out of chaos: phylogenomics of Asian Sonerileae

Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with more than 70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as wel..., , , # Data from: out of chaos: phylogenomics of Asian Sonerileae

[https://doi.org/10.5061/dryad.p2ngf1vs1](https://doi.org/10.5061/dryad.p2ngf1vs1)

## Description of the data and file structure

\### Plastome_alignment.fasta

Description: Alignment of 223 whole chloroplast genomes

\### genomic_dataset.vcf

Description: vcf file of genomic dataset, generated by mapping whole genome resequencing data of 223 samples to **Tigridiopalma magnifica** reference genome, further filtered based on hard filtering by GATK and LD by Plink.

\### SCO_dataset.vcf

Description:  vcf file of single copy ortholog dataset, generated by mapping whole genome resequencing data of 223 samples to 332 reference single copy orthologs, further filtered based on hard filtering by GATK.

\### reference_sequeces_of_332_SCO.fasta

Description: 332 reference single copy orthologs assembled using Mitobim, based on 332 single copy genes identified by OrthoFinder.

\### supplementary_appendix.docx

Description: supplementa...