Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax. Using syntR, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservat..., , syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers.
The documentation and tutorial for syntR can be found here](https://ksamuk.github.io/syntR/index.html
You can install syntR from Github with:
``` rinstall.packages(\"devtools\")devtools::install_github(\"ksamuk/syntR\")```
Also see the README file.