Results of GO enrichment analyses of 6,689 conserved genes in <i>B</i>. <i>humilis</i>.

<p>GO enriched terms (<i>p</i> < 0.01) were analyzed using the Classification SuperViewer Tool and normalized (A) results are presented. (B) Venn diagram representation to show the conserved genes between <i>B</i>. <i>humilis</i> and the other five other sequenced species. Abbreviations: AT, <i>A</i>. <i>thaliana</i>; AL, <i>A</i>. <i>lyrata</i>; CR, <i>C</i>. <i>rubella</i>; TP, <i>T</i>. <i>parvula</i>; ATr, <i>A</i>. <i>trichopoda</i>.</p

A comparative transcriptomic analysis reveals the core genetic components of salt and osmotic stress responses in <i>Braya humilis</i>

<div><p><i>Braya humilis</i> is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, <i>B</i>. <i>humilis</i> is mainly found on the Qinghai—Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78.41% were annotated by BLASTing versus public protein databases. The <i>B</i>. <i>humilis</i> transcriptome is characterized by a high level of sequence conservation compared with its close relative, <i>Arabidopsis thaliana</i>. We also used reciprocal blast to identify shared orthologous genes between <i>B</i>. <i>humilis</i> and four other sequenced Brassicaceae species (i.e. <i>A</i>. <i>thaliana</i>, <i>A</i>. <i>lyrata</i>, <i>Capsella rubella</i>, and <i>Thellungiella parvula</i>). To enable precise characterization of orthologous genes, the early-diverging basal angiosperm <i>Amborella trichopoda</i> was also included. A total of 6,689 orthologous genes were identified before stricter criteria for the determination of e-values, amino acid hit lengths, and identity values was applied to further reduce this list. This led to a final list of 381 core orthologous genes for <i>B</i>. <i>humilis</i>; 39 out of these genes are involved in salt and osmotic stress responses and estimations of nonsynonymous/synonymous substitution ratios for this species and <i>A</i>. <i>thaliana</i> orthologs show that these genes are under purifying selection in <i>B</i>. <i>humilis</i>. Expression of six genes was detected in <i>B</i>. <i>humilis</i> seedlings under salt and osmotic stress treatments. Comparable expression patterns to their counterparts in <i>Arabidopsis</i> suggest that these orthologous genes are both sequence and functional conservation. The results of this study demonstrate that the environmental adaptations of <i>B</i>. <i>humilis</i> are mainly the results of preexisting genetic components. Future work will be required to characterize the expression patterns of these orthologous genes in natural populations and will provide further insights into the adaptive mechanisms underlying the wide range of <i>B</i>. <i>humilis</i> adaptations.</p></div

Characteristics of the conserved (5441 genes) and lost (560 genes) gene sets common to both <i>R</i>. <i>soongorica</i> and sand rice.

<p>At, <i>A</i>. <i>thaliana</i>; Os, <i>O</i>. <i>sativa</i>; Bv, <i>B</i>. <i>vulgaris</i>; Rs, <i>R</i>. <i>soongorica</i>; As, <i>A</i>. <i>squarrosum</i>.</p

GO biological process term annotation of the conserved and lost genes common to both <i>R</i>. <i>soongorica</i> and sand rice.

<p>The (A) 5441 conserved and (B) 560 lost genes common to both species.</p

GO biological process annotation of the species-specific conserved genes.

<p>(A) Annotation of the 1912 <i>R</i>. <i>soongorica</i> conserved genes; (B) annotation of the 723 sand rice conserved genes.</p

Expression profile of 36 <i>Arabidopsis</i> PEDG orthologs during seed development.

<p>Forty sand rice-specific conserved PEDGs and 36 corresponding <i>Arabidopsis</i> genes showed specific probes on the microarray.</p

Summary of unigene annotations within the <i>B</i>. <i>humilis</i> transcriptome.

<p>Summary of unigene annotations within the <i>B</i>. <i>humilis</i> transcriptome.</p

Analyses of the <i>B</i>. <i>humilis</i> trancriptome.

<p>(A) Histogram to show the length distribution of assembled unigenes. (B) Distribution of GC content in unigenes. (C) Length distribution of annotated and un-annotated unigenes inferred using ln(Length). (D) Expression levels of annotated and un-annotated unigenes inferred using ln(RPKM).</p

Expression patterns of the six core stress responsive genes in <i>B</i>. <i>humilis</i>.

<p>(A) Heatmap to show six <i>Arabidopsis</i> gene expression profiles under osmotic and salt stress treatments. This graphic was created using the BAR Expression Browser [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183778#pone.0183778.ref031" target="_blank">31</a>]. The expression profiles of these six genes in response to other abiotic stresses are shown in Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183778#pone.0183778.g004" target="_blank">Fig 4</a>. (B) The transcript levels of six core stress genes in <i>B</i>. <i>humilis</i> seedlings were determined after treatments with 150 mM NaCl and 300 mM mannitol. Error bars represent ± SE.</p

Ka/Ks results of the 39 salt and osmotic stress genes in <i>B</i>. <i>humilis</i> versus <i>A</i>. <i>thaliana</i> orthologs.

<p>Ka/Ks results of the 39 salt and osmotic stress genes in <i>B</i>. <i>humilis</i> versus <i>A</i>. <i>thaliana</i> orthologs.</p