Inference of subgenomes resulting from polyploid events using synteny based dynamic linking and maximum neighbourhood

Polyploidy is common in flowering plants, resulting in extra sets of chromosomes, known as subgenomes. These events are widespread in plant evolution, making the assignment of synteny blocks to subgenomes challenging due to gene fractionation and gene order rearrangements. Current methods for subgenome identification are labor-intensive and require expertise, lacking automation. To address this challenge, we introduce the SyntenyLink algorithm, which automates subgenome reconstruction from synteny blocks. This algorithm considers differences in substitution and fractionation patterns in synteny blocks and maintains the continuity of gene order. SyntenyLink starts by identifying synteny blocks using BLASTP and DAGchainer, then Automatically partitions them into subgenomes by traversing the maximum weighted path on the "super-synteny graph". We validated the SyntenyLink algorithm using verified subgenomes of Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus, and Sinapis alba. The results demonstrate its effectiveness, especially for subgenome 1, with accuracy ranging from 82% to 88%. Subgenomes 2 and 3 showed slightly lower accuracy (60%-85%) due to their similar fractionation patterns. Furthermore, we applied SyntenyLink to separate the six subgenomes in Brassica juncea and Brassica carinata, illustrating its versatility. In summary, the SyntenyLink algorithm offers a powerful and automated approach for reconstructing subgenomes in complex polyploid genomes. This advancement has significant implications for studying the evolutionary history of flowering plants and other polyploid organisms.