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).