The complete chloroplast genome of a Tertiary relict species Liriodendron chinense (Magnoliaceae)
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TECHNICAL NOTE
The complete chloroplast genome of a Tertiary relict species Liriodendron chinense (Magnoliaceae) Bin Li1 • Yanda Li1,3 • Qifei Cai1 • Furong Lin1 Qinyang Meng1,2 • Yongqi Zheng1
•
Received: 15 May 2016 / Accepted: 25 May 2016 Ó Springer Science+Business Media Dordrecht 2016
Abstract Liriodendron chinense is a rare Tertiary relict tree species. In this study, we report the complete chloroplast genome of a Chinese tulip tree, L. chinense. The total genome size was 159,429 bp in length, containing a pair of inverted repeats (IRs) of 26,333 bp, separated by large single copy (LSC) and small single copy (SSC) of 87,766 and 18,997 bp, respectively. The chloroplast genome contained the conservative quadripartite structure present in most Magnoliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbored a single intron, and 2 contained a couple of introns. The overall G?C content of the cpDNA is 39.2 %, while the corresponding values of the LSC, SSC and IR regions are 37.8, 34.3 and 43.2 % respectively. A maximum likelihood phylogenomic analysis showed that L. chinense is closely related to L. tulipifera that belongs to the tribe Magnoliaceae. Keywords Chloroplast genome Liriodendron chinense Phylogeny Next-generation sequencing Liriodendron chinense (Hemsl.) Sarg is a rare Tertiary relict tree species belonging to the magnolia family (Magnoliaceae). It grows fast with a good quality of lightness and softness, and therefore, is cultivated in China & Yongqi Zheng [email protected] 1
State Key Laboratory of Tree Breeding and Forest Genetics, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
2
Henan University of Science and Technology, Zhengzhou, China
3
Peking University, Beijing, China
for wood production. This species has been regarded as an endangered plant because it occurs in small populations scattering in montane broad-leaved forests of southern China and northern Vietnam (Tang et al. 2013). Chloroplast genome was widely used in phylogeny (Xue et al. 2012), DNA barcoding (Dong et al. 2012, 2014), species conservation and genome evolution (Dong et al. 2013b). Here, we reported the complete chloroplast genome sequence of the L. chinense based on the next-generation sequencing method (Dong et al. 2013a). The annotated cpDNA has been deposited into GenBank with the accession number KU170538. Total Genomic DNA was extracted from fresh young leaves of a L. chinense plant found in the Experiment Center of Subtropical Forestry, Chinese Academy of Forestry, Jiangxi province (collection number: EZQ-2) using the mCTAB method (Li et al. 2013a). DNA was sheared by sonication, fragments around 500 bp were recycled in agarose gel. Paired-end libraries were prepared with NEBNext Ultra DNA Library Prep Kit for Illumina in accordance with the manufacture’s instructions. The library was sequenced using the HiSeq 4000 platform. The pairedend reads were qualitatively assessed and assembled with SPAdes 3.6.1 (Bankevich et al. 2012).
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