Characterization of the complete chloroplast genome of the relict Chinese false tupelo, Camptotheca acuminata
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of the relict Chinese false tupelo, Camptotheca acuminata Si‑Yun Chen2 · Xian‑Zhi Zhang1
Received: 11 September 2017 / Accepted: 13 October 2017 © Springer Science+Business Media B.V. 2017
Abstract The Chinese false tupelo, Camptotheca acuminata, is a Tertiary relict species with dramatically fragmented and declined populations. Here we characterized the complete chloroplast (cp) genome of C. acuminata using Illumina pair-end sequencing data. The C. acuminata cp genome was 157,806 bp in length, containing a pair of inverted repeats (IRs) of 25,771 bp which separated a large single copy region (LSC) of 87,504 bp and a small single copy region (SSC) of 18,760 bp. The genome contained 134 genes, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Most of genes occurred as single-copy in the LSC or SSC, while 18 genes had two copies in the IRs. The GC content of C. acuminata cp genome is 37.8%. Phylogenomic analysis strongly supported the close relationship of C. acuminata and Davidia involucrata. This complete cp genome will be useful for further conservation genomics studies of C. acuminata. Keywords Camptotheca acuminata · Chloroplast genome · Phylogenomics Camptotheca acuminata Decne., commonly called false tupelo or happy tree, is a deciduous tree in the family Nyssaceae, native to southern China and Vietnam (Qin and Phengklai 2007). It is a Tertiary relict tree species with * Xian‑Zhi Zhang [email protected] 1
College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
2
important scientific, medicinal and ornamental values (Zhang et al. 2004). Unfortunately, the wild populations of C. acuminata have been dramatically fragmented and decreased over the past decades, largely due to the anthropogenic agricultural activities and overexploitation for commerce as medicine (Jordi and Zhao 2004). It is urgent to take protective action to conserve this valuable forest tree species. A complete chloroplast (cp) genome will be useful for population and phylogenetic studies of C. acuminata, and such comprehensive genomic information will also provide essential resource for both conservation and utilization of this relict tree species. In the present study, we assembled and characterized the complete cp genome of C. acuminata using the Illumina pair-end sequencing data. Fresh leaves of a single individual of C. acuminata were collected from the Arboretum of Northwest A&F Univeristy, Shaanxi province of China, and total genomic DNA was extracted using the modified CTAB method (Doyle and Doyle 1987). The voucher specimen was deposited at the Trees Herbarium of Northwest A&F University (Accession No. ZXZ16006). The genome skimming sequencing was conducted with 100 bp paired-end (PE) reads on the Illumina HiSeq 2000 platform in Beijing Genomics Institute (BGI) in Shenzhen, China. Approxim
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