Additional file 4: of SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis

Figure Schematic of identification capacity analysis of 20 SSR primers in all 86 C. indicum germplasm samples. (TIF 1428 kb

Additional file 1: of SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis

Some information extracted from the doctoral thesis about phenotypic difference betwwen two C. indicum germplasms. (DOCX 2701 kb

Additional file 2: of SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis

Table Information for 86 C. indicum samples. (DOC 121 kb

Sequencing success, sequence quality, and barcode recovery of six regions.

<p>Sequencing success, sequence quality, and barcode recovery of six regions.</p

Minimum spanning tree analysis of 29 Amomi Fructus landraces based on the data set of 35 SNPs from four loci (ITS, <i>LSU</i> D1–D3, <i>rbcL</i>, and <i>matK</i>).

<p>Each circle in the tree represents a different SNP genotype (ST). The circle size is proportional to the number of landraces belonging to a ST. Numbers between circles represent the number of SNP differences. Two or more STs differing at two or fewer SNPs were regarded as a group (indicated by the gray shadow) and are connected with solid lines; those that differ by more than 2 SNPs are connected with dashed lines.</p

Geographic origins of 29 landraces of Amomi Fructus (<i>A. villosum</i> Lour., <i>A. xanthioides</i> Wall. ex Baker and <i>A. longiligulare</i> T. L. Wu) sampled in this study.

<p>The locations of samples are illustrated on the map based on longitudes and latitudes.</p

Phylogenetic tree of 29 Amomi Fructus landraces constructed by the maximum parsimony method based on 35 single nucleotide polymorphisms (SNPs) from 4 loci (ITS, <i>LSU</i> D1–D3, <i>rbcL</i>, and <i>matK</i>).

<p>Each circle in the tree represents a unique SNP genotype (ST). Accession codes for each ST are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114940#pone-0114940-g002" target="_blank">Fig. 2</a>. Numbers on the tree branches are bootstrap values from 1,000 replicates. Only bootstrap values >60% are included.</p

SNP Typing for Germplasm Identification of <i>Amomum villosum</i> Lour. Based on DNA Barcoding Markers

<div><p><i>Amomum villosum</i> Lour., produced from Yangchun, Guangdong Province, China, is a <i>Daodi</i> medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three <i>Amomum</i> species (<i>A</i>. <i>villosum</i> Lour., <i>A. xanthioides</i> Wall. ex Baker and <i>A. longiligulare</i> T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, <i>LSU</i> D1–D3, <i>matK, rbcL</i> and <i>trnH-psbA</i>) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, <i>LSU</i> D1–D3, <i>matK</i>, and <i>rbcL</i>) except <i>trnH-psbA</i>. Three ribosomal regions, namely, ITS, ITS2, and <i>LSU</i> D1–D3, contained more SNP genotypes (STs) than the plastid genes <i>rbcL</i> and <i>matK</i>. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, <i>LSU</i> D1–D3, <i>rbcL</i>, and <i>matK</i>). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1–8 and ST11) of <i>A. villosum</i> Lour., and group II was composed of 3 STs (ST16–18) of <i>A. longiligulare</i> T.L. Wu. Our results suggested that ITS and <i>LSU</i> D1–D3 should be incorporated with the core barcodes <i>rbcL</i> and <i>matK</i>. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas.</p></div

Primers and PCR reaction conditions used in this study.

<p>Primers and PCR reaction conditions used in this study.</p