Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

• 成果类型: Article
• 署名作者: David, Kyle T.; Schraiber, Joshua G.; Crandall, Johnathan G.; Labella, Abigail L.; Opulente, Dana A.; Harrison, Marie- Claire; Wolters, John F.; Zhou, Xiaofan; Shen, Xing - Xing; Groenewald, Marizeth; Hittinger, Chris Todd; Pennell, Matt; Rokas, Antonis
• 署名单位: Vanderbilt University; Vanderbilt University; University of Southern California; University of Southern California; University of Wisconsin System; University of Wisconsin Madison; University of North Carolina; University of North Carolina Charlotte; Villanova University; Guangdong Laboratory for Lingnan Modern Agriculture; South China Agricultural University; Cornell University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9423
• DOI: 10.1073/pnas.2500165122
• 发表日期: 2025-06-10
• 关键词: evolution; duplication; MODEL; contingency; inference; TREE

摘要

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times, many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,785 gene families from 993 Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we found that gene family expansion and contraction were significantly linked to trait gain and loss in 45/56 (80%) traits. While 595/739 (81%) significant gene families were associated with only one trait, we also identified several keystone gene families that were significantly associated with up to 13/56 (23%) of all traits. Strikingly, most of these families are known to encode metabolic enzymes and transporters, including all members of the industrially relevant MAL tose fermentation loci in the baker's yeast Saccharomyces cerevisiae. These results indicate that convergent evolution on the gene family level may be more widespread across deeper timescales than previously believed.