Histogram of the gene ontology classifications of annotated unigenes from the <i>W</i>. <i>ugandensis</i> transcriptome.

<p>BP, Biological process; CC, Cell component; MF, Molecular function.</p

Phylogenetic tree of terpene synthases.

<p>Phylogenetic analysis of 14 putative <i>W</i>. <i>ugandensis</i> WuTPS protein sequences with their homologs from other plants indicates that they are clustered into three main clades including: monoterpenoid synthase (WuMts), sesquiterpenoid synthase (WuSps), and diterpenoid synthase (WuDts). WarbTPS-c (ACJ46047.1, putative sesquiterpene synthase, <i>W</i>. <i>ugandensis</i>); WarbTPS-g (ACJ46048.1, putative sesquiterpene synthase, <i>W</i>. <i>ugandensis</i>); WuSps1, CL29873Contig1; WuSps2, CL29511Contig1; WuSps3, CL3178Contig1; WuSps4, CL4160Contig1; WuSps5, comp68897_c0_seq1; WuSps6, CL24969Contig1; WuSps7, CL30258Contig1; WuMts1, CL27268Contig1; WuMts2, CL27339Contig1; WuMts3, CL30385Contig1; WuMts4, CL276Contig2; WuMts5, CL1Contig9269; WuMts6, CL29966Contig1; WuMts7, CL14869Contig1; WuDts1, CL9128Contig1; WuDts2, CL28648Contig1; Citsi_Germacrene_D (XP_006494713.1, (-)-germacrene D synthase-like isoform X2, <i>Citrus sinensis</i>); Popeu_Valencene (XP_011015484.1, valencene synthase-like, <i>Populus euphratica</i>); Nelnu_Germacrene_D (XP_010258444.1, (-)-germacrene D synthase-like, <i>Nelumbo nucifera</i>); Eletr_Copaene (ADK94034.1, alpha-copaene synthase, <i>Eleutherococcus trifoliatus</i>); Gosar_Germacrene_D (KHG04103.1, (-)-germacrene D synthase, <i>Gossypium arboretum</i>); Vitvi_Germacrene_D (XP_010644711.1, (-)-germacrene D synthase, <i>Vitis vinifera</i>); Vitvi_Germacrene_A (ADR66821.1, Germacrene A synthase, <i>Vitis vinifera</i>); Citja_Elemene (BAP74389.1, delta-elemene synthase, <i>Citrus jambhiri</i>); Theca_Cadinene (EOY12648.1, Delta-cadinene synthase isozyme A, <i>Theobroma cacao</i>); Ricco_Cadinene (EEF38721.1, (+)-delta-cadinene synthase isozyme A, <i>Ricinus communis</i>); Aqusi_Guaiene (AIT75875.1, putative delta-guaiene synthase, <i>Aquilaria sinensis</i>); Vitvi_Caryophyllene (AEP17005.1, (E)-beta-caryophyllene synthase, <i>Vitis vinifera</i>); Maggr_Cubebene (ACC66281.1, beta-cubebene synthase, <i>Magnolia grandiflora</i>); Cinos_Linalool (AFK09265.1, S-(+)-linalool synthase, <i>Cinnamomum osmophloeum</i>); Nelnu_Nerolidol (XP_010248179.1, (3S,6E)-nerolidol synthase 1-like, <i>Nelumbo nucifera</i>); Vitvi_Nerolidol (XP_010646919.1, (3S,6E)-nerolidol synthase 1, chloroplastic-like isoform X1, <i>Vitis vinifera</i>); Vitvi_Linalool (ADR74212.1, (3S)-linalool/(E)-nerolidol synthase, <i>Vitis vinifera</i>); Actpo_Linalool (ADD81295.1, linalool synthase, <i>Actinidia polygama</i>); Nelnu_Ent-copalyl (XP_010277558.1, ent-copalyl diphosphate synthase, chloroplastic-like, <i>Nelumbo nucifera</i>); Theca_Ent-copalyl (XP_007050589.1, Copalyl diphosphate synthase, <i>Theobroma cacao</i>); Morno_Ent-copalyl (XP_010090409.1, Ent-copalyl diphosphate synthase, <i>Morus notabilis</i>); Gosar_Ent-copalyl (KHG01750.1, Ent-copalyl diphosphate synthase, chloroplastic, <i>Gossypium arboreum</i>); Nelnu_Ent-kaurene (XP_010260722.1, ent-kaur-16-ene synthase, chloroplastic isoform X1, <i>Nelumbo nucifera</i>); Phoda_Ent-kaurene (XP_008809130.1, ent-kaur-16-ene synthase, chloroplastic, <i>Phoenix dactylifera</i>); Ricico_Ent-kaurene (XP_002533694.1, Ent-kaurene synthase B, chloroplast precursor, <i>Ricinus communis</i>); Popeu_Ent-kaurene (XP_011014299.1, ent-kaur-16-ene synthase, chloroplastic, <i>Populus euphratica</i>); Nicta_Epi-Aristolochene (3M02.A, 5-Epi-Aristolochene Synthase, <i>Nicotiana tabacum</i>); Soltu_Vetispiradiene (Q9XJ32.1, vetispiradiene synthase 1, <i>Solanum tuberosum</i>); Litcu_Ocimene (AEJ91554.1, trans-ocimene synthase, <i>Litsea cubeba</i>); Litcu_Thujene (AEJ91555.1, alpha-thujene synthase, <i>Litsea cubeba</i>); Citli_Limonene (AAM53946.1, (+)-limonene synthase 2, <i>Citrus limon</i>); Vitvi_Ocimene/Myrcene (ADR74206.1, (E)-beta-ocimene/myrcene synthase, <i>Vitis vinifera</i>); Queil_Pinene (CAK55186.1, pinene synthase, <i>Quercus ilex</i>).</p

