Paper
We developed the CLfinder-OrthNet pipeline that detects co-linearity in gene arrangement among multiple closely related genomes; find ortholog groups; and encodes the evolutionary history of each ortholog group into a representative network (OrthNet). Using a search based on network topology, out of a total of 17,432 OrthNets in six Brassicaceae genomes, we identified 1,394 that included gene transposition-duplication (tr-d) events in one or more genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. They also had a higher chance of being expressed and derived from older tr-d events. We also found an enrichment, compared to random chance, of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3. The CLfinder-OrthNet pipeline provides a flexible and a modular toolkit to compare gene order, encode and visualize evolutionary paths among orthologs as networks, and identify all gene loci that share the same evolutionary history using network topology searches.\n\nFunding source: This work was supported by National Science Foundation (MCB 1616827) and the Next Generation BioGreen21 Program (PJ011379) of the Rural Development Administration, Republic of Korea.\n\nOnline-only Supplementary materials includes supplementary text (S1-S10), methods (M1-M4), figures (S1-S7), and tables (S1-S3), in two PDF files, one for text and methods and the other for figures and tables. Additionally, Supplementary Dataset S1 is available at the Figshare repository (https://doi.org/10.6084/m9.figshare.5825937) and Dataset S2 and S3 as separate Excel files.
