Co-expression network of the <i>PgNBS</i> gene transcripts in the 4-year-old roots of different ginseng genotypes.

<p>The network was constructed at a cutoff of <i>P</i> ≤ 0.05. (A) The overall view of the network consisting of all 206 nodes indicated by colorful balls, 2,446 edges indicated by the lines between the balls and 14 clusters indicated by different colors. (B) 14 different clusters constituting the network.</p

Origin, evolution and phylogeny of the <i>PgNBS</i> gene family.

<p>(A) Phylogeny of the <i>PgNBS</i> gene family. The number nearby each clade or branch indicates the bootstrap confidence derived from 1000 replications. (B) Phylogeny of <i>P</i>. <i>ginseng</i> and selected plant species as references for inference of origin and evolution of the <i>PgNBS</i> gene family. The phylogenic tree of the species was from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181596#pone.0181596.ref025" target="_blank">25</a>]. <i>Pg</i>, <i>Panax ginseng</i>; <i>At</i>, <i>Arabidopsis thaliana</i>; <i>Ca</i>, <i>Cicer arietinum</i>; <i>Cs</i>, <i>Camelina sativa</i>; <i>Ha</i>, <i>Helianthus annuus</i>; <i>Os</i>, <i>Oryza sativa; St</i>, <i>Solanum tuberosum</i>.</p

Functional categorization of the <i>PgNBS</i> gene transcripts by gene ontology (GO).

<p>(A) Venn diagram of the <i>PgNBS</i> gene transcripts among the biological process (BP), molecular function (MF) and cellular component (CC) functional categories. (B) The <i>PgNBS</i> gene transcripts were categorized into 36 functional categories (Level 2), including seven MF functional categories, 12 CC functional categories and 17 BP functional categories.</p

Expression heatmap of the <i>PgNBS</i> gene transcripts in the roots of different year-old plants.

<p>One hundred fifty-two of the 412 NBS gene transcripts were found to express in the roots of these different year-old plants and therefore, used for the heatmap construction.</p

Conserved amino acid motifs in the NBS domain of the <i>PgNBS</i> gene proteins identified using the MEME 4.0 software.

<p>(A) Sequence logo of seven prominent conserved motifs in the NBS domain of the CC type. (B) Sequence logo of seven prominent conserved motifs in the NBS domain of the TIR type. (C) Sequence logo of six prominent conserved motifs in the NBS domain of the RPW8 type.</p

Conserved amino acid motifs in the N terminal region of the <i>PgNBS</i> gene proteins identified using the MEME 4.0 software.

<p>(A) Sequence logo of prominent conserved motifs in the N terminal region of the TIR type. (B) Sequence logo of prominent conserved motifs in the N terminal region of the RPW8 type.</p

Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, <i>Panax ginseng</i> C.A. Meyer

<div><p>Ginseng, <i>Panax ginseng</i> C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (<i>PgNBS</i> genes). Four hundred twelve <i>PgNBS</i> gene transcripts, derived from 284 gene models, were identified from the transcriptomes of 14 ginseng tissues. These genes were classified into eight types, including TNL, TN, CNL, CN, NL, N, RPW8-NL and RPW8-N. Seven conserved motifs were identified in both the Toll/interleukine-1 receptor (TIR) and coiled-coil (CC) typed genes whereas six were identified in the RPW8 typed genes. Phylogenetic analysis showed that the <i>PgNBS</i> gene family is an ancient family, with a vast majority of its genes originated before ginseng originated. In spite of their belonging to a family, the <i>PgNBS</i> genes have functionally dramatically differentiated and been categorized into numerous functional categories. The expressions of the across tissues, different aged roots and the roots of different genotypes. However, they are coordinating in expression, forming a single co-expression network. These results provide a deeper understanding of the origin, evolution and functional differentiation and expression dynamics of the NBS-encoding gene family in plants in general and in ginseng particularly, and a NBS gene toolkit useful for isolation and characterization of disease resistance genes and for enhanced disease resistance breeding in ginseng and related species.</p></div

Co-expression network of the 403 <i>PgNBS</i> gene transcripts in ginseng different tissues.

<p>The network was constructed at a cutoff of <i>P</i> ≤ 0.05. (A) The overall view of the network consisting of all 403 transcript nodes indicated by colorful balls, 21,140 interaction edges indicated by the lines between the balls and 17 clusters indicated by different colors. (B) 17 different clusters constituting the network.</p

Expression heatmap of the <i>PgNBS</i> gene transcripts in the four-year-old roots of different farmers’ cultivars (e.g., S43).

<p>Two hundred and six of the 412 NBS gene transcripts were found to express in the roots of these cultivars and therefore, used for the heatmap construction.</p

Expression of the <i>PgNBS</i> gene transcripts in ginseng.

<p>(A) Expression of the <i>PgNBS</i> gene transcripts in different numbers of tissues. (B) Expression of the <i>PgNBS</i> gene transcripts in differently-aged roots. The percentages of each part of the pie indicates the percentage of the 412 <i>PgNBS</i> gene transcripts; the number behind the percentage in each part of the pie indicates the number of the 14 tissues (A) or the number of four aged roots (B) in which the gene transcripts expressed.</p