The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China

Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. They were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IR, and the whole cp genome. Each inversion was replaced with its reverse complement and coded as a single-nucleotide variant (SNV). Unique cpDNA haplotypes were determined by DnaSP v.6.12.03 based on four datasets: 1) the alignment of whole cp genome sequences with IRa excluded and indels considered; 2) the same as dataset 1 except that indels were not considered; 3) the concatenated alignment of IGSs and introns excluding indels; and 4) the concatenated alignment of CDSs excluding indels.