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Scientific Publications on Next Generation Sequencing Applications in Plant and Algae Genetics

This page introduces a selection of scientific publications of next generation sequencing (NGS) applications in plant and algae genetics. The major fields of NGS application is crop breeding. Some publications refer to diagnostics aspects of infectious diseases in plants and algae. 

 Publications on NGS applications in Plant and Algae Genetics

Application of Genomic Tools in Plant Breeding

A.M. Pérez-de-Castro et al. 2012
This review presents and discusses advances in the development and application of genomic tools for plant breeding.
The review discusses the possible application of NGS in plant genetics. And describes the problems of WGS of plants with large and complex genomes and introduces the transcriptome sequencing as alternative and useful tool for breeding.
Different NGS technologies and its application in plant genomics are briefly introduced. The author introduce different bioinformatics solutions for NGS data analysis.
The application of microarrays as another tool for expression studies is introduced and discussed.

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Comparative whole-genome analyses of selection marker-free rice-based cholera toxin B-subunit vaccine lines and wild-type lines

In this publication, the authors investigated the development of a rice-based oral cholera vaccine named MucoRice-CTB (Cholera Toxin B-subunit) using an Agrobacterium tumefaciens–mediated co-transformation system. NGS was applied in order to study the genome-wide effects of the Agrobacterium tumefaciens transformation system. Various transfected MucoRice-CTB rice lines and wild type (WT) rice lines were compared in order to determine mutation rates and variant distribution. The distribution of the average numbers of variants along the genome was similar in MucoRice-CTB and WT. In summary, the results showed that the MucoRice-CTB lines and the WT lines were virtually identical at a genomic level.
Kashima et al 2015

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De novo transcriptome sequencing in Frankliniella occidentalis to identify genes involved in plant virus transmission and insecticide resistance

Here, the global gene expression of Frankliniella occidentalis (western flower thrips (WFT)), a common insect pest, was investigated using Illumina sequencing. Genes were annotated in order to identify those linked to insecticide resistance and plant virus transmission. The identified gene families can provide further information on the mechanism of virus entry, infection, replication, diffusion within the thrips vector, and the vector immune response. A number of putative insecticide-resistant genes were identified, including nicotinic acetylcholine receptor-related sequences. Furthermore, a genome-wide expression profiling comparison was performed between TSW virus-infected and non-infected insects in order to evaluate differences in gene expression. A functional annotation analysis of the differentially-expressed genes was also performed. In summary, the findings of this study contribute substantially to existing sequence resources related to thrips, and support research into mechanisms of insecticide resistance and improved molecular strategies for virus infection control.
Zhang et al. 2013

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Global Analysis of Chlorella variabilis NC64A mRNA Profiles during the Early Phase of Paramecium bursaria Chlorella Virus-1 Infection

Algae are a potential source of bioproducts, such as biofuels. This publication describes the first global algae transcriptome study during the early stage of virus infection. At different time points (0, 7, 14, 20, 40 and 60 min) after infection, mRNA was extracted for NGS analysis. The changes observed in host mRNA expression indicate a rapid reprogramming of the host transcription machinery after virus infection.
A rapid change in host mRNA expression following virus infection was observed as early as seven minutes post-infection. Different functional gene categories were identified that modulate expression levels after virus infection. Changes in host mRNA expression were observed, for example, in jasmonic acid and the APC/C complexes, in the shikimate pathway, and in parts of the RNA polymerase complexes.
Rowe et al. 2014
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Molecular marker database for efficient use in agricultural breeding programs

The National Agricultural Biotechnology Information Center (NABIC) constructed a web-based molecular marker database to provide information about 7,847 sequence-tagged site (STS) markers identified in 11 species using a next generation sequencing (NGS) technologies. The database uses a BioSQL database in order to cover public and private platforms. Access to the database is free. The database has three major features these are marker search, detailed viewer, and data download.
Kim et al. 2015

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Nuclear processes associated with plant immunity and pathogen susceptibility

This publication starts with a general introduction to the plant defence response against biotic threats, followed by a focus on nuclear processes associated with plant immune responses. Some of the processes discussed in more detail are nuclear transport, post translational modifications, chromatin remodelling and DNA modification, transcriptional and post transcriptional regulation, RNA interference, alternative splicing, and alternative polyadenylation. Furthermore, the authors give a brief overview of functional assays in plant genomics, such as reporter and phenocopy assays.
Motion et al 2015

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The impact and origin of copy number variations in the Oryza species

29. March 2016, BMC genomics published the study of Bai et al. "The impact and origin of copy number variations in the Oryza species".

Copy number variations (CNVs) are widespread in eukaryotic genomes. CNVs can have significant effects on gene functions and can play important roles in phenotypic variations.
In this study a high resolution CNV map of the Oryza genome was generated by next generation sequencing. Three different analysis methods were applied for CNV detection; paired-end (PE) mapping, split-read (SR) analysis, and read-depth (RD) analysis. The BreakDancer, CNVnator, and Pindel tools were used for CNV analysis. The Nipponbare genome was used as reference genome. Over 9000 deletions were detected.
The CNVs were validated by PCR experiments, compared with a microarray-based study and a BAC-based report between rice and three of its closest relatives.
Furthermore, the impact of the CNVs on gene functions was investigated. In this study 28 functional CNV genes were detected and validated. In five genes the coding regions were affected by CNVs. Functional consequences of these CNVs are not clear, it is supposed that variation effects might be rather quantitative than qualitative.
In conclusion, this CNV map will be very beneficial to study genome evolution and phenotypic variation in the Oryza species.

The publication is free available at BMC Genomics

The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm

TRIM (terminal-repeat retrotransposons in miniature) are small retrotransposons found in plants and animals.
This study describes the identification of Wukong elements, a highly conservative TRIM family found in the maize genome.
The newly-discovered Wukong elements are characterised, and their distribution in the genome is described. Furthermore, the insertion time was determined and the occurrence of Wukong elements in three germplasm groups was investigated in order to determine whether these elements can be used as molecular markers.
Liu et al 2015

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