The complete chloroplast genome sequence of <i>Epipremnum aureum</i> and its comparative analysis among eight Araceae species

<div><p><i>Epipremnum aureum</i> is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of <i>E</i>. <i>aureum</i> by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes. Tandem repeats comprise the majority of the 43 long repetitive sequences. In addition, 111 simple sequence repeats are present, with mononucleotides being the most common type and di- and tetranucleotides being infrequent events. Positive selection pressure on <i>rps12</i> in the <i>E</i>. <i>aureum</i> chloroplast has been demonstrated via synonymous and nonsynonymous substitution rates and selection pressure sites analyses. <i>Ycf15</i> and <i>infA</i> are pseudogenes in this species. We constructed a Maximum Likelihood phylogenetic tree based on the complete chloroplast genomes of 38 species from 13 families. Those results strongly indicated that <i>E</i>. <i>aureum</i> is positioned as the sister of <i>Colocasia esculenta</i> within the Araceae family. This work may provide information for further study of the molecular phylogenetic relationships within Araceae, as well as molecular markers and breeding novel varieties by chloroplast genetic-transformation of <i>E</i>. <i>aureum</i> in particular.</p></div

The selection pressure sites of <i>rps12</i> in Araceae species identified by different methods.

<p>The selection pressure sites of <i>rps12</i> in Araceae species identified by different methods.</p

Relative synonymous codon usage (RSCU) for protein-coding genes in <i>Epipremnum aureum</i>.

<p>Relative synonymous codon usage (RSCU) for protein-coding genes in <i>Epipremnum aureum</i>.</p

Nucleotide alignments of <i>InfA</i> (A) and <i>ycf15</i> (B) in <i>Colocasia esculenta</i> (<i>Ce</i>), <i>Dieffenbachia seguine</i> (<i>Ds</i>), <i>Epipremnum aureum</i> (<i>Ea</i>), <i>Pinellia ternata</i> (<i>Pt</i>), <i>Lemna minor</i> (<i>Lm</i>), <i>Spirodela polyrhiza</i> (<i>Sp</i>), <i>Wolffia australiana</i> (<i>Wa</i>), and <i>Wolffiella lingulata</i> (<i>Wl</i>), with <i>Camellia crapnelliana</i> (<i>Cc</i>) as reference.

<p>Nucleotide alignments of <i>InfA</i> (A) and <i>ycf15</i> (B) in <i>Colocasia esculenta</i> (<i>Ce</i>), <i>Dieffenbachia seguine</i> (<i>Ds</i>), <i>Epipremnum aureum</i> (<i>Ea</i>), <i>Pinellia ternata</i> (<i>Pt</i>), <i>Lemna minor</i> (<i>Lm</i>), <i>Spirodela polyrhiza</i> (<i>Sp</i>), <i>Wolffia australiana</i> (<i>Wa</i>), and <i>Wolffiella lingulata</i> (<i>Wl</i>), with <i>Camellia crapnelliana</i> (<i>Cc</i>) as reference.</p

Gene distribution map for cp genome of <i>Epipremnum aureum</i>.

<p>Genes in inner and outer rings are transcribed in clockwise and counter-clockwise directions, respectively. Functional gene groups are indicated by different colors. For inner circles, dark grey and light grey represent GC and AT content, respectively.</p

Comparison of chloroplast sequences for <i>E</i>. <i>aureum</i> and other species within Araceae family.

<p>Comparison of chloroplast sequences for <i>E</i>. <i>aureum</i> and other species within Araceae family.</p

Maximum Likelihood (ML) tree based on coding sequences of 53 protein-coding genes from 38 species, using <i>G</i>. <i>biloba</i> as outgroup.

<p>Numbers on each node are bootstrap support values.</p

Comparison of IR boundaries among Araceae members.

<p>Comparison of IR boundaries among Araceae members.</p

Split genes and size of introns in the chloroplast genome of <i>E</i>. <i>aureum</i>.

<p>Split genes and size of introns in the chloroplast genome of <i>E</i>. <i>aureum</i>.</p

Statistical analysis of SSRs in <i>Epipremnum aureum</i> chloroplast genome.

<p>(A) Sorted by type of SSR. (B) Frequency by type. (C) Sorted by region of genome.</p