Abstract
The first complete chloroplast genome (cpDNA) sequence of Altingia yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,860 bp in length, contains a large single-copy region (LSC) of 89,162 bp and a small single-copy region (SSC) of 19,008 bp, which were separated by a pair of inverted repeat (IR) regions of 26,325 bp each. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further, the phylogenomic analysis showed that A. yunnanensis and Altingia excelsa clustered in a clade in Saxifragales order.
Keywords: Altingia yunnanensis, chloroplast, Illumina sequencing, phylogenetic analysis
Altingia yunnanensis is the species of the genus Altingia within the family Altingiaceae. It distributes in the southeast of Yunnan (Yang et al. 1996). This species is of great significance for studying the taxonomic status of Altingia and Hamamelidaceae (Ickert-Bond et al. 2007). Altingia yunnanensis is also constructive species in the tropical rain forest of China (Xu et al. 2004). However, there have been no genomic studies on A. yunnanensis.
Herein, we reported and characterized the complete A. yunnanensis plastid genome. The GenBank accession number is MN106248. One A. yunnanensis individual (specimen number: 201807060) was collected from Puwen, Yunnan Province of China (22°25′25′′N, 101°6′31′′E). The specimen is stored at Yunnan Academy of Forestry Herbarium, Kunming, China and the accession number is YAFH0012862. DNA was extracted from its fresh leaves using DNA Plantzol Reagent (Invitrogen, Carlsbad, CA).
Paired-end reads were sequenced by using Illumina HiSeq system (Illumina, San Diego, CA). In total, about 24.5 million high-quality clean reads were generated with adaptors trimmed. Aligning, assembly, and annotation were conducted by CLC de novo assembler (CLC Bio, Aarhus, Denmark), BLAST, GeSeq (Tillich et al. 2017), and GENEIOUS v11.0.5 (Biomatters Ltd., Auckland, New Zealand). To confirm the phylogenetic position of A. yunnanensis, the other 13 species of order Saxifragales from NCBI were aligned using MAFFT v.7 (Katoh and Standley 2013). The Auto algorithm in the MAFFT alignment software was used to align the 16 complete genome sequences and the G-INS-i algorithm was used to align the partial complex sequences. The maximum likelihood (ML) bootstrap analysis was conducted using RAxML (Stamatakis 2006); bootstrap probability values were calculated from 1000 replicates. Chloranthus spicatus (EF380352) and Buxus microphylla (EF380351) were served as the out-group.
The complete A. yunnanensis plastid genome is a circular DNA molecule with the length of 160,860 bp, contains a large single-copy region (LSC) of 89,162 bp and a small single-copy region (SSC) of 19,008 bp, which were separated by a pair of inverted repeat (IR) regions of 26,325 bp each. The overall GC content of the whole genome is 37.9%, and the corresponding values of the LSC, SSC, and IR regions are 36.0, 32.2, and 43.1%, respectively. The plastid genome contained 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis showed that A. yunnanensis and Altingia excelsa clustered in a unique clade in Saxifragales order (Figure 1). The determination of the complete plastid genome sequences provided new molecular data to illuminate the order Saxifragales evolution.
Figure 1.
The maximum-likelihood tree based on the fourteen chloroplast genomes of order Saxifragales. The bootstrap value based on 1000 replicates is shown on each node.
Funding Statement
This work was supported by Yunnan Key Research and Development Project in Forestry [2018BB007] and Construction project of xishuangbanna high-efficiency cultivation test and demonstration base for valuable timber tree plantation.
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Ickert-Bond SM, Pigg KB, Wen J. 2007. Comparative infructescence morphology in Altingia (Altingiaceae) and discordance between morphological and molecular phylogenies. Am J Bot. 94(7):1094–1115. [DOI] [PubMed] [Google Scholar]
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. [DOI] [PubMed] [Google Scholar]
- Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq-versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Xu JX, Ferguson DK, Li CS, Wang YF, Du NQ. 2004. Climatic and ecological implications of Late Pliocene palynoflora from Longling, Yunnan, China. Quat Int. 117(1):91–103. [Google Scholar]
- Yang SZ, Wang RR, Wang DM. 1996. A studv on forestation techniques of Altingta excelsa and A. yunnanensis. J West China for Sci. 75(2):41–49. [Google Scholar]