The alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species

This dataset includes the alignment of 163 plastome haplotypes of East Asian Cerris oaks and 29 plastomes of related oak species. The alignment was generated through four steps: (1) We used PhyloSuite v.1.2.2 to extract protein-coding genes (PCGs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) from the plastomes of 761 East Asian Cerris oak trees and 29 accessions of 22 related oak species. (2) The extracted regions were aligned individually with MAFFT v.7.313 and adjusted manually using BioEdit v.7.2.5. Specifically, inversions and length variations in simple sequence repeats were excluded because of their tendency for homoplasy. Eight ambiguously aligned regions in rps16-trnQ, psbM-trnD, ndhF-rpl32, rpl32-trnL, ndhD-psaC, and psaC-ndhE IGSs, and ndhF and ycf1 PCGs were also discarded to reduce phylogenetic noise. (3) The individual alignments were concatenated according to their respective positions in the plastome to generate a whole-plastome alignment with only one inverted repeat (IR) retained. (4) Unique plastome haplotypes were determined by DnaSP v.5.10.01.