Common Ancestry of the Id Locus: Genetic Clues and Polygenic Possibilities DOI Open Access
Ashutosh Sharma, Nagarjun Vijay

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 29, 2023

Abstract The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting overexpression of EDN3 (a gene central to melanocyte regulation). In contrast, inhibition regulated Id locus. Although prior studies using genetic crosses, GWAS, expression analysis have investigated underpinnings its precise location functional details remain elusive. Our study aims precisely locate identify associated rearrangements candidate genes influencing pigmentation, examine ancestral status locus BBC breeds. Using public genomic data from non-BBC breeds, we refined ∼1.6 Mb region that co-localizes Z amplicon repeat units distal end q-arm within 10.36 inversion Silkie BBC. Phylogenetic population structure analyses reveal shares common ancestry across all much like Selection signatures highly differentiated BBC-specific SNPs MTAP position it as prime CCDC112 additional genes, suggesting possible polygenic nature. results suggest shared breeds may function supergene cluster shank variation.

Язык: Английский

Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities DOI
Ashutosh Sharma, Nagarjun Vijay

Journal of Molecular Evolution, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

Язык: Английский

Процитировано

1
Fitness consequences of structural variation inferred from a House Finch pangenome DOI Creative Commons
Bohao Fang, Scott V. Edwards

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(47)

Опубликована: Ноя. 12, 2024

Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied wild animal populations. We constructed for House Finches ( Haemorhous mexicanus ), model studies of host-pathogen coevolution, using long-read sequence data on 16 individuals (32 de novo - assembled haplotypes) one outgroup. identified 887,118 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, reduced SV diversity the eastern US as result its introduction by humans. The distribution genome-wide was estimated maximum likelihood approaches revealed that both coding noncoding regions were more deleterious smaller indels or single nucleotide polymorphisms. reference-free facilitated identification > 10-My-old, 11-megabase-long pericentric inversion chromosome 1. found genotype frequencies inversion, from 135 birds widely sampled temporally geographically, increased steadily over 25 y since first exposed to bacterial pathogen Mycoplasma gallisepticum showed signatures balancing selection, capturing genes related immunity telomerase activity. also observed shorter telomeres populations greater number years exposure . Our study illustrates utility sequencing methods understanding populations, estimating SVs, advancing our evolution through variation.

Язык: Английский

Процитировано

3
Fitness consequences of structural variation inferred from a House Finch pangenome DOI Creative Commons
Bohao Fang, Scott V. Edwards

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 17, 2024

Abstract Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied wild animal populations. We constructed for House Finches, model studies of host-pathogen coevolution, using long-read sequence data on 16 individuals (32 de novo- assembled haplotypes) one outgroup. identified 643,207 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, reduced SV diversity the eastern US as result its introduction by humans. The distribution genome-wide was estimated maximum likelihood approaches showed both coding non-coding regions to be more deleterious smaller indels or single nucleotide polymorphisms. reference-free facilitated discovery 10-million-year-old, 11-megabase-long pericentric inversion chromosome 1. found that genotype frequencies inversion, from 135 birds widely sampled geographically temporally, increased steadily over 25 years since Finches were first exposed bacterial pathogen Mycoplasma gallispecticum signatures balancing selection, capturing genes related immunity telomerase activity. also observed shorter telomeres populations greater number exposure . Our study illustrates utility applying methods populations, helps estimate SVs, advances our understanding evolution through variation. Significance Statement Prevailing genomic research neutral has focused primarily polymorphisms (SNPs). However, variation (SV) plays critical often directly underlying fitness-relevant traits, although less well understood. constructs Finch sequencing, full spectrum without use reference genome. In addition detecting half million we document large shows evidence contributing disease resistance. sequencing pangenomic bird population presents compelling approach complexities molecular ecology evolution. Graphical abstract

Язык: Английский

Процитировано

2
Common Ancestry of the Id Locus: Genetic Clues and Polygenic Possibilities DOI Open Access
Ashutosh Sharma, Nagarjun Vijay

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 29, 2023

Abstract The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting overexpression of EDN3 (a gene central to melanocyte regulation). In contrast, inhibition regulated Id locus. Although prior studies using genetic crosses, GWAS, expression analysis have investigated underpinnings its precise location functional details remain elusive. Our study aims precisely locate identify associated rearrangements candidate genes influencing pigmentation, examine ancestral status locus BBC breeds. Using public genomic data from non-BBC breeds, we refined ∼1.6 Mb region that co-localizes Z amplicon repeat units distal end q-arm within 10.36 inversion Silkie BBC. Phylogenetic population structure analyses reveal shares common ancestry across all much like Selection signatures highly differentiated BBC-specific SNPs MTAP position it as prime CCDC112 additional genes, suggesting possible polygenic nature. results suggest shared breeds may function supergene cluster shank variation.

Язык: Английский

Процитировано

0