Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae)
2016
Hu, Yiheng | Chen, Xi | Feng, Xiaojia | Woeste, Keith E. | Zhao, Peng
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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