Landscape of Lineage-Specific Gene Translocation and Duplication Events within the Crucifer Family

Gene duplication and translocations erode co-linearity between closely related genomes over time, providing a source of variations that may be critical for organismal adaptation. We developed a pipeline to identify and trace gene duplication and translocation unique to or shared among lineages within multiple closely related genomes. The CL_finder-OrthNet pipelines encode and visualize gene duplication and translocation events in a set of networks that connect nodes of orthologous loci with edges indicating co-linearity (CL) relationship among them.

We characterized the gene duplication and translocation events among six crucifer genomes, including a model plant (Arabidopsis thaliana) and extremophytes adapted to various extreme environmental challenges (Eutrema salsugineum and Schrenkiella parvula) from both Lineage I and II. The OrthNet pipeline effectively identified lineage-specific (LS) gene translocation-duplication (Tlc-d) events. The ratio of open reading frame (ORF) size between the duplicates and the ancestral gene models in LS Tlc-d events showed two distinct distributions, with two peaks indicating a truncated duplication and a putative selection for additional gene copies, respectively. We found signatures of selection among stress response-related genes in E. salsugineum and S. parvula lineage-specific Tlc-d events that contain additional duplicates with ORF size conserved.

The flexible CL_finder-OrthNet pipelines can provide insights into the landscape of co-linearity and its erosion within any set of multiple closely related genomes. The pipelines also can identify candidate genes that have played roles in adaptation with an increasing resolution, as more de novo assembled genomes for closely related species and comparative genome-wide data on gene expression and regulation become available.