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

James R P Worth; Luxian Liu; Fu-Jin Wei; Nobuhiro Tomaru

doi:10.7717/peerj.7026

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

PeerJ. 2019 Jun 7:7:e7026. doi: 10.7717/peerj.7026. eCollection 2019.

Authors

James R P Worth¹, Luxian Liu², Fu-Jin Wei¹, Nobuhiro Tomaru³

Affiliations

¹ Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan.
² Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, China.
³ Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.

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.

Keywords: Beech; Chloroplast SSRs; Chloroplast microsatellites; Fagaceae phylogeny; Fagus crenata; Whole chloroplast genome.

Grants and funding

This work was supported by the Japanese Society for the Promotion of Science Grant-in-Aid for Young Scientists A (Grant number 16748931); and a Forestry and Forest Products Research Institute grant (Grant number 201430). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.