Abstract
Myricaria prostrata is a critically endangered plant mainly distributed in Qinghai–Tibetan Plateau and adjacent areas. In the current research, we report the complete chloroplast genome sequence of M. prostrata. The total length of the genome was 155,230 bp with the GC content of 36.39%. 129 genes including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. Maximum-likelihood (ML) analysis revealed that Myricaria forms a clade with Tamarix which showed close relationship with the clade of Hololachna and Reaumuria.
Keywords: Myricaria prostrata, chloroplast genome, phylogenetic analysis
Myricaria prostrata is a prostrate shrub mainly distributed in rocky mountain slopes, sandy places in river valleys, and lakesides of high mountain regions in the Qinghai–Tibetan plateau and adjacent areas with an altitude of 4000–5200 m (Wu et al. 2007). Myricaria prostrata is an excellent species for soil and water conservation in plateau due to its characteristics of cold, drought, and salt resistance (Hai et al. 2003). However, the populations of M. prostrata is decreasing sharply on account of the snow line elevation and the lake area decreasing on the Qinghai–Tibetan plateau (Wang et al. 2009). Thus M. prostrata was listed as a critically endangered plant in the list of wild plants under key protection in Xinjiang Uygur Autonomous Region of China (http://www.iplant.cn/rep/prot/Myricaria%20prostrata). Until now, little research concerning M. prostrata was reported. In the current study, we report the completed chloroplast genome of M. prostrata based on the next-generation sequencing method. We hope that the chloroplast genome will contribute to molecular phylogeny, genetic improvement, conservation, and sustainable management for this threatened species.
Myricaria prostrata was collected from Qinghai, China (35°04′54″N, 93°01′18″E) and the specimen was deposited in the Qinghai–Tibetan Plateau Museum of Biology (Voucher specimen: chen2015179, HNWP). The total DNA was extracted from the fresh leaves through Cetyltriethyl Ammnonium Bromide (CTAB) method (Doyle 1987) with modification. Sequencing was conducted on Illumina HiSeq2500 platform (San Diego, CA, USA), and a total of 24,164,723 paired-end reads were obtained. The chloroplast genome was then assembled by SPAdes (Bankevich et al. 2012), annotated by GeSeq (Tillich et al. 2017). The total length of M. prostrata chloroplast genome (MN088847) was 155,230 bp and the GC content was 36.39%. The lengths of two inverted repeats (IR), large single copy region (LSC) and small single copy region (SSC) were 25961, 85026, 18282 bp, respectively. A total of 129 genes were predicted including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Seventeen genes including seven tRNA (tRNA-ACG, tRNA-CAA, tRNA-CAU, tRNA-GAC, tRNA-GUU, tRNA-UGC, tRNA-UUC), four rRNA (rrn4.5, rrn5, rrn16, rrn23), six protein-coding genes (ndhB, rpl2, rpl23, rps7, ycf2, ycf15) were duplicated in the IR regions. There were 18 intron-containing genes, one of which (clpP) contained two introns.
The completed chloroplast genome sequences of M. prostrata together with 13 representative species from Caryophyllales and Artemisia frigida (outgroup) were aligned by MAFFT (Kazutaka and Standley 2013) and removed ambiguously aligned sites by Gblocks (Castresana 2000). Maximum-likelihood (ML) analysis was implemented using RAxML-HPC2 on CIPRES Science Gateway (http://www.phylo.org/) based on the GTR + G + I nucleotide substitution model. Phylogenetic analysis showed that Myricaria forms a clade with Tamarix which is sister to the clade of Hololachna and Reaumuria (Figure 1).
Figure 1.
Maximum-likelihood phylogenetic tree based on 15 complete chloroplast genome sequences. Accession numbers: Agrostemma githago NC_023357.1, Artemisia frigida NC_020607.1, Drosera rotundifolia NC_029770.1, Fagopyrum esculentum NC_010776.1, Frankenia laevis MK397868.1, Frankenia pulverulenta MK397869.1, Hololachna songarica NC_041273.1, Limonium tenellum MK397871.1, Myricaria paniculata MK397878.1, Myricaria prostrata MN088847, Plumbago auriculata NC_041245.1, Reaumuria trigyna NC_041265.1, Reaumuria trigyna MK397893.1, Rheum palmatum NC_027728.1, Silene noctiflora NC_016728.1, Tamarix chinensis NC_040943.1.
Disclosure statement
No potential conflict of interest was reported by authors.
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