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 .