Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

Background: The great diversity in plant genome size and chromosome number
is partly due to polyploidization (i.e., genome doubling events). The
differences in genome size and chromosome number among diploid plant
species can be a window into the intriguing phenomenon of past genome
doubling that may be obscured through time by the process of
diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of
chromosome numbers and a complex genomic history. Hibiscus is ideal for
exploring past genomic events because although two ancient genome
duplication events have been identified, more are likely to be found due
to its diversity of chromosome numbers. To reappraise the history of whole
genome duplication events, we tested  three alternative scenarios
describing different polyploidization events. Results: Using target
sequence capture, we designed a new probe set for Hibiscus and generated
87 orthologous genes from four diploid species. We detected paralogues in
>54% putative single-copy genes. 34 of these genes were selected
for testing three different genome duplication scenarios using gene
counting. All species of Hibiscus sampled shared one genome duplication
with H. syriacus and one whole genome duplication occurred along the
branch leading to H. syriacus. Conclusions: Here, we corroborated the
independent genome doubling previously found in the lineage leading to H.
syriacus and a shared genome doubling of this lineage and the remainder of
Hibiscus. Additionally, we found a previously undiscovered genome
duplication shared by the /Pavonia and /Malvaviscus clades (both nested
within Hibiscus) with the occurrences of two copies in what were otherwise
single-copy genes. Our results highlight the complexity of genomic
diversity in some plant groups, which makes orthology assessment and
accurate phylogenomic inference difficult.