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. 2023 Jan 27;45(2):1024-1036.
doi: 10.3390/cimb45020067.

Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants

Thuy Thi Thu Vu  1 , Lien Thi Kim Vu  2   3 , Lam Tung Le  4 , Thu Thi Mai Lo  5 , Mau Hoang Chu  1
Affiliations

Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants

Thuy Thi Thu Vu et al. Curr Issues Mol Biol. .

Abstract

Ficus simplicissima Lour. is an Asian species of fig tree in the family Moraceae. The chloroplast (cp) genome of F. simplicissima m3 was sequenced using the Pacbio sequel platform. The F. simplicissima cpDNA has a size of 160,321 bp in length, of which GC content accounts for 36.13%. The cp genome of F. simplicissima consists of a single large copy (LSC) with a size of 91,346 bp, a single small copy (SSC) with a size of 20,131 bp, and a pair of inverted repeats with a size of 24,421 to 24,423 bp. The cp genome of F. simplicissima has 127 genes, including 85 protein-coding genes, eight rRNA genes, and 34 tRNA genes; 92 simple sequence repeats and 39 long repeats were detected in the cpDNA of F. simplicissim. A comparative cp genome analysis among six species in the Ficus genus indicated that the genome structure and gene content were highly conserved. The non-coding regions show more differentiation than the coding regions, and the LSC and SSC regions show more differences than the inverted repeat regions. Phylogenetic analysis supported that F. simplicissima m3 had a close relationship with F. hirta. The complete cp genome of F. simplicissima was proposed as a chloroplast DNA barcoding for genus-level in the Moraceae family and the psbA-trnH gene region for species-level identification.

Keywords: DNA barcode; Ficus simplicissima; chloroplast genome; medicinal plants; phylogeny.

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Conflict of interest statement

All authors declare that the research was conducted in the absence of any commercial or financial relationships which could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Sample image of Ficus simplicissima Lour. m3 regenerated from seeds collected in the Thai Nguyen province (Hung Son township, Dai Tu district). (a) Plants regenerated in vitro from seeds grown in the experimental garden and (b) grown in pots, they are kept at the Department of Biology, Thai Nguyen University of Education; (c,d) fruit of F. simplicissima.
Figure 2
Figure 2
Circular map of the chloroplast genome of F. simplicissima m3. Genes located outside of the circle are transcribed counter-clockwise, while genes shown inside are transcribed clockwise. The darker gray in the inner circle indicates GC content, and the lighter gray corresponds to AT content. Genes marked with the sign ‘*’ are the gene with intron.
Figure 3
Figure 3
Number of different repeat units of SSRs.
Figure 4
Figure 4
Phylogenetic relationships among Moraceae family based on complete cp genome (a) and psbA-trnH intergenic region (b).
Figure 5
Figure 5
Contiguous positions between LSC, SSC, and IR regions of six Ficus cp genomes.
Figure 6
Figure 6
Sequence alignment of chloroplast genomes among six Ficus species. The x-axis shows the coordinates in the cp genome. The y-axis shows the recognition percentage (50% to 100%).
See this image and copyright information in PMC

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