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

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

doi:10.7717/peerj.7026

James R. P. Worth, Fu-Jin Wei + Show 2 more

Open Access

https://doi.org/10.7717/peerj.7026

Copy DOI

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.

Highlights

The genus Fagus is a major tree of temperate forests of the northern hemisphere with two informal subgenera recognized (Shen, 1992): Engleriana with three species and Fagus with seven species (Oh, 2015; Renner et al, 2016)
This study reports the whole chloroplast genome of the Japanese endemic Fagus crenata, the first reported of subgenus Fagus
Of chloroplast DNA from the whole genomic sequencing data was undertaken in Novoplasty 2.6.3 (Dierckxsens, Mardulyn & Smits, 2016), a seed-and-extend algorithm that is designed for the specific purpose of assembling chloroplast genomes from whole genome sequencing data, starting from a chloroplast seed sequence

Summary

Introduction

The genus Fagus is a major tree of temperate forests of the northern hemisphere with two informal subgenera recognized (Shen, 1992): Engleriana with three species and Fagus with seven species (Oh, 2015; Renner et al, 2016). Despite the significance of the genus there remains a dearth of Generation Sequencing based-genetic resources for Fagus, including for the chloroplast genome, with the whole chloroplast genome of only a single species, the Chinese endemic F. engleriana of subgenus Engleriana (Yang et al, 2018), so far published. The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana).

Methods

Results

Conclusion