JackmanWarrenGibbEtAl2016

Référence

Jackman, S.D., Warren, R.L., Gibb, E.A., Vandervalk, B.P., Mohamadi, H., Chu, J., Raymond, A., Pleasance, S., Coope, R., Wildung, M.R., Ritland, C.E., Bousquet, J., Jones, S.J.M., Bohlmann