2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2017

Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Mark Fishbein, Roswitha Schmickl, Angela McDonnell, Aaron Liston. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. Appl Plant Sci, 2(9). 2014.

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PREMISE OF THE STUDY: Hyb-Seq, the combination of target enrichment
and genome skimming, allows simultaneous data collection for low-copy nuclear
genes and high-copy genomic targets for plant systematics and evolution studies. 
* METHODS AND RESULTS: Genome and transcriptome assemblies for milkweed
(Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768
genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq
of 12 individuals (10 Asclepias species and two related genera) resulted in at
least partial assembly of 92.6% of exons and 99.7% of genes and an average
assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA
cistrons were assembled using off-target reads. Phylogenomic analyses
demonstrated signal conflict between genomes. * CONCLUSIONS: The Hyb-Seq approach
enables targeted sequencing of thousands of low-copy nuclear exons and flanking
regions, as well as genome skimming of high-copy repeats and organellar genomes, 
to efficiently produce genome-scale data sets for phylogenomics.