title: Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.
abstract: The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: René L
authors.initials: RL
authors.lastname: Warren
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Ewan A
authors.initials: EA
authors.lastname: Gibb
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Vandervalk
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Hamid
authors.initials: H
authors.lastname: Mohamadi
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Justin
authors.initials: J
authors.lastname: Chu
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Anthony
authors.initials: A
authors.lastname: Raymond
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Stephen
authors.initials: S
authors.lastname: Pleasance
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Robin
authors.initials: R
authors.lastname: Coope
authors.affiliation: School of Molecular Biosciences, Washington State University.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Wildung
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Carol E
authors.initials: CE
authors.lastname: Ritland
authors.affiliation: Department of Forest and Environmental Genomics, Université Laval, Québec, QC, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada Department of Botany, University of British Columbia, Vancouver, BC, Canada bohlmann@msl.ubc.ca ibirol@bcgsc.ca.
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada Department of Computer Science, University of British Columbia, Vancouver, BC, Canada bohlmann@msl.ubc.ca ibirol@bcgsc.ca.
authors.forename: Inanç
authors.initials: I
authors.lastname: Birol
mesh_terms: D001483:Base Sequence; D020451:Contig Mapping; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D028222:Picea / Q000235:genetics*
keywords: ABySS; genome assembly; gymnosperms; organelle; sequencing; white spruce