Sequencing Technologies and Their Use in Plant Biotechnology and Breeding

Llaca, Víctor

doi:10.5772/37918

Cited by 6 publications

(5 citation statements)

References 149 publications

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“…The differences in dye excitation profiles are recorded and translated by a computer to generate the sequence. Primary analysis software then calls nucleotides from the raw sequences, assigning a corresponding quality score at each position [6,14].…”

Section: The Development Of Sanger Sequencing For De Novo Assembly Ofmentioning

confidence: 99%

“…This approach minimized problems associated with the misassembly of highly repetitive DNA and therefore provided a better, more complete assembly in plants and other complex eukaryotic genomes. WGS projects were computationally intensive and were less effective bridging repetitive regions in complex genomes but benefited from considerably lower cost, time and logistics [14].…”

Section: The Development Of Sanger Sequencing For De Novo Assembly Ofmentioning

confidence: 99%

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Strategies for Sequence Assembly of Plant Genomes

Deschamps¹,

Llaca²

2016

Plant Genomics

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The field of plant genome assembly has greatly benefited from the development and widespread adoption of next-generation DN" sequencing platforms. Very high sequencing throughputs and low costs per nucleotide have considerably reduced the technical and budgetary constraints associated with early assembly projects done primarily with a traditional Sanger-based approach. Those improvements led to a sharp increase in the number of plant genomes being sequenced, including large and complex genomes of economically important crops. "lthough next-generation DN" sequencing has considerably improved our understanding of the overall structure and dynamics of many plant genomes, severe limitations still remain because next-generation DN" sequencing reads typically are shorter than Sanger reads. In addition, the software tools used to de novo assemble sequences are not necessarily designed to optimize the use of short reads. These cause challenges, common to many plant species with large genome sizes, high repeat contents, polyploidy and genome-wide duplications. This chapter provides an overview of historical and current methods used to sequence and assemble plant genomes, along with new solutions offered by the emergence of technologies such as single molecule sequencing and optical mapping to address the limitations of current sequence assemblies.

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Section: The Development Of Sanger Sequencing For De Novo Assembly Ofmentioning

confidence: 99%

Section: The Development Of Sanger Sequencing For De Novo Assembly Ofmentioning

confidence: 99%

Strategies for Sequence Assembly of Plant Genomes

Deschamps¹,

Llaca²

2016

Plant Genomics

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“…This is because it does not require fluorescence or chemiluminence to work and therefore does not employ the use of optics (e.g., CCD camera). 28 Substituting fluorescence detection by electric signals has numerous advantages. For one, it does not require tailored nucleotides or costly optical detection instruments.…”

Section: Reversible Terminator-based Sequencingmentioning

confidence: 99%

Plant exomics: Concepts, applications and methodologies in crop improvement

Hashmi

Shafqat

Khan

et al. 2014

Plant Signaling & Behavior

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“…In contrast to first-generation sequencing, second-and thirdgeneration technologies produce an enormous volume of sequence data at a much lower cost, making the system versatile for plenty of applications (Metzker, 2009;Llaca, 2012). Today, second-generation sequencing is extensively used in the discovery of genetic markers, gene expression profiling through mRNA sequencing, and comparative and evolutionary studies to answer a diverse set of biological questions Jia et al, 2013;Nystedt et al, 2013;Dohm et al, 2014;Sierro et al, 2014).…”

Section: Sequencing Applicationsmentioning

confidence: 99%

“…For instance, draft genomes of several crop species such as einkorn (Ling et al, 2013), as well as wheat and A. tauschii (Jia et al, 2013), were produced using the WGS approach. Apart from this, resequencing is mostly used in transcriptome profiling and SNP discovery for marker development (Llaca, 2012). Thus, a high-quality reference genome of potato was revealed utilizing the WGS approach and SNP identification was performed to compare a homozygous doubled-monoploid line with its heterozygous diploid line (Xu et al, 2011).…”

Section: Whole-genome Sequencingmentioning

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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Sequencing Technologies and Their Use in Plant Biotechnology and Breeding

Cited by 6 publications

References 149 publications

Strategies for Sequence Assembly of Plant Genomes

Strategies for Sequence Assembly of Plant Genomes

Plant exomics: Concepts, applications and methodologies in crop improvement

Sequencing of plant genomes – a review

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