Fitness consequences of structural variation inferred from a House Finch pangenome

• 成果类型: Article
• 署名作者: Fang, Bohao; Edwards, Scott V.
• 署名单位: Harvard University; Harvard University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11314
• DOI: 10.1073/pnas.2409943121
• 发表日期: 2024-11-19
• 关键词: copy number variant; mycoplasma-gallisepticum; carpodacus-mexicanus; comparative genomics; natural-populations; EVOLUTION; inversions; reveals; repeats; susceptibility

摘要

Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied in wild animal populations. We constructed a pangenome for House Finches (Haemorhous mexicanus), a model for studies of host- pathogen coevolution, using long- read sequence data on 16 individuals (32 de novo- assembled haplotypes) and one outgroup. We identified 887,118 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, with reduced SV diversity in the eastern US as a result of its introduction by humans. The distribution of fitness effects of genome- wide SVs was estimated using maximum likelihood approaches and revealed that SVs in both coding and noncoding regions were on average more deleterious than smaller indels or single nucleotide polyfrequencies of the inversion, estimated from 135 birds widely sampled temporally and selection, capturing genes related to immunity and telomerase activity. We also observed Our study illustrates the utility of long- read sequencing and pangenome methods for and advancing our understanding of adaptive evolution through structural variation.