Abstract
Altingia chinensis is an important native broad-leaved tree in southern China. Its wood can be used as an excellent edible fungus culture medium, in addition, aromatic oil can be extracted for medicine and spices. Its full-length chloroplast genome is 160,410 bp, including a large single copy (LSC) region of 88,936 bp, a small single copy (SSC) region of 18,917 bp, and a pair of inverted repeat (IR) regions of 26,274 bp. Furthermore, we also found 132 genes, 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes in the chloroplast genome of Altingia chinensis. Phylogenetic analysis shows that Altingia chinensis is most closely related to Liquidambar formosana and Semiliquidambar cathayensis. This study can provide basic data for research on molecular-assisted breeding of Altingia chinensis,and phylogeny of Hamamelidaceae.
Altingia chinensis is an evergreen tree belonging to Hamamelidaceae, mainly distributed in valleys or along streams in southern China and northern Vietnam. Liquidambar formosana is its main associated species (Peng and Zhong Citation2007). A. chinensis is rich in volatile aromatic essential oil, which can be extracted mushroom oil. It is an effective ingredient in many Chinese herbs and spices for medicinal purposes or for spices. Its wood is strong and perishable, so it can be used as an excellent medium for edible fungi (Wang et al. Citation2016). However, up to now, the research on A. chinensis mainly focuses on seedling cultivation and chemical composition determination, and there is no relevant report on the molecular level (Long et al. Citation2009). The results of this study are of great significance for molecular-assisted breeding of A. chinensis and phylogeny of Hamamelidaceae.
The materials of this experiment were collected from the fresh tender leaves of a big tree of A. chinensis in the Forest Orchid Garden of Fujian Agriculture and Forestry University (118°13′23″E, 25°38′16″N), Fuzhou, China, and its specimen was preserved in the Herbarium of Fujian Agriculture and Forestry University (FAFU20190168). The PE150 of the Illumina Hiseq XTen platform was used to construct the library of A. chinensis, generating approximately 2 Gb of data. Raw data quality was cropped by CLC Genomics Workbench version 10 (CLC Bio, Aarhus, Denmark) using default parameters. The complete chloroplast genome of A. chinensis was assembled and annotated using online tools GetOrganelle (https://github.com/Kinggerm/GetOrganelle) (Wick et al. Citation2015) and GENEIOUS version R11.15 (Kearse et al. Citation2012). The annotation results of this test were drawn by online tool OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. Citation2013). MAFFT version 7.388 (Katoh and Standley Citation2013) was used to align the sequences, and RAxML(http://epa.h-its.org/raxml/submit_single_gene) (Stamatakis Citation2014) was used to construct the phylogenetic tree. Furthermore, the chloroplast genome data of A. chinensis was uploaded to the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/, NCBI), and its number was MT193687.
The length of complete chloroplast genome sequence of A. chinensis is 160410 bp, in which the length of large single-copy (LSC) region is 88936 bp, the length of small single copy (SSC) region is 18917 bp, and the length of a pair of inverted repeats repeat (IR) region is 26274 bp. The complete chloroplast genome contains 132 genes, including 86 Coding sequence (CDS), 37 transfer ribonucleic acid (tRNA) genes, and 8 ribosomal ribonucleic acid (rRNA) genes. In addition, 26 exons were found in the whole genome of A. chinensis, and the content of GC in the complete genome is 37.9%. In order to study the relationship between A. chinensis and other Hamamelidaceae plants, the chloroplast genome data of twelve species of Hamamelidaceae (Parrotia subaequalis, Distylium tsiangii, Hamamelis mollis, Sinowilsonia henryi, Fortunearia sinensis, Corylopsis coreana, Corylopsis spicata, Loropetalum subcordatum, Chunia bucklandioides, Rhodoleia championii, L. formosana and Semiliquidambar cathayensis), two species of Fagaceae (Qercus glauca and Castanea henryi), and one species of Lauraceae (Cinnamomum camphora) have been published in the NCBI gene library were used to construct phylogenetic trees () . It shows that A. chinensis and L. formosana are most closely related, and then they are grouped with S. cathayensis, which is different from other Hamamelidaceae plants. It shows that A. chinensis, S. cathayensis and L. formosana are most closely related, which is consistent with the previous research conclusions (Shi et al. Citation2019; Zhang et al. Citation2020). Our research indirectly confirms that S. cathayensis is generated from the natural hybridization of Altingia and Liquidambar (Wu et al. Citation2010).
Figure 1. Maximum-likelihood (ML) tree based on 13 complete cp-genome in Hamamelidaceae,with Qercus glauca, Castanea henryi and Cinnamomum camphora as out group, bootstrap supp-ort value near the branch.
Acknowledgements
We are particularly grateful to editor and anonymous reviewers for their valuable comments on the manuscript.
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References
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