The complete chloroplast genome sequence of Myristica yunnanensis (Myristicaceae)

Abstract

Myristica yunnanensis is a member of Myristicaceae. The M. yunnanensis chloroplast genome is found to be 155,923 bp in length and has a base composition of A (30.04%), G (19.28%), C (19.91%), and T (30.77%). The genome contained two short inverted repeat (IRa and IRb) regions (48,004 bp) which were separated by a large single-copy (LSC) region (87,088 bp) and a small single-copy (SSC) region (20,731 bp). The genome encodes 120 unique genes, including 85 protein-coding genes, 27 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Further, complete chloroplast sequence of M. yunnanensis was aligned together with Horsfieldia pandurifolia and other Magnoliales and basal angiosperms species which have reported the complete chloroplast sequence. This complete chloroplast genome will provide valuable information for the development of DNA markers for future species resource development and phylogenetic analysis of M. yunnanensis.

Keywords:

• Myristica yunnanensis
• chloroplast genome
• Myristicaceae

Myristica yunnanensis belongs to the genus Myristica of Myristicaceae, it is a tall arbor tree and distributed only in China (Yunnan Institute of Botany 1977). For Myristicaceae, the taxonomic position of some species is controversial (Ye, 2004). Regarding M. yunnanensis, there have been no reports on molecular genetics and dispute over taxonomic status. So far, it has been analyzed on chemical constituents (Li and Ding 2001) and as the taxonomic group with the other 10 species of Myristicaceae to discuss the taxonomic position of Horsfieldia pandurifolia (Wu et al. 2015). The existing research showed that M. yunnanensis was a potential species for herbal development and volatile oil extraction. In this study, we characterized the complete chloroplast genome sequence of M. yunnanensis for phylogenetic analysis. The annotated genome sequence has been deposited in the Genbank under the accession number MK285565.

The fresh leaves of M. yunnanensis was collected in 2017 from plantation base of Yunnan Institute of Tropical Crops (YITC), Jinghong, China (100°47′E, 22°00′N), and its genome DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, Valencia, CA). A specimen of this tree was conserved in YITC. Genome sequencing was performed using Roche/454, sequencing libraries were prepared by the GS Titanium library preparation kit. The chloroplast genome assembled using CLC Genomic Workbench v3.6 (http://www.clcbio.com). The genes in the chloroplast genome were predicted using the DOGMA program (Wyman et al. 2004).

The circular genome is 155,923 bp in size, and comprises a large single-copy (LSC) region (87,088 bp), a small single-copy (SSC) region (20,731 bp), and two short inverted repeat (IRa and IRb) regions (48,004 bp). The base composition of the circular chloroplast genome is A (30.04%), G (19.28%), C (19.91%), and T (30.77%). GC content of 39.19% was observed for the whole M. yunnanensis chloroplast genome. The M. yunnanensis chloroplast genome encodes a total of 120 unique genes, including 85 protein-coding genes, 27 transfer RNA genes, and 8 ribosomal RNA genes. There were 50 genes duplicated in the IR regions. The LSC region contained 65 genes, which including 44 protein-coding genes, 18 tRNA genes, and 3 rRNA genes, whereas 6 protein-coding genes and 2 tRNA gene were including in the SSC region. The introns were detected in 11 genes, among them, psbB, rpoB, atpH, rpl23, rps19-fragment, trnQ-UUG, trnS-GGA, trnV-GAC, ndhH, trnL-CAA have 1 intron and rps7 gene has 2 introns.

To study M. yunnanensis phylogenetic relationship with the angiosperms, Horsfieldia pandurifolia of Myristicaceae (Changli et al. 2019) and other complete chloroplast genome sequences of angiosperms were download for analyses. The maximum likelihood phylogenetic was performed using MEGA X (Kumar et al. 2018) (Figure 1). A bootstrap analysis was performed on the resulting phylogenetic tree, and values were obtained after 1000 replications. The result shows that M. yunnanensis was clustered with other species and closely to Horsfieldia pandurifolia chloroplast complete genome.

Figure 1. Maximum likelihood phylogenetic tree of M. yunnanensis with 6 species based on complete chloroplast genome sequences. The gene’s accession number is listed in the figure and the data of H. pandurifolia was obtained from author.

The complete chloroplast genome of M. yunnanensis would provide information on development of molecular markers and phylogenetic analysis in the future.

Acknowledgements

We thank the editor and anonymous reviewers for providing valuable comments on the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by National Science Foundation of China [31560214].