Corylus chinensis, the only macrophanerophyte species in the genus Corylus, is natively distributed in the southern region of China. As a fruit–timber tree, C. chinensis has been seriously threatened by human activities in the last few decades. Recently, several chloroplast (cp) DNA markers have been used for phylogenetic analysis of hazelnut species (Erdogan et al. 2000; Palmé et al. 2002; Boccacci et al. 2009; Bassil et al. 2013; Martins et al. 2013). However, little is known about the chloroplast genome of the Corylus genus. This study was the first to report the complete chloroplast genome of C. chinensis on the basis of the Illumina pair-end sequencing dataset. The annotated chloroplast genome of C. chinensis has been deposited into GenBank with the Accession No. KX426347.

Fresh leaves were collected from a single C. chinensis plant planted at the germplasm nursery of the Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China. DNA extractions were performed using the Plant Genomic DNA Kit (Tiangen Biotech Co., China) according to the manufacturer’s instructions, and the high-throughput sequencing was carried out on the Hiseq2500 System (Illumina, USA) by Ori-Gene Technology Co., Beijing, China. In all, 14.55 M of 126-bp raw reads were trimmed with SolexaQA (Cox et al. 2010). About 1.487G high-quality base pairs of sequencing data were obtained and used for the chloroplast genome assembly using SOAPdenovo software (Luo et al. 2012). Then, reference-guided assembly was performed to reconstruct the chloroplast genomes with the program BLAST (Altschul et al. 1990) using closely related species as the references. A 159,915-bp chloroplast genome of C. chinensis was obtained after filling the gap with GapCloser (http://soap.genomics.org.cn/index.html). The annotation was performed using CPGAVAS (Liu et al. 2012). Finally, a physical map of the chloroplast genome was generated.

The circular genome contains a pair of inverted repeat (IRa and IRb) regions of 26,989 bp, a large single-copy region, and a small single-copy region with the lengths of 88,115 and 17,822 bp, respectively (Fig. 1). The chloroplast genome of C. chinensis comprises 132 genes, including 95 protein-coding genes, 8 ribosomal RNA genes, and 29 transfer RNA genes. Among the annotated genes, 11 protein-coding genes contain introns, including 9 genes with a single intron each (atpF, rpoC1, rpl2, ycf15, ndhB, ndhA, ndhB, ycf15, and rpl2) and 2 genes with 2 introns each (clpP and ycf3). The overall AT content of C. chinensis cp genome is 63.51 %.

Fig. 1
figure 1

Gene map of the Corylus chinensis chloroplast genome

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On the basis of the cpDNA sequences of C. chinensis and the other 11 species of the families Fagaceae, Juglandaeceae, and Betulaceae from the Fagales, a neighbor-joining phylogenetic tree was conducted using MEGA6 (Tamura et al. 2013). The cpDNA sequences of 12 plants were analyzed to identify the phylogenetic position of C. chinensis using MEGA6. The phylogenetic analysis showed that the cp genome of C. chinensis was closely related to that of Ostrya rehderiana of the family Betulaceae (Fig. 2).

Fig. 2
figure 2

Neighbor-joining phylogenetic tree inferred using MEGA6 from 12 complete cp genomes

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The aforementioned complete chloroplast genome can be subsequently used for population, phylogenetic, and cp genetic engineering studies of C. chinensis, and such information would be fundamental to formulate potential new conservation and management strategies for this important Betulaceae species.