Additional file 2: Figure S1. of Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

Percentage distribution of GC content between Spartina alterniflora and rice genes. Figure S2 Gene family distribution among the four monocots, Spartina alterniflora (Sa), Oryza sativa (Os), Sorghum bicolor (Sb) and Zea mays (Zm). The homologous genes from each monocot species were clustered to represent gene family. The number of homologous genes shared by different species is represented by gene families at intersection. Figure S3 Functional GO terms for gene families specific to Spartina alterniflora indicating coverage of different functional category genes specific to S. alterniflora. Figure S4 A histogram showing the GC content distribution in different sets of genes of Spartina alterniflora. NP, set of genes having similarity outside of poaceae; PS, poaceae specific genes; All, whole S. alterniflora transcriptome; and SS, S. alterniflora-specific genes. Figure S5 Distribution of different repeat unit size of the SSRs identified in Spartina alterniflora transcriptome. Figure S6 Distribution of different types of SSR motifs in Spartina alterniflora unigenes. Figure S7 Representative gel showing DNA profile of 13 (CP1 through CP13) Spartina alterniflora accessions produced by five SSR primers derived from the contigs. (PPTX 778 kb

Additional file 3: Table S1. of Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

Protein families found in Spartina alterniflora unigenes retrieved from Pfam database. (XLSX 229 kb

Additional file 1: of Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

The comparative analysis among Spartina alterniflora reads with reads of Salterniflora [34] and unigenes of S. pectinata [78]. (XLSX 154 kb

Principal component analysis (PCA) showing the variability (72% variance) of DEGs of cotton in pericarp and seed tissue in response to infection by toxigenic and atoxiganic strains of <i>A</i>. <i>flavus</i>.

<p>Expression of genes under different experimental conditions in seed (small oval) and pericarp (large oval) were distinct with the variability of expression higher in pericarp compared to seed. PC1, PC2 and PC3 explained 32%, 24% and 16% of the total variance.</p

Gene ontology enrichment analysis of DEGs in pericarp and seed tissues of cotton in response to infection with atoxigenic and toxigenic strains of <i>A</i>. <i>flavus</i>.

<p>The X-axis represents the GO categories and Y-axis represents enrichment in terms of P-value.</p

Gene expression profile of cotton in pericarp and seed tissue in response to <i>A</i>. <i>flavus</i> infection.

<p>A) Heatmap showing differentially expressed genes (DEGs) of cotton in response to infection by atoxigenic and toxigenic strains of <i>A</i>. <i>flavus</i>. The up-regulated genes (log2FC> = 2 and P<0.05) and down-regulated genes (log2FC< = -2 and P<0.05) are represented by blue and yellow color, respectively. Genes with similar expression profiles were clustered together by hierarchical clustering. For description of the gene names represented in the heatmaps please refer to the <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138025#pone.0138025.s002" target="_blank">S1 Table</a>, sheet 2.</b> Venn diagram shows the unique and common DEGs in pericarp (B) and seed (C) tissues under different experimental conditions.</p

Lengthwise (in bp) distribution of transcripts in RNA-Seq libraries from pericarp and seed tissues of cotton with and without <i>Aspergillus flavus</i> infection.

<p>NIP = non-inoculated pericarp, NTP = non-toxigenic pericarp, TP = toxigenic pericarp, NIS = non-inoculated seed, NTS = non-toxigenic seed, TS = toxigenic seed.</p

Heatmaps showing DEGs involved in transcriptional regulation (A), involved in oxidative burst (B) and stress response (C).

<p>The green color represents up-regulated (log2FC≥2) genes and red color represents down-regulated (log2FC≤2) genes. For gene names represented in the heatmaps please refer to the <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138025#pone.0138025.s002" target="_blank">S1 Table</a></b>.</p

Genome-Wide Transcriptome Analysis of Cotton (<i>Gossypium hirsutum</i> L.) Identifies Candidate Gene Signatures in Response to Aflatoxin Producing Fungus <i>Aspergillus flavus</i>

<div><p>Aflatoxins are toxic and potent carcinogenic metabolites produced from the fungi <i>Aspergillus flavus</i> and <i>A</i>. <i>parasiticus</i>. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. United States federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies have been proposed for controlling aflatoxin contamination, and much success has been achieved by the application of an atoxigenic strain of <i>A</i>. <i>flavus</i> in cotton, peanut and maize fields. Development of cultivars resistant to aflatoxin through overexpression of resistance associated genes and/or knocking down aflatoxin biosynthesis of <i>A</i>. <i>flavus</i> will be an effective strategy for controlling aflatoxin contamination in cotton. In this study, genome-wide transcriptome profiling was performed to identify differentially expressed genes in response to infection with both toxigenic and atoxigenic strains of <i>A</i>. <i>flavus</i> on cotton (<i>Gossypium hirsutum</i> L.) pericarp and seed. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to <i>A</i>. <i>flavus</i> infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp as compared to seed. The genes involved in auxin and cytokinin signaling were also induced. Most of the genes involved in defense response in cotton were highly induced in pericarp than in seed. The global gene expression analysis in response to fungal invasion in cotton will serve as a source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research.</p></div

Sequence and assembly statistics of six cotton libraries with/without <i>A</i>. <i>flavus</i> infection.

<p>*NIP = non-inoculated pericarp</p><p>NTP = atoxigenic pericarp; TP = toxigenic pericarp; NIS = non-inoculated seed; NTS = atoxigenic seed; TS = toxigenic seed.</p><p>Sequence and assembly statistics of six cotton libraries with/without <i>A</i>. <i>flavus</i> infection.</p