Gross chromosomal shuffling reassembled the C.
rotundifolia genome
We collected a total of 342 single copy genes (61,639 homologous amino
acids) among 13 representative angiosperms to clarify the divergence ofC. rotundifolia (hereafter Cissus ) and V. vinifera(hereafter grape) (Figure S3, Table S1). Reconstruction of the phylogeny
indicated these two species had separated as early as 60.19–84.68
million years ago (mya) (Figure 1b), coincided with the distribution
pattern of synonymous substitutions per synonymous site (Ks ) (a
peak of distribution as Ks = 0.33) (Figure 1e). The subsequentKs analysis of all paralogous genes in the genomes ofCissus and grape and syntenic regions support a shared
whole-genome triplication, namely WGT-γ, the ‘pivot’ palaeo-hexaploidy
event that occurred in the most recent common ancestors (MRCA) of all
eudicots (Albert et al., 2013; Jaillon et al., 2007) (Figure 1b and 1e).
No more signatures of whole-genome duplication (WGD) were observed inCissus and grape genomes. Nevertheless, in Cissus , there
is another small peak of duplicated genes with Ks =
~ 0.1, and the majority of the paired genes were devoid
of inter-chromosomal regions (Figure 1e, Figure S4). Approximately 236
duplication events occurred inside their chromosome and were
characterized as segmental duplications. Such recent local gene cluster
duplication burst finally accounted for 8.31 % of Cissusfunctional genome profiles (4.75 % in grape, Table S12).
Interestingly, gene ontology analysis (GO) of the segmental duplications
gene clusters in two species revealed similar function enrichments
mostly associated with basic biological processes such as phosphorus
metabolic process and cellular protein metabolic process. Meanwhile,
specific biochemical pathways (e.g., brassinosteroid homeostasis) and
chromosome dynamics (e.g., meiotic chromosome condensation and meiotic
sister chromatid cohesion) are only enriched in Cissus (Table
S12). It would be worthy of further investigation on the role of the
‘connected’ gene cluster as a module of function during speciation and
the retention of duplicated segments with gene dosage relationship
preserved (Freeling, 2009).
Considerable high collinearity was observed between Cissus and
grape chromosomes, presenting a pattern as a combination of each two of
the 19 chromosomes in grape often correspond to one chromosome inCissus , leading to fewer monoploid chromosome numbers in the
latter (n=12) (Figure 2a). To search for genomic features that might
contribute to Cissus ’ modern 12 chromosomes, we compared the
ancestral eudicot karyotype (AEK) reconstructed from an integration of
the Vitales (grape), Malvales (cacao) and Rosales (peach) major
subfamilies to uncover that at least five fusions occurred inCissus after inheriting 21 AEK post-γ chromosomes from the MRCA
of eudicots (Murat et al., 2017) (Figure 2b). Specifically, pairwise
comparisons among Cissus , grape and AEK post-γ revealed that
82.59 % of grape genomic regions were linked to AEK post-γ, higher than
the number (71.24 %) of Cissus (Table S2). This may partly be
due to the ancestral reference derived from a comparison of
grape-cacao-peach, particularly when the grape preserved more ancestral
genomic organizations. Alternatively, the Cissus genome may have
lost more ancestral gene arrays than the grape, probably attributed to a
higher frequency of chromosomal rearrangement and recombination (Wan et
al., 2021; Xiong et al., 2011). Beyond that, 17.7 % of grape genes
(4,757 genes) were embedded in syntenic blocks with a 3:1 relationship
to each Amborella trichopoda (Albert et al., 2013) region that
resulted from WGT-γ, higher than syntenic block genes in Cissusgenome (13.7 %, 3,687 genes) (Figure 2c and 2d, Table S3). Likewise,
the number of syntenic genes was lower in Cissus (19.3 %, 4,188
genes) than in grape (23.4 %, 5,089 genes) when aligned withAristolochia fimbriata (Qin et al., 2021) (A species that is
similar to Amborella lack of further WGDs since the origin of
extant angiosperms). Moreover, 2,419 genes harbored in chromosome 1 were
identified as 76 %, of which were specific to Cissus (Figure 2b,
Figure S5, Table S13). Together with the above, it would imply a more
diverged genome of Cissus reshaped after long-term separation
with Vitis .