Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)

The recent recognition of the five-subgenera classification within Crataegus has prompted discussion about the maternal phylogenetic relationships among these subgenera, with inconsistencies in taxon sampling, marker selection, and inference methods contributing to differing interpretations. In this study, we performed deep genome skimming sequencing and assembled 63 whole plastomes, including 58 from Crataegus and five from related genera as the outgroups. We employed multiple phylogenetic inference methods (Maximum Likelihood and Bayesian Inference) to reconstruct an accurate phylogeny. The whole plastome-based, maternally inherited trees consistently supported two major clades within Crataegus: one comprising C. subg. Crataegus and C. subg. Brevispinae, the other encompassing the remaining three subgenera. Within the latter clade, C. subg. Sanguineae and C. subg. Americanae formed a sister group, which together were sister to C. subg. Mespilus. Our analysis also revealed a close..., , , [https://doi.org/10.5061/dryad.z612jm6nc](https://doi.org/10.5061/dryad.z612jm6nc)

## Description of the data and file structure

# Data from: Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of *Crataegus shandongensis* (Rosaceae, Maleae)

### Files and variables

#### File: Crataegus_whole_plastomes_IQTREE.treefile

**Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through maximum likelihood analysis using IQ-TREE2.

#### File: Crataegus_whole_plastomes_RAxML.tre

**Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through maximum likelihood analysis using RAxML.

#### File: Crataegus_whole_plastomes_Mrbayes.tre

**Description:** Whole plastome-based phylogenetic backbone of *Crataegus* estimated through Bayesian Inference analysis using MrBayes.

#### File: Crataegus.mafft.trimal.fasta

**Description:** Alignment of *Crataegus* and outgroups...,