Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum).
SNPs
axolotl
genome
hybrid
salamander
Journal
Developmental dynamics : an official publication of the American Association of Anatomists
ISSN: 1097-0177
Titre abrégé: Dev Dyn
Pays: United States
ID NLM: 9201927
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
revised:
14
09
2020
received:
01
07
2020
accepted:
24
09
2020
pubmed:
2
10
2020
medline:
11
3
2022
entrez:
1
10
2020
Statut:
ppublish
Résumé
Recent efforts to assemble and analyze the Ambystoma mexicanum genome have dramatically improved the potential to develop molecular tools and pursue genome-wide analyses of genetic variation. To better resolve the distribution and origins of genetic variation with A mexicanum, we compared DNA sequence data for two laboratory A mexicanum and one A tigrinum to identify 702 million high confidence polymorphisms distributed across the 32 Gb genome. While the wild-caught A tigrinum was generally more polymorphic in a genome-wide sense, several multi-megabase regions were identified from A mexicanum genomes that were actually more polymorphic than A tigrinum. Analysis of polymorphism and repeat content reveals that these regions likely originated from the intentional hybridization of A mexicanum and A tigrinum that was used to introduce the albino mutation into laboratory stocks. Our findings show that axolotl genomes are variable with respect to introgressed DNA from a highly polymorphic species. It seems likely that other divergent regions will be discovered with additional sequencing of A mexicanum. This has practical implications for designing molecular probes and suggests a need to study A mexicanum phenotypic variation and genome evolution across the tiger salamander clade.
Sections du résumé
BACKGROUND
Recent efforts to assemble and analyze the Ambystoma mexicanum genome have dramatically improved the potential to develop molecular tools and pursue genome-wide analyses of genetic variation.
RESULTS
To better resolve the distribution and origins of genetic variation with A mexicanum, we compared DNA sequence data for two laboratory A mexicanum and one A tigrinum to identify 702 million high confidence polymorphisms distributed across the 32 Gb genome. While the wild-caught A tigrinum was generally more polymorphic in a genome-wide sense, several multi-megabase regions were identified from A mexicanum genomes that were actually more polymorphic than A tigrinum. Analysis of polymorphism and repeat content reveals that these regions likely originated from the intentional hybridization of A mexicanum and A tigrinum that was used to introduce the albino mutation into laboratory stocks.
CONCLUSIONS
Our findings show that axolotl genomes are variable with respect to introgressed DNA from a highly polymorphic species. It seems likely that other divergent regions will be discovered with additional sequencing of A mexicanum. This has practical implications for designing molecular probes and suggests a need to study A mexicanum phenotypic variation and genome evolution across the tiger salamander clade.
Identifiants
pubmed: 33001517
doi: 10.1002/dvdy.257
pmc: PMC8715502
mid: NIHMS1764885
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
822-837Subventions
Organisme : NIH HHS
ID : P40 OD019794
Pays : United States
Organisme : NIH HHS
ID : R24 OD010435
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130349
Pays : United States
Informations de copyright
© 2020 Wiley Periodicals LLC.
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