Ostrya chisosensis, common name Big Bend hop-hornbeam or Chisos hop-hornbeam, is a kind of tall deciduous tree species endemic to Texas. It is known only from the Chisos Mountains inside Big Bend National Park, in Brewster County, although related populations in northern Chihuahua have not been studied in detail and may be the same species (F.o.N.A.E Committee 1997). This species is reported only 639 mature individuals in the wild and listed as critically endangered species in the IUCN red list (Shaw et al. 2014; http://www.iucnredlist.org/details/194284/0). Due to small population and limited habitat, it is more susceptible to stochastic events. Therefore, measures of conservation and restoration are urgently needed. In this case, its genomics information is definitely fundamental to formulate a comprehensive conservation strategy. Here, we presented the complete chloroplast genome of O. chisosensis (GenBank: MG584735) based on the next-generation sequencing data.

A fresh leaf was collected from a mature individual of O. chisosensis in Big Bend National Park (Texas, USA, 29.33°N, 103.25°W), then it was dried using silica gel. Genomic DNA was isolated using the modified CTAB method (Doyle 1987). The whole-genome sequencing was conducted with 150 bp pair-end reads on the Illumina Hiseq Platform (Illumina, San Diego, CA). In total, 174 million high quality base pairs of sequence data were obtained and used for the cp genome assembly using the Fast-Plast pipeline (https://github.com/mrmckain/Fast-Plast; McKain and Wilson, unpublished). Annotation was performed with a newly developed command-line application called Plann (Plastome Annotator), which is suitable for plastomes annotation with a well-annotated sequenced relative (Huang and Cronk 2015). Then, we corrected the annotation with Geneious (Kearse et al. 2012). The plastid genome map was generated with OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013). We also constructed the phylogenetic trees with the maximum likelihood (ML, RaxML version 8, Stamatakis 2014) and bayesian analysis (BI, MrBayes version 3, Ronquist and Huelsenbeck 2003) methods based on the alignments created by the MAFFT (Katoh and Standley 2013) within the nine species plastid genomes.

The complete chloroplast genome of O. chisosensis was a quadripartite circular and 159,107 bp in length, comprising a large single copy (LSC) of 88,458 bp and a small single copy (SSC) of 18,792 bp, separated by two inverted repeat (IR) regions of 51,857 bp (Fig. 1). It contained 123 genes, included 85 protein-coding, 8 ribosomal RNA, and 30 tRNA genes. The plastome contained 95 unique genes, 14 genes duplicated in the IR regions. Among annotated genes, 10 genes contained a single intron, and four genes had two introns (i.e., clpP, ycf3, rps12 and rpl2). The base compositions of the whole chloroplast genome were uneven (31.4% A, 18.6% C, 18.6% G, 32.17% T), with an overall GC content of 36.5%, and the corresponding values of the LSC, SSC and IR regions reaching 34.3, 30.1 and 42.5%, respectively.

Fig. 1
figure 1

Gene map of the Ostrya chisosensis chloroplast genome

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To ascertain the phylogenetic position of O. chisosensi, we conducted a phylogenetic analysis using nine complete chloroplast genomes including O. rehderiana, O. trichocarpa, Carpinus putoensis, Carpinus tientaiensis, Corylus chinensis and Corylus fargesii representatives in Fagales and two outgroups (Fig. 2). The results indicated that all three species from the Ostrya were clustered together and O. chisosensi was most closely related to Ostrya rehderiana. This complete chloroplast genome can be readily used for population genomic studies of O. chisosensis, and such information would be fundamental to formulate potential new conservation and management strategies for this endangered species.

Fig. 2
figure 2

The phylogenetic tree based on the 9 complete chloroplast genome sequences. Bayesian posterior probabilities/ML bootstrap values are shown at nodes. Accession numbers: Carpinus tientaiensis KY117036, Carpinus putoensis KX695124, Corylus chinensis NC_032351, Corylus fargesii NC_031854, Juglans regia NC_028617, Ostrya chisosensis MG584735, Ostrya rehderiana KT454094, Ostrya trichocarpa KY088271, Betula pendula LT855378

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