De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

Clustering of Short Read Sequences for de novo Transcriptome Assembly

Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...

De Novo Sequencing, Assembly, and Analysis of the Root Transcriptome of Persea americana (Mill.) in Response to Phytophthora cinnamomi and Flooding

Avocado is a diploid angiosperm containing 24 chromosomes with a genome estimated to be around 920 Mb. It is an important fruit crop worldwide but is susceptible to a root rot caused by the ubiquitous oomycete Phytophthora cinnamomi. Phytophthora root rot (PRR) causes damage to the feeder roots of trees, causing necrosis. This leads to branch-dieback and eventual tree death, resulting in severe...

The Phosphite Responsive Transcriptome of Phytophthora Cinnamomi

De novo transcriptome assembly with ABySS

MOTIVATION Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. RESUL...

De Novo Assembly with the Genome Analyzer

The utility of the Illumina Genome Analyzer for a broad range of applications is evidenced by an amazing rate of publication by the research community1. In addition to human-scale resequencing2 –4 and other applications requiring a reference genome, researchers are performing de novo assembly. Several important organisms have been sequenced for the first time as a direct result of the consisten...