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Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.

Authors
  • Yoshida, Kentaro1
  • Sasaki, Eriko2
  • Kamoun, Sophien3
  • 1 Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University Kobe, Japan ; The Sainsbury Laboratory, Norwich Research Park Norwich, UK. , (Japan)
  • 2 Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Austria. , (Austria)
  • 3 The Sainsbury Laboratory, Norwich Research Park Norwich, UK.
Type
Published Article
Journal
Frontiers in Plant Science
Publisher
Frontiers Media SA
Publication Date
Jan 01, 2015
Volume
6
Pages
771–771
Identifiers
DOI: 10.3389/fpls.2015.00771
PMID: 26442080
Source
Medline
Keywords
License
Unknown

Abstract

The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

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