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

Abstract

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable 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.

Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea

“…Consistent with previous reported values for Fagus plastomes (35.5% for F . crenata [ 32 ]; 37.0% for F . engleriana [ 34 ]; and 37.1% for F .…”

“…crenata (subgenus Fagus ) and F . engleriana (subgenus Engleriana ) [ 32 ]. The study found substantially lower pairwise nucleotide differences (p-distances) between the two species of Fagus than between those of its sister genus Quercus (0.0018 vs. 0.0042) [ 32 ].…”

“…multinervis from Buk-myeon, Ulleung Island, Korea (37°30′57 N 130°52′10 E). A previously sequenced accession of F. crenata (NC041252) was collected from Daisengen Peak on the northern island Hokkaido, Japan (41.616° N, 140.1333° E) [ 32 ]. The accession sequenced in this study represents a sample from southern Japan.…”

“…Therefore, such information is particularly fundamental to provide a greater resolution and stronger support at lower taxonomic levels [ 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Recently, several studies have reported the whole plastome sequences of Fagus and related genera, such as Quercus and Castanea , in Fagaceae [ 30 , 31 , 32 , 33 , 34 ]. Previous phylogenetic studies of Fagus were based primarily on nuclear ITS region and LEAFY intron and rarely on plastid coding or noncoding regions, which are either highly variable or highly conserved, providing unsupported congeneric relationships [ 2 , 9 ].…”

“…To determine the precise phylogenetic position of F. multinervis based on plastome data, F. japonica must be included in the analysis. Furthermore, structural variation and molecular evolution of plastomes within Fagus have been addressed only to a limited extent based on two species ( F. crenata and F. engleriana ) [ 32 , 34 ], which cannot clarify the whole scenario of plastome evolution within this genus.…”