Whole-genome duplication
Li et al. (2018) inferred the occurrence of a whole-genome duplication
(WGD) event in F. candida , but Roelofs et al. (2020) refuted this
assumption and proposed a large number of small-scale gene duplications.
We tested the WGD hypothesis in both genomes using three methods: 1)
examination of patterns of collinearity within genomes: intraspecific
genomic collinear blocks were identified as in the above syntenic
analyses except that the mode was intraspecific rather than
interspecific (‘-b 1’); 2) evaluation of the paranome distributions of
synonymous distances (Ks, Blanc & Wolfe, 2004): the paralogue Ks
distribution and WGD signal were calculated from coding sequences using
wgd v1.1.1 (Zwaenepoel & Van de Peer, 2019), and kernel density
estimation (KDE) and BGMM mixture modelling were used to fit Ks
distributions; and 3) observation of the number of HOX gene clusters
(Ferrier & Minguillón, 2003): Hox genes were manually annotated by
TBLASTN-like MMseqs2 searches, with a sensitive mode and an e-value of
1e-10, using reference HOX protein sequences of F. candida mined
from the NCBI. Synteny, circus and HOX distribution figures were
visualized using TBtools v1.095 (Chen et al., 2020).