Phylogenetic relationships among STB03, BTS02, and 30 <i>Echinochloa</i> accessions based on the nucleotide sequences of <i>trn</i>T-L-F region of the chloroplast genome.

<p>See the study by Yamaguchi <i>et al.</i> (2005) for code numbers of the 30 accessions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113657#pone.0113657-Aoki1" target="_blank">[12]</a>. The tree was constructed using NJ method. Bootstrap values with less than 50 are not shown.</p

<i>Echinochloa</i> Chloroplast Genomes: Insights into the Evolution and Taxonomic Identification of Two Weedy Species

<div><p>The genus <i>Echinochloa</i> (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus <i>Echinochloa</i>. In this study, we completed the entire chloroplast genomes of two <i>Echinochloa</i> species (<i>Echinochloa oryzicola</i> and <i>Echinochloa crus-galli</i>) based on high-throughput sequencing data from their fresh green leaves. The two <i>Echinochloa</i> chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus <i>Echinochloa</i> and <i>Panicum</i> occurred about 21.6 million years ago, whereas the divergence between <i>E. oryzicola</i> and <i>E. crus-galli</i> chloroplast genes occurred about 3.3 million years ago. The two reported <i>Echinochloa</i> chloroplast genome sequences contribute to better understanding of the diversification of this genus.</p></div

Divergence time of the genus <i>Echinochloa</i>.

<p>Divergence time was estimated using BEAST based on the complete chloroplast genomes of six species (<i>E. oryzicola</i>, <i>E. crus-galli</i>, <i>P. virgatum</i>, <i>S. bicolor</i>, <i>Z. mays</i>, and <i>O. sativa</i>). The numbers showed at nodes indicate divergence time.</p

Visualization of alignments of chloroplast genome sequences.

<p>The sequence identity was plotted with the <i>E.oryzicola</i> chloroplast genome as the reference. Sequence identity with 50%–100% is shown. Exonic regions and conserved non-coding sequences (CNS) are colored in blue and red, respectively.</p