Abstract Detail



Revolutionizing systematics: Herbaria in the Genomics Age

Johnson, Matthew [1].

Including herbarium specimens in targeted sequencing projects for phylogenies and population genetics: data analysis challenges and solutions.

The use of sub-genome datasets has greatly improved our ability to reconstruct phylogeneies and calcualte population genetics statistcs using a large amount of nuclear data. The application of one method, targeted sequencing (i.e. HybSeq), also promises to revolutionize the importance of herbarium specimens. DNA extracted from herbarium specimens may be degraded and prove ineffective in traditional PCR-based sequencing, but the same extract may be used effectively in targeted sequencing. This allows for the increased availability of rare taxa and accessions from inaccessible locations for analysis. However, the nature of degraded DNA in herbarium specimens leads to unique challenges in the analysis of datasets tha include both herbarium and fresh specimens. Strategies to overcome these challenges include the use of higher-depth sequencing platforms with shorter read length, post-sequencing error correction using read mapping, and aggressively trimming alignments to remove regions of poor depth. These steps will ensure that sub-genome scale datasets that include herbarium specimens are free of systemic bias.


1 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States

Keywords:
HybSeq
HybPiper
degraded DNA
Phylogenetics
Next generation sequencing
herbarium.

Presentation Type: Colloquium Presentations
Number:
Abstract ID:224
Candidate for Awards:None


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