The complete chloroplast genome of Fagus crenata (subgenus Fagus ) and comparison with F. engleriana (subgenus Engleriana )

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus ), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagu s chloroplast genome, F. engeleriana (subgenus Engleriana ) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psb K- psb I, trn G- psb fM, trn V, rpl 32, ndhD - psa C and ndh I- ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.