Intergenomic synteny and whole-genome duplication
All seven corresponding
chromosomes between the FCDK and FCSH genomes exhibit conserved syntenic
relationships (Figure 2a). MCScanX identified 212 syntenic blocks
containing 27,559 (59.55%) PCGs from the two genomes. Both chromosomes
1 and 4 of FCDK showed perfect matches with the corresponding
chromosomes of FCSH; however, some obvious large-scale chromosomal
structural variations were present between other corresponding
chromosomes of the two strains. Large-scale inversions occurred at least
one, three, two, and four times on corresponding chromosomes 2, 3, 5 and
7, respectively, of FCDK and FCSH. Meanwhile, many translocation events
occurred on corresponding chromosomes 6 and 7, respectively of the two
strains.
Several large distal regions of FCDK chromosomes 1
(~10.51 Mb), 3 (~3.76 Mb), 4
(~7.71 Mb) and 7 (~9.13 Mb) did not
share any syntenic blocks with FCSH (Figure 2a). The top enrichment GO
terms of ~2,300 PCGs located in these FCDK-specific
regions were mainly related to nutrient responses, immunity, stress
tolerance and protein conformation, etc. (Figure 2b), which may
associate with the better adaptation of this strain to the environment
relative to FCSH. Most of other enriched GO terms (Figure 2b) and most
enriched KEGG pathways (Figure 2c) were associated with viruses,
bacteria and fungi as well as interactions between these organisms and
FCDK. A large number of genes may have been generated from ancient
horizontal gene transfers (HGTs), as revealed by Faddeeva-Vakhrusheva et
al. (2017) in the FCBL strain.
We tested the WGD hypotheses using within-genome collinear patterns,
paranome Ks distributions, and the estimated number of HOX gene
clusters. First, 14 syntenic blocks (198 genes) were identified within
the FCDK genome, and nine (131 genes) were found within the FCSH genome
(Figure 1i), among which only nine FCDK blocks were distributed on
different chromosomes. Most of the blocks occurred in genomic regions
with a high density of transposons. Second, KDEs fit the distributions
very well without obvious peaks in the Ks distributions (Figure 2d).
When BGMM mixture components were fit to Ks distributions, none of the
four default hypotheses (1~4 components/WGDs) was found
to be predominant (Figure S2). Third, only a single, complete HOX gene
cluster was identified on chromosome 5 (Figure 1i), with a length of
approximately 5 Mb, in both the FCDK and FCSH genomes. The Hox gene
cluster showed the same order of Scr , Ftz , Antp ,Ubx , lab , pb , Hox3 , Dfd , Abd-Aand Abd-B reported in a previous study (Faddeeva-Vakhrusheva et
al., 2007). Therefore, three lines of evidence (i.e., few within-genome
syntenic blocks, an absence of obvious peaks in Ks distribution plots,
and single HOX clusters in the genome) absolutely supported an absence
of WGD events in F. candida .