Abstract
The whole chloroplast (cp) genome sequence of Bennettiodendron leprosipes has been characterized from Illumina pair-end sequencing. The complete cp genome was 157,872 bp in length containing a large single copy region (LSC) of 85,643 bp and a small single copy region (SSC) of 16,439 bp, which were separated by a pair of 27,895 bp inverted repeat regions (IRs). The genome contained 130 genes, including 86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of B. leprosipes cp genome is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.5, 30.7, and 41.9%, respectively. Further, phylogenetic analysis suggested that the location of B. leprosipes is an outgroup to the genera of Salix and Populus.
Bennettiodendron leprosipes is a species of flowering plant in the family Salicaceae. The tree is 8–12 meters high and its fruit is scarlet when it matures. It is born in a mixed forest of hillsides and valleys with an altitude of 200–1450 meters (mostly over 1000 meters). Since we know little about genomic information of B. leprosipes at present, getting the complete chloroplast genome is helpful to understand the evolutionary analysis of Salicaceae. In this study, we assembled and characterized the complete chloroplast genome sequence of B. leprosipes based on the Illumina pair-end sequencing data. The voucher specimen was collected at XiShuangBanNa Tropical Botanical Garden (101°25′E, 21°41′N) and stored at Chinese Field Herbarium.
The total genomic DNA was extracted from fresh leaves using a modified CTAB method (Doyle and Doyle Citation1987). The filtered reads were assembled by the program NOVOPlasty (Dierckxsens et al. Citation2017) for B. leprosipes using the sequenced plastome of its close relative Flacourtia indica (GenBank accession no. MG262341) as the reference. Next, the assembled plastome was annotated using Plann (Huang and Cronk 2015) and the annotation was corrected using Geneious (Kearse et al. Citation2012). In addition, the physical map of the plastome was generated using OGDRAW (Lohse et al. Citation2013). The complete plastome together with gene annotations was submitted to GenBank under the accession number of MK281360. To further investigate its phylogenetic placement, a neighbor-joining tree (Saitou and Nei Citation1987) was constructed based on complete plastome sequences of 12 seed plants. Here, DNA sequences from these 12 plastomes were first aligned using MAFFT (Katoh and Standley Citation2013) and a phylogenetic tree was then constructed using MEGA7 (Kumar et al. Citation2016) with 1000 bootstrap replicates.
Our assembled plastome of B. leprosipes is 157,872 base pairs (bp) in size, containing a large single-copy (LSC) region of 85,643 bp, a small single-copy (SSC) region of 16,439 bp, and two inverted repeat (IR) regions of 27,895 bp. In addition, the plastome possesses total of 130 genes including 86 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. Most of these genes are in a single copy, however, four rRNA genes (i.e. 4.5S, 5S, 16S, and 23S rRNA), eight protein-coding genes (i.e. ndhB, rpl2, rpl23, rps12, rps19, rps7, ycf15, and ycf2), and seven tRNA genes (i.e. trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC) occur in double copies. The overall GC-content of the whole plastome is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.5, 30.7, and 41.9%, respectively. Furthermore, the location of B. leprosipes is an outgroup to the genera of Salix and Populus with over 90% bootstrap support (). The location of some species consists of previous study (Zhang et al. Citation2018).
Figure 1. Phylogenetic relationships of 12 seed plants based on plastome sequences. Bootstrap percentages are indicated for each branch. GenBank accession numbers: Flacourtia indica (MG262341), Passiflora vitifolia (MF807947.1), Idesia polycarpa (KX229742), Itoa orientalis (MG262342), Populus tremula (KP861984.1), Populus rotundifolia (KX425853.1), Populus euphratica (KJ624919), Populus trichocarpa (EF489041), Populus wilsonii (MG262359), Salix chaenomeloides (MG262362), Salix oreinoma (MF189168.1).
The complete plastome can provide valuable information to develop highly variable DNA markers for population genetic survey, species delimitation, and other ecological and evolutionary studies. In addition, our study will benefit the study of the relationships between Salicaceae species.
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The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
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References
- Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45:e18
- Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15.
- Huang DI, Cronk Q. 2015. Plann: a command-line application for annotating plastome sequences. Appl Plant Sci. 3:1500026.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28:1647–1649.
- Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger Datasets. Mol Biol Evol. 33:1870–1874.
- Lohse M, Drechsel O, Kahlau S, Bock R. 2013. Organellar Genome DRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41:W575–W581.
- Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406–425.
- Zhang L, Xi Z, Wang M, Guo X, Ma T. 2018. Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows. Ecol Evol. 8:7817–7823.