Open AccessIAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios
Author(s) -
Shenghan Gao,
Xiaofei Yang,
Jianyong Sun,
Xixi Zhao,
Bo Wang,
Kai Ye
Publication year - 2022
Publication title -
molecular biology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.637
H-Index - 218
eISSN - 1537-1719
pISSN - 0737-4038
DOI - 10.1093/molbev/msac041
Subject(s) - genome , ancestor , biology , most recent common ancestor , evolutionary biology , range (aeronautics) , gene duplication , computational biology , genomics , genetics , gene , materials science , archaeology , composite material , history
Significant improvements in genome sequencing and assembly technology have led to increasing numbers of high-quality genomes, revealing complex evolutionary scenarios such as multiple whole-genome duplication events, which hinders ancestral genome reconstruction via the currently available computational frameworks. Here, we present the Inferring Ancestor Genome Structure (IAGS) framework, a novel block/endpoint matching optimization strategy with single-cut-or-join distance, to allow ancestral genome reconstruction under both simple (single-copy ancestor) and complex (multicopy ancestor) scenarios. We evaluated IAGS with two simulated data sets and applied it to four different real evolutionary scenarios to demonstrate its performance and general applicability. IAGS is available at https://github.com/xjtu-omics/IAGS.