Biology subjects

Peng, M.-S.

Publications and source records attributed to Peng, M.-S..

3 recordsLinked to original sources

bioRxiv2024

Two distinct structural variants involving EDN3 cause hyperpigmentation in chicken

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant causing upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed structural arrangement and functional consequences of the variant remained unclear. In this study, we conducted a comprehensive genomic survey of 692 FM chickens representing 55 breeds and uncovered two distinct structural variants causing the FM phenotype: FM*A, the previously reported complex rearrangement involving the EDN3 locus1, and FM*B, a tandem duplication of a 16 kb region upstream of EDN3. We demonstrate that both structural variants (SVs) significantly upregulate EDN3 expression, with FM*B associated with even higher expression than FM*A. A luciferase reporter assays showed that the 16 kb region in FM*B contains powerful enhancers and the copy number expansion of this element is a likely explanation for EDN3 upregulation and hyperpigmentation. Furthermore, our analysis of linkage disequilibrium patterns allowed us to resolve the complex arrangement of duplications and inversion on the FM*A haplotype.

genomics↗

bioRxiv2024

Rapid evolution of fine-scale recombination during domestication

Recombination serves as a pivotal force propelling the evolution of genomic diversity in sexually reproducing organisms. Despite its fundamental role, the evolutionary dynamics of recombination rates and their implications for genome evolution remain largely elusive. The domestication of animals, which is characterized by dynamic selection pressures, offers a unique lens to explore this issue. Here, we constructed a fine-scale recombination map leveraging whole-genome data from domestic chickens, encompassing both contemporary commercial breeds and the wild progenitor, the Red Junglefowl (RJF). Our analysis revealed the rapid evolution of the recombination landscape within and across chicken populations, with significant variation in recombination coldspots and hotspots, particularly in commercial breeds. The occurrence of coldspots and the disappearance of hotspots are closely associated with selective sweeps.Contrary to prevailing observations in most species, we observed a weakly negative correlation between recombination rates and the frequency of introgressed ancestry from other RJF subspecies. Our findings provide valuable insights into the intricate interplay of evolutionary forces shaping the evolution of recombination.

evolutionary biology↗

bioRxiv2020

Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2

Understanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.

microbiology↗