Summary of unigenes related to lipid and terpenoid metabolism.

<p>Summary of unigenes related to lipid and terpenoid metabolism.</p

Statistic of sequencing and <i>de novo</i> assembling of transcriptome in <i>W</i>. <i>ugandensis</i>.

<p>Statistic of sequencing and <i>de novo</i> assembling of transcriptome in <i>W</i>. <i>ugandensis</i>.</p

qRT-PCR analysises.

<p>qRT-PCRwas performed to validate the 12 differentially expressed unigenes related to terpenoid biosynthesis and/or unsaturated fatty acid metabolisms. The gene names, serial numbers and primer sequences used for qRT-PCR analysis are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135724#pone.0135724.s012" target="_blank">S8 Table</a>.</p

Statistics of annotations for assembled unigenes in <i>W</i>. <i>ugandensis</i>.

<p>^a The percent of annotated unigenes in the total 72591 assembled unigene.</p><p>Statistics of annotations for assembled unigenes in <i>W</i>. <i>ugandensis</i>.</p

The phytochemical analysis of terpenoid and fatty acid compositions in <i>W</i>. <i>ugandensis</i> bark and leaf.

<p>The relative content of monoterpenes (A), sesquiterpenes (B), and fatty acid compositions (C) were shown.</p

Putative structural genes involved in terpenoid backbone biosynthesis pathway.

<p>The values in the bracket indicate the number of unigenes in the corresponding gene families. ACCT, acetyl-CoA C-acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MVD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; IDI, isopentenyl-diphosphate delta-isomerase; GPPS, geranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase; STS, Sesquiterpenoid synthase; MTS, Monoterpenoid synthase.</p

Additional file 1: Figure S1. of Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

Fiber length of two cotton species in the early stages of fiber elongation process. (TIF 44 kb

Additional file 4: of Comparative proteomic analyses of Asian cotton ovules with attached fibers in the early stages of fiber elongation process

Annotated PMF spectra for 55 DDP spots. (PPT 728 kb