#35 · Genomics

Graph pangenomes and simulation reveal structural variation driving genome evolution

The dominant thread is comparative inference of genome-wide variation from isolate genomes and its functional consequences. A graph pangenome of 1060 Brettanomyces bruxellensis isolates detects 5972 structural variants, with allopolyploids carrying more SVs and hybridization-associated SVs strongly affecting function. A comparative analysis of gut bacterial isolate genomes links industrialized-host origin to expanded proteomes and fluid pangenomes. PrinTE, a forward-time whole-genome simulator, infers transposable element insertion and deletion rates with under 6% error and is applied to the study of genome expansion and contraction. What is new is pairing pangenome-scale structural variant detection with explicit simulation of transposable element dynamics. The items do not test a shared mechanism, so the common thread is comparative inference rather than a single demonstrated process.