Advancing Pyrus phylogeny: Deep genome skimming-based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)

The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single-copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree-based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one-to-one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid ana..., Taxon sampling, DNA extraction, and sequencing. — Multi-source genomic data have been collected to infer a comprehensive phylogenomic backbone. We acquired DGS data for wild pear species from public databases, namely the National Center for Biotechnology Information (NCBI) and the National Genomics Data Center (NGDC), encompassing 63 individuals, and also generated new data from silica-gel dried materials or museum/herbarium specimens for 15 individuals, exclusively for this study. In total, we sampled 78 individuals of Pyrus, representing 32 species. We sampled several individuals of each of the widespread species, i.e., P. betulifolia Bunge (4 individuals), P. calleryana (5), P. elaeagrifolia Pall. (3), P. pashia Buch.-Ham. ex D.Don (5), P. phaeocarpa Rehder (4), and P. ussuriensis (7). It is important to note that we aimed to propose an updated infrageneric classification of Pyrus in this study rather than focus on species delimitation. In addition,..., , # Advancing Pyrus phylogeny: Deep genome skimming-based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)

Phylogenomic analyses from hundreds of single-copy nuclear genes and plastomes via deep genome skimming data support an updated infrageneric classification of the pear genus Pyrus (Maleae, Rosaceae)

This package contains the data and software outputs - Analyses_data.tar.gz

## Description of the Data and file structure

#### Analyses_data.zip

**ALIGNMENTS**

* Data 1. Pyrus_nuclear.fasta = 801 nuclear single-copy reference genes filtered from thirteen genomes
* Data 2. Pyrus_72_plastid_coding_genes.fasta = concatenated alignments of 72 plastid coding genes of Pyrus
* Pyrus_72_plastid_coding_genes.partitions.txt = partition file for concatenated alignments of 72 plastid coding genes of Pyrus
* Data 3. Pyrus_513_1to1_genes_dataset.fasta = concatenated alignments of 513 1to1...,