Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae).

BACKGROUND AND AIMS

Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies, and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by, using organelle-scale "barcodes" (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes.

METHODS

To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe, and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR boundaries, nucleotide divergence, pttRNA structures, and codon aversions. Additionally, phylogenetic inferences were inferred using both plastomic dataset (79 genes) and nuclear dataset (1,054 genes).

KEY RESULTS

Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC lengths. Informative diversities existed in the gene content at SSC/IRa, with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 CDSs revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic.

CONCLUSIONS

This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified high-informative unique markers at the subfamily, genus, and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.

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