Research on Plant Pathogenic Fungi in the Genomics Era: From Sequence Analysis to Systems Biology

Part of the Fungal Biology book series (FUNGBIO)


Recent years have seen the development of a variety of so-called “next-generation” sequencing platforms, with several others anticipated to become available shortly. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses. Plant pathology stands to gain from the new sequencing technologies that are already making a big impact in academic research. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. The management and analysis of next-generation sequencing data requires the development of informatics tools able to assemble, map, and interpret huge quantities of relatively or extremely short nucleotide sequence data. In this review, we summarize some applications of these high-throughput sequencing methods, useful genomics and bioinformatics resources available to plant pathologists with emphasis on the associated computational and bioinformatics challenges and their solutions. The increasing availability of high-throughput technology and the reduction of costs of these technologies have moved genomics from the sequencing of a few model species to sequencing any organism that is economically important. It has opened new avenues in research, as well as poses new challenges to plant pathologists.


Horizontal Gene Transfer Fungal Community Flux Balance Analysis Fungal Genome Coalescent Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Indian Institute of Spices ResearchKozhikodeIndia
  2. 2.Division of Crop ProtectionIndian Institute of Spices ResearchKozhikodeIndia

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