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Title: Multiplexed fragaria chloroplast genome sequencing
Author: Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N.V.;
Source: ISHS Acta Horticulturae 859: 315-321
Publication Series: Scientific Journal (JRNL)
Description: A method to sequence multiple chloroplast genomes using ultra high throughput sequencing technologies was recently described. Complete chloroplast genome sequences can resolve phylogenetic relationships at low taxonomic levels and identify informative point mutations and indels. The objective of this research was to sequence multiple Fragaria chloroplast genomes using the Illumina Genome Analyzer. Sixty-three PCR fragments from 22 species were sequenced in four multiplex sequencing runs. Plastome sequences were assembled using a combination of de novo and reference guided assembly with F. vesca ‘Hawaii 4’ providing the reference. De novo assembly resulted in plastome coverage of 43-74%, and reference guided assembly increased the plastome coverage to 76-82%. The alignment of sequenced chloroplast genomes was 96,438 bp and contained 319 parsimony-informative sites which will be useful in identifying chloroplast genome regions of high sequence variation for testing evolutionary relationships.
Keywords: high-throughput sequencing, polyploidy, reference genome, sequence alignments, microreads
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Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N.V. 2010. Multiplexed fragaria chloroplast genome sequencing. In: Basil, N.V.; Martin, R., eds. International Symposium on Molecular Markers in Horticulture. ISHS Acta Horticulturae 859: 315-321.
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