3.5 Gene family cluster identification and phylogenetic
analysis
We compared genomes of Chinese walnut and eight other plants based on
523 single-copy orthologs (Figure 4a). The number of single-copy
orthologs in the genome of Chinese walnut was similar to Arabidopsis,
the percentage of the Chinese walnut genome occupied by single-copy
orthologs was higher than all other species in the comparison exceptQ. robur and C. sinensis . (Figure 4a). We identified
125,530 orthologous gene families that consist of 310,273 genes, with
9,906 orthogroups containing proteins from all species (Figure 4b, Table
S10). We further compared Chinese walnut with three cultivated woody
species: Persian walnut (J. regia ), apple (M. domestica )
and olive (O. europaea ). We found 17.4 % (10,321/59,377) of all
gene families existed in all four species, while 5 % (2,972) were
specific to walnuts (Juglans ) (Figure 4a; Figure S5). When the
two Juglans species were compared, 457 genes were specific to
Chinese walnut, and 1,704 gene families were shared in both walnut
genomes. We discovered 399 gene families were expanded in Chinese walnut
compared to all other species in the phylogenetic tree, and 1,528 were
contracted (Figure 4b). As a comparison, Chinese walnut’s close relativeJuglans regia , showed 2,025 expanded gene families (5-fold more
than J. cathayensis ) and 243 contracted gene families (about 1/7
the number in the Chinese walnut genome) (Figure 4b).
We constructed a phylogenetic tree of these nine plant species with the
monocot rice (Oryza sativa ) as outgroup. The phylogeny was based
on 552 single-copy orthologous genes (Figure 4b). As expected, the two
closely related walnut species clustered on a branch with 100 %
bootstrap support (Figure 4b). The divergence between Chinese walnut and
Persian walnut was estimated to have occurred ~28 Mya
(Figure 4b).
We investigated whether any whole genome duplication (WGD) events have
occurred during Chinese walnut evolution. We identified a total of 86
synteny blocks and 5,614 genes in all blocks that covered 20.1 % of
Chinese walnut genome (Figure 3; Table S11). We calculated the density
distribution of the Ks values for the paired genes within each syntenic
genomic block based on the collinear blocks between the genomes of
Chinese walnut and Persian walnut (Figure 5). The peak of Ks was
~0.25 and ~1.5 for orthologous gene
pairs between the two walnuts, indicating that ancestors of these two
walnuts evolved through two ancient WGD events (Figure 5). Because the
peak of Ks was ~0 for orthologous gene pairs between
Chinese walnut and Persian walnut, their genomes reflect recent species
differentiation (Figure 5).