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Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae)

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Abstract

Carya sinensis (Chinese Hickory, beaked walnut, or beaked hickory) is an endangered species that needs urgent conservation action. Here, we reported the complete chloroplast (cp) genome sequence and the genomic features of the C. sinensis cp, which is the first complete cp genome of any member of Carya. The C. sinensis cp genome was 160,195 bp, containing a large single copy region (LSC) of 89,541 bp and a small single copy region (SSC) of 18,538 bp separated by a pair of 26,058 bp inverted repeat regions (IRs). The genome contained 135 genes, including 87 protein-coding genes (79 species), 40tRNA genes (30tRNA species) and eight ribosomal RNA genes (four rRNA species). Most genes occurred as a single copy; 22 were duplicated. The overall GC content of the C. sinensis cp genome was 36.3 %; the corresponding GC content values of the LSC, SSC and IR regions were 33.9, 30.0 and 42.5 %, respectively. A maximum likelihood (ML) phylogenetic analysis showed that C. sinensis is closely related to Juglans, as expected based on taxonomic affinity. The complete cp genome of C. sinensis will be useful for further investigations of genetic diversity and conservation of this endemic relict woody plant.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 41471038, No. 31200500 and No. J1210063), the Program for Excellent Young Academic Backbones funding by Northwest University, Changjiang Scholars and Innovative Research Team in University (IRT1174).Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply its approval to the exclusion of other products or vendors that also may be suitable.

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Authors and Affiliations

  1. Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Taibaibei Road 229, Xi’an, 710069, Shaanxi Province, China

    Yiheng Hu, Xi Chen, Xiaojia Feng & Peng Zhao

  2. USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN, 47907, USA

    Keith E. Woeste

Authors
  1. Yiheng Hu
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  2. Xi Chen
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  3. Xiaojia Feng
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  4. Keith E. Woeste
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  5. Peng Zhao
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Correspondence to Peng Zhao.

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Hu, Y., Chen, X., Feng, X. et al. Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae). Conservation Genet Resour 8, 467–470 (2016). https://doi.org/10.1007/s12686-016-0601-4

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  • DOI: https://doi.org/10.1007/s12686-016-0601-4

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