De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

Abstract

We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. We applied this method to two isolates of the phytopathogenic bacteria Pseudomonas syringae. Sequencing and reassembly of the well-studied tomato and Arabidopsis pathogen, Pto DC3000 , facilitated development and testing of our method. Sequencing of a distantly related rice pathogen, Por 1_6 , demonstrated our method's efficacy for de novo assembly of novel genomes. Our assembly of Por 1_6 yielded an N50 scaffold size of 531,821 bp with >75% of the predicted genome covered by scaffolds over 100,000 bp. One of the critical phenotypic differences between strains of P. syringae is the range of plant hosts they infect. This is largely determined by their complement of type III effector proteins. The genome of Por 1_6 is the first sequenced for a P. syringae isolate that is a pathogen of monocots, and, as might be predicted, its complement of type III effectors differs substantially from the previously sequenced isolates of this species. The genome of Por 1_6 helps to define an expansion of the P. syringae pangenome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species.

Analysis of Achromobactin Biosynthesis byPseudomonas syringaepv. syringae B728a

“…phaseolicola 1448A [21], P. syringae pv. oryzae 1_6 [39], and P. syringae pv. tabaci ATCC 11528 (accession no.…”

Global Phosphoproteomic Analysis Reveals Diverse Functions of Serine/Threonine/Tyrosine Phosphorylation in the Model Cyanobacterium Synechococcus sp. Strain PCC 7002

“…The Syn6803 proteins were substituted by Synechococcus 7002 proteins if the sequence similarity of reciprocal aligned sequences was not lower than 40%. 47 All identified phosphoproteins interaction network was constructed according to the Synechococcus 7002 protein−protein interaction map. This interaction networks were imported into and visualized by Cytoscape v2.8.1 (http://www.cytoscape.…”

Next‐generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation

“…Many organisms have unique features, but lack the genomic characterization that stems from advances such as genome assembly. Last year, the feasibility of de novo genome assembly using short reads was demonstrated for bacterial genomes [26,27] and we can expect that de novo assemblies of more complex genomes will follow. While good reference genomes are available for both mouse and rat, resequencing additional strains will require some degree of de novo assembly as well, as genomic segments that are lacking in a reference genome are not automatically included in de novo assemblies based on short read-based shotgun resequencing.…”