Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

Cahill, Matt J.; Köser, Claudio U.; Ross, Nicholas E.; Archer, John

doi:10.1371/journal.pone.0011518

Cited by 36 publications

(29 citation statements)

References 29 publications

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“…Recently, some studies evaluated assembly qualities of secondgeneration platforms, involving hundreds of prokaryote genomes (Cahill et al, 2010;Kingsford et al, 2010), but they are based on ideal models, including error-free reads with exact read length and sufficiently high sequencing depth. So these studies just give an upperbound on the performance of de novo assembler across different read lengths.…”

Section: Introductionmentioning

confidence: 99%

6–10× pyrosequencing is a practical approach for whole prokaryote genome studies

Jiang

Leung

2012

Gene

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Section: Introductionmentioning

confidence: 99%

6–10× pyrosequencing is a practical approach for whole prokaryote genome studies

Jiang

Leung

2012

Gene

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“…Recent advancements in transcriptome characterization, through techniques such as RNA-seq, have contributed to improved resolution of transcripts, and the subsequent ability to quantify gene expression in thousands of genes at a time (Conesa et al 2016; Kanitz et al 2015). Short read technologies, available through the numerous Illumina platforms, provide substantial depth at a low cost with reads that typically range from 50 to 300 nucleotides (nt) in length (Cahill et al 2010). In the absence of a contiguous genome assembly, researchers rely on de novo assembly techniques to organize those short reads into full-length transcripts (Moreton et al 2015).…”

mentioning

confidence: 99%

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

González-Ibeas

Martínez-García

Famula

et al. 2016

G3 Genes|Genomes|Genetics

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Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.

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“…Repetitive elements are one of the challenging issues for assembly procedures. In fact, the majority of the gaps in an assembly are caused by repeated sequences (Cahill et al, 2010). Sequencing with longer reads emerges as a good way out.…”

Section: Genome-sequence Analysis Toolsmentioning

confidence: 99%

Sequencing of plant genomes – a review

Türktaş¹,

Kurtoğlu²,

Dorado³

et al. 2015

Turk J Agric For

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The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second-and third-generation sequencing platforms called "next-generation" sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.

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Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

Cited by 36 publications

References 29 publications

6–10× pyrosequencing is a practical approach for whole prokaryote genome studies

6–10× pyrosequencing is a practical approach for whole prokaryote genome studies

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

Sequencing of plant genomes – a review

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