Additional file 4: Figure S4. of Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

DMRs length analysis in each chromosome between drought and control sample (PNG 107 kb

Gene ontology (GO) enrichment of lncRNAs and KEGG enrichment of lncRNA-targets.

<p>(a) The results of GO analysis based on the differently expressed lncRNAs. (b) Main enrichments of differentially expressed lncRNAs based on Gene ontology (GO) analysis. (c) Statistical KEGG enrichment of lncRNA-targets genes using KOBAS software.</p

Alignment of GhSOS1 and SOS1 homologs of other plant species.

<p><i>Arabidopsis thaliana</i> (AtSOS1, AF256224), <i>Populus euphratica</i> (PeSOS1, DQ517530), <i>Kosteletzkya virginica</i> (KvSOS1, KJ577576) and <i>Theobroma cacao</i> (TcSOS1, XM_007045345). Identical peptides are highlighted in black, and conservative substitutions are indicated in pink. Putative GhSOS1 transmembrane domains are underlined.</p

Expression levels of stress-responsive genes (<i>RD29A</i>, <i>RD29B</i>, <i>SOS2</i> and <i>CBL1</i>) in control plants and transgenic lines.

<p>Columns marked with different lower case letters indicate a significant difference (p < 0.05) from the WT treatment.</p

The phylogenetic relationship between GhSOS1 and SOS1 from other plant species.

<p>The phylogenetic tree was constructed using MEGA ver. 5.0. The following protein sequences were used to construct of the phylogenetic tree: <i>Arabidopsis thaliana</i> AtSOS1 (AF256224) and AtNHX1 (AF510074), <i>Chrysanthemum crassum</i> CcSOS1 (AB439132), <i>Halostachys caspica</i> HcNHX1 (GU188850), <i>Helianthus tuberosus</i> HtSOS1 (KC410809), <i>Kosteletzkya virginica</i> KvSOS1 (KJ577576), <i>Limonium gmelinii</i> LgSOS1 (EU780458), <i>Oryza sativa</i> OsSOS1 (AY785147) and OsNHX1 (AB021878), <i>Populus euphratica</i> PeSOS1 (DQ517530) and PeNHX1 (FJ866610), <i>Pennisetum glaucum</i> PgNHX1 (DQ071264), <i>Salicornia brachiata</i> SbSOS1 (EU879059), <i>Salicornia europaea</i> SeNHX1 (AY131235), <i>Suaeda japonica</i> SjSOS1 (AB198179), <i>Suaeda salsa</i> SsSOS1 (KF914414), <i>Theobroma cacao</i> TcSOS1 (XM_007045345) and TcNHX1 (XM_007030729), <i>Thellungiella halophila</i> ThSOS1 (EF207775), <i>Vitis vinifera</i> VvSOS1 (CAO42437) and <i>Zoysia japonica</i> ZjNHX1 (EU333827).</p

Morphological changes of seedlings after treatments and identification of long noncoding RNAs (lncRNAs).

<p>(a) Morphological changes of cotton seedlings after drought and re-watering treatments at trefoil stage. (b) The classification of transcripts by RNA-seq. (c) The Pipeline for the identification of lncRNAs in <i>Gossypium hirsutum</i> L.</p

Transposable elements (TEs) prediction and expression patterns analysis of lncRNAs.

<p>(a) The results of repeat sequences and transposable elements (TEs) prediction. GhAt, GhDt and GhUn represent A subgroup, D subgroup and ungrouped, respectively. (b) The faction of lncRNAs with different characteristics. (c) Overall expression levels difference between lncRNAs and mRNAs. (d) Expression patterns analysis of different lncRNAs in response to the drought stress. D-C, Re_W-D means drought vs control, Re-Watering vs drought, respectively and +, - represents up-regulated and down-regulated, respectively.</p

Functional complementation of a salt-sensitive AXT3 yeast cell mutant using <i>GhSOS1</i>.

<p>AXT3 cells transformed with empty vector (pYES2) or the indicated combination of the <i>GhSOS1</i> gene were grown overnight on selective medium. Three microliters of serial dilutions (10⁻¹) were spotted onto plates containing SC-U medium (as SC but lacking uracil) supplemented with 0, 50, 100 and 150 mM NaCl. The plates were incubated at 30°C for 2–4 days.</p

Salt tolerance of <i>GhSOS1</i> transgenic <i>Arabidopsis</i> plants.

<p>(A) <i>GhSOS1</i> expression in wild type (WT) and transgenic lines (L12 and L14). (B) Responses of transgenic and WT <i>Arabidopsis</i> plants grown in pots under normal conditions and salt stress. (C) MDA content of WT and transgenic plants with or without salt stress treatments. Columns marked with different lower case letters indicate a significant difference (p < 0.05) from the WT treatment.</p