Additional file 1: of Capturing judgement strategies in risk assessments with improved quality of clinical information: How nurses’ strategies differ from the ecological model

Clinical background. (DOCX 18 kb

Transcriptome Sequencing and <em>De Novo</em> Analysis for Ma Bamboo (<em>Dendrocalamus latiflorus</em> Munro) Using the Illumina Platform

<div><h3>Background</h3><p>Bamboo occupies an important phylogenetic node in the grass family with remarkable sizes, woodiness and a striking life history. However, limited genetic research has focused on bamboo partially because of the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bamboo research. In the present study, we performed <em>de novo</em> transcriptome sequencing for the first time to produce a comprehensive dataset for the Ma bamboo (<em>Dendrocalamus latiflorus</em> Munro).</p> <h3>Results</h3><p>The Ma bamboo transcriptome was sequenced using the Illumina paired-end sequencing technology. We produced 15,138,726 reads and assembled them into 103,354 scaffolds. A total of 68,229 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 28,165 were annotated in the Swiss-Prot database. Of these annotated unigenes, 11,921 and 10,147 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 45,649 unigenes onto 292 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. The annotated unigenes were compared against Moso bamboo, rice and millet. Unigenes that did not match any of those three sequence datasets are considered to be Ma bamboo unique. We predicted 105 unigenes encoding eight key enzymes involved in lignin biosynthesis. In addition, 621 simple sequence repeats (SSRs) were detected.</p> <h3>Conclusion</h3><p>Our data provide the most comprehensive transcriptomic resource currently available for <em>D. latiflorus</em> Munro. Candidate genes potentially involved in growth and development were identified, and those predicted to be unique to Ma bamboo are expected to give a better insight on Ma bamboo gene diversity. Numerous SSRs characterized contributed to marker development. These data constitute a new valuable resource for genomic studies on <em>D. latiflorus</em> Munro and, more generally, bamboo.</p> </div

Ma bamboo unigene similarity comparison with rice and millet and functional classification by GO analysis.

<p>(A) Similarity search of Ma bamboo sequence against rice and millet. (B) Functional classification of Ma bamboo unigenes with and without homologs with rice and millet.</p

Overview of the <i>Dendrocalamus latifloru</i>s Munro transcriptome sequencing and assembly.

<p>(A) Length distribution of <i>D. latifloru</i>s Munro transcripts. (B) Size distribution of <i>D. latifloru</i>s Munro unigenes. (C) Log-log plot showing the dependence of unigene lengths on the number of reads assembled into each unigene.</p

Summary of Illumina transcriptome assembly for <i>D. latiflorus</i> Munro.

<p>Summary of Illumina transcriptome assembly for <i>D. latiflorus</i> Munro.</p

Functional annotation of assembled sequences based on gene ontology (GO) categorization.

<p>GO analysis was performed at the level 2 for three main categories (cellular component, molecular function and biological process).</p

Number of bamboo FL-cDNAs and number of genes found in the rice genome that encode nine key enzymes in the lignin biosynthesis pathway.

a<p>The results were cited from Peng et al (2010).</p

Clusters of orthologous groups (COG) classification.

<p>In total, 10,147 of the 68,229 sequences with Nr hits were grouped into 25 COG classifications.</p

Functional annotation of the <i>D. latiflorus</i> Munro transcriptome.

<p>Functional annotation of the <i>D. latiflorus</i> Munro transcriptome.</p

Summary of simple sequence repeat (SSR) types in the <i>D. latiflorus</i> Munro transcriptome.

a<p>Number of the total SSRs detected in unigenes</p>b<p>The relative percentage of SSRs with different repeat motifs among the total SSRs</p