Phylogenomics with Hyb-Seq Unravels Korean Hosta Evolution

A total of 246 nuclear gene sequences and whole plastid genomes were captured from 55 accessions of Korean Hosta species using the Hyb-Seq method. The captured nuclear sequences were processed with the pipeline of HybPiper (v1.2). In short, the trimmed data were aligned onto the reference file with BWA aligner, and retrieved exon and intron sequences were assembled as contigs which were combined into a supercontig by SPAdes (v3.10.1) assembler. Each supercontig was aligned by MAFFT (v7.402). Because some of the bases exist in only a few samples, they were removed via Phyutility (v2.2.6) with -clean 0.7 option. Every clean supercontig file was concatenated according to sample ID. For chloroplast genome assembly, 55 constructed DNA libraries were sequenced on an Illumina platform (2 X 150 bp). Reconstruction of the chloroplast genome was performed in Geneious v. 2019.2.3 where the published Hosta chloroplast genome sequences were used as the reference.<br>The nuclear dataset includes a total of 246 genes (489,796 bp) from 55 Hosta species, while the chloroplast dataset contains 159,590 bp from 63 Hosta species and four outgroup taxa.<br>Three files (ASR_R_script.R, DNA_nr.csv, Hosta.tre) were used in ancestral state reconstruction of genome sizes in Korean Hosta species.