools that are capable of capturing large amounts of genetic information in a single application, and represent a unique opportunity to identify genomic variation in closely related species that currently have a paucity of genomic information available. A candidate list of MDGA loci that can be utilized in cross-species hybridization studies was identified and may prove to be informative for rodent species that are known as environmental sentinels. Future studies may evaluate the utility of candidate SNP loci in populations of non-model rodents. Author Summary There is a need for a tool that can assay DNA sequence differences in species for which there is little or no DNA information available. One method of analyzing differences in DNA sequences in species with well-understood genomes is through a genotyping microarray, which has demonstrated utility cross-species. The Mouse Diversity Genotyping Array (MDGA) is a tool designed to examine known differences across the genome of the house mouse, Mus musculus . Given that related organisms share genetic similarity, the MDGA was tested for utility in identifying genome variation in other wild mice and rodents. Variation identified from distantly related species that were not of the same genus as the house mouse was an underestimate of the true amount of variation present in the genomes of wild species. Utility of the MDGA for wild species is best suited to mice from the same genus as the house mouse, and candidate variation identified can be tested in rodent populations in future studies. Identifying changes in genetic variation within populations of wild rodents can help researchers understand the links between specific genome changes and the ability to adapt to pressures in the environment, as well as better understand the evolution of rodents.
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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 | 0,001 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,001 |
| 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 | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,001 |
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 ».