title: Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.
abstract: The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis). Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Lauren
authors.initials: L
authors.lastname: Coombe
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: René L
authors.identifier: http://orcid.org/0000-0002-9890-2293
authors.initials: RL
authors.lastname: Warren
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: Chen
authors.initials: C
authors.lastname: Yang
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: Richard A
authors.initials: RA
authors.lastname: Moore
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 J
authors.initials: RJ
authors.lastname: Coope
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D018745:Genome, Plant; D010802:Phylogeny; D028222:Picea / Q000145:classification / Q000235:genetics*