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

Yoshida K, Sasaki E, Kamoun S - Front Plant Sci (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University Kobe, Japan ; The Sainsbury Laboratory, Norwich Research Park Norwich, UK.

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.

No MeSH data available.


Related in: MedlinePlus

Local haplotype reconstruction using the linkage method for a single diploid individual. Scheme was adapted from Sasaki et al. (2013).
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Figure 1: Local haplotype reconstruction using the linkage method for a single diploid individual. Scheme was adapted from Sasaki et al. (2013).

Mentions: In the linkage method, haplotype construction is performed using SNP linkage (Figure 1). Briefly, the current diploid algorithm is composed of two parts: local haplotype construction and local haplotype concatenation (Sasaki et al., 2013). In local haplotype construction, short DNA sequencing reads are aligned to the reference genome. Then, the reads are connected using heterozygous SNPs. In Figure 1, red and blue boxes indicate different nucleotides at heterozygous SNP positions. In this example, three blocks called local haplotypes are estimated using SNP linkage. Next, minor local haplotypes with low frequency are excluded, resulting in two local haplotypes. This process is performed on partial genomic regions called “windows”. In the second part, the “window” is moved along the chromosome. The local haplotypes obtained can then be assembled into major haplotypes. The local haplotypes are ranked based on scores calculated using their frequency in each of the windows. Based on their rank, local haplotypes are then concatenated. Finally, the two major haplotypes with the highest scores are selected. Ideally, two homologous chromosomes are generated for a diploid organism although in most cases only haplotype blocks are identified, which can range from gene size to much larger regions.


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

Yoshida K, Sasaki E, Kamoun S - Front Plant Sci (2015)

Local haplotype reconstruction using the linkage method for a single diploid individual. Scheme was adapted from Sasaki et al. (2013).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585160&req=5

Figure 1: Local haplotype reconstruction using the linkage method for a single diploid individual. Scheme was adapted from Sasaki et al. (2013).
Mentions: In the linkage method, haplotype construction is performed using SNP linkage (Figure 1). Briefly, the current diploid algorithm is composed of two parts: local haplotype construction and local haplotype concatenation (Sasaki et al., 2013). In local haplotype construction, short DNA sequencing reads are aligned to the reference genome. Then, the reads are connected using heterozygous SNPs. In Figure 1, red and blue boxes indicate different nucleotides at heterozygous SNP positions. In this example, three blocks called local haplotypes are estimated using SNP linkage. Next, minor local haplotypes with low frequency are excluded, resulting in two local haplotypes. This process is performed on partial genomic regions called “windows”. In the second part, the “window” is moved along the chromosome. The local haplotypes obtained can then be assembled into major haplotypes. The local haplotypes are ranked based on scores calculated using their frequency in each of the windows. Based on their rank, local haplotypes are then concatenated. Finally, the two major haplotypes with the highest scores are selected. Ideally, two homologous chromosomes are generated for a diploid organism although in most cases only haplotype blocks are identified, which can range from gene size to much larger regions.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University Kobe, Japan ; The Sainsbury Laboratory, Norwich Research Park Norwich, UK.

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.

No MeSH data available.


Related in: MedlinePlus