Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae)

Advances in new next-generation sequencing (NGS) methods have revolutionized phylogenetics, yet challenges remain in effectively utilizing data from a wide range of sources. A well-resolved and broadly sampled phylogeny for Sonerileae, the second-largest tribe in Melastomataceae, is still lacking, hindering our understanding of its phylogenetic relationships and evolutionary history.

We combined target enrichment, genome skimming, RNA-Seq, and deep genome skimming (DGS) data to reconstruct the phylogenetic relationships within Sonerileae. We sampled 184 accessions representing 41 of the 47 genera in the tribe, including new sequences obtained with Hyb-Seq and DGS, and publicly available sequences. A newly developed reference comprising 5626 loci was employed to integrate data from different sources.

Our analyses produced a well-supported, near-comprehensive phylogeny for the tribe, outperforming previous and current studies that used only target enrichment probe sets as the reference for loci extraction. For the long-unresolved Asian Sonerileae, our phylogeny is comparable to that of a study focused specifically on that group, where a draft genome was required to identify orthologs.

Our analyses demonstrate that using an inclusive reference file enables the integration of genomic data generated with different sequencing strategies. We provide an effective approach for combining heterogeneous data for phylogenomic analysis.