Dataset Information

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

ABSTRACT: The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the loss and gain of mobile genetic elements, horizontal gene transfer through recombination and genomic rearrangements. De novo assembly is the reconstruction of the underlying genome sequence, an essential step to understanding bacterial genome diversity. Here we present a high-throughput bacterial assembly and improvement pipeline that has been used to generate nearly 20?000 annotated draft genome assemblies in public databases. We demonstrate its performance on a public data set of 9404 genomes. We find all the genes used in multi-locus sequence typing schema present in 99.6?% of assembled genomes. When tested on low-, neutral- and high-GC organisms, more than 94?% of genes were present and completely intact. The pipeline has been proven to be scalable and robust with a wide variety of datasets without requiring human intervention. All of the software is available on GitHub under the GNU GPL open source license.

SUBMITTER: Page AJ

PROVIDER: S-EPMC5320598 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Robust high-throughput prokaryote <i>de novo</i> assembly and improvement pipeline for Illumina data.

Page Andrew J AJ De Silva Nishadi N Hunt Martin M Quail Michael A MA Parkhill Julian J Harris Simon R SR Otto Thomas D TD Keane Jacqueline A JA

Microbial genomics 20160825 8

The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the loss and gain of mobile genetic elements, horizontal gene transfer through recombination and genomic rearrangements. <i>De novo</i> assembly is the reconstruction of the underlying genome sequence, an e ...[more]

PMID: 28348874

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Project description:BackgroundAs an important perennial herbaceous flower, Salvia splendens possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although Salvia splendens is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for Salvia splendens through de novo high-throughput transcriptome sequencing.Methodology/principal findingsWe performed de novo transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for Salvia splendens were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).ConclusionsWe obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of Salvia splendens in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on Salvia splendens.

Dataset Information

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

Publications

Robust high-throughput prokaryote <i>de novo</i> assembly and improvement pipeline for Illumina data.

Similar Datasets

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