Functional classification of assembled unigenes.

<p>Functional classification of assembled unigenes based on Gene Ontology (GO) categorisation. The results are summarised in three main GO categories: biological process, cellular component and molecular function. The x-axis indicates the subcategories, and the y-axis indicates the numbers related to the total number of GO terms present; the unigene numbers that are assigned the same GO terms are indicated on the top of the bars.</p

Summary of functional annotation of assembled unigenes.

<p>Summary of functional annotation of assembled unigenes.</p

De Novo Assembly of Transcriptome Sequencing in <i>Caragana korshinskii Kom</i>. and Characterization of EST-SSR Markers

<div><p><i>Caragana korshinskii Kom</i>. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in <i>Caragana Fabr</i>. genus. In this study, more than two billion bases of high-quality sequence of <i>C. korshinskii</i> were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp). The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO) database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%), suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in <i>Fabraceae</i>. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in <i>Caranaga Fabr</i>. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.</p></div

Comparasion of three types of motifs for EST-SSR in all the five species.

<p>*： The numbers in the bracket showed the percentage of the specific SSR motif type.</p><p>Comparasion of three types of motifs for EST-SSR in all the five species.</p

Summary of the EST-SSRs that were identified in the transcriptome.

<p>Summary of the EST-SSRs that were identified in the transcriptome.</p

SSRs motif distribution analysis in <i>Caragana korshinskii Kom</i>. and 4 supplementary materials from public database.

<p>The bars from left to right in each species represent di-, tri-, tetra-, penta- and hexa-nucleotides.</p

Summary of the <i>Caragana korshinskii</i> transcriptome.

<p>Summary of the <i>Caragana korshinskii</i> transcriptome.</p

Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG).

<p>(A) Classification based on cellular process categories, (B) classification based on environmental information processing categories, (C) classification based on genetic information processing categories, (D) classification based on metabolism categories, and (E) classification based on organismal systems categories.</p

De Novo Foliar Transcriptome of <em>Chenopodium amaranticolor</em> and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response

<div><h3>Background</h3><p>The hypersensitive response (HR) system of <em>Chenopodium</em> spp. confers broad-spectrum virus resistance. However, little knowledge exists at the genomic level for <em>Chenopodium</em>, thus impeding the advanced molecular research of this attractive feature. Hence, we took advantage of RNA-seq to survey the foliar transcriptome of <em>C. amaranticolor</em>, a <em>Chenopodium</em> species widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance.</p> <h3>Methodology and Principal Findings</h3><p>Using Illumina HiSeq™ 2000 platform, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,452 unigenes (3,847 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 61,698 sequences with a cut-off E-value above 10⁻⁵. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms, respectively. A total number of 738 resistance gene analogs (RGAs) and homology sequences of 6 key signaling proteins within the R proteins-directed signaling pathway were identified. Based on this transcriptome data, we investigated the gene expression profiles over the stage of HR induced by <em>Tobacco mosaic virus</em> and <em>Cucumber mosaic virus</em> by using digital gene expression analysis. Numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR were identified, and the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were particularly emphasized.</p> <h3>Conclusions</h3><p>To our knowledge, this study is the first description of the genetic makeup of <em>C. amaranticolor</em>, providing deep insight into the comprehensive gene expression information at transcriptional level in this species. The 738 RGAs as well as the differentially regulated genes, particularly the common genes regulated by both TMV and CMV, are suitable candidates which merit further functional characterization to dissect the molecular mechanisms and regulatory pathways of the HR-type of virus resistance in <em>Chenopodium</em>.</p> </div

GO categories of biological process (BP), cellular component (CC) and molecular function (MF) for the early water-stress responding genes (P-6h <i>vs</i>. P-0h) in <i>A</i>. <i>sparsifolia</i> primary roots.

<p>(A) the early water-stress inducible genes; (B) the early water-stress repressed genes. The right y-axis shows the number of genes in a category, and the left y-axis indicates the percentage of a specific category of genes in that main category.</p