ArticlePloS one2016
Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Repeated loss of plastid NDH during evolution of land plants.Annals of botany · 2026Review
- Whole-genome de novo sequencing reveals genomic variants associated with differences of sex development in SRY negative pigs.Biology of sex differences · 2024Article
- The First High-Quality Genome Assembly of Freshwater Pearl MusselInternational journal of molecular sciences · 2024Article
- Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.G3 (Bethesda, Md.) · 2023Article
- Assembly and Annotation of Red Spruce (International journal of molecular sciences · 2022Article
- Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.Genome biology and evolution · 2020Article
- Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding.Frontiers in microbiology · 2020Article
- A Reference Genome Sequence for the European Silver Fir (G3 (Bethesda, Md.) · 2019Article
- Complete Chloroplast Genome Sequence of an Engelmann Spruce (Microbiology resource announcements · 2019Article
- Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.Microbiology resource announcements · 2019Article
- Linked read technology for assembling large complex and polyploid genomes.BMC genomics · 2018Article
- Hardwood Tree Genomics: Unlocking Woody Plant Biology.Frontiers in plant science · 2018Article
- Single cell sequencing: a distinct new field.Clinical and translational medicine · 2017Review
- Genome graphs and the evolution of genome inference.Genome research · 2017Review
- International Standards for Genomes, Transcriptomes, and Metagenomes.Journal of biomolecular techniques : JBT · 2017Review
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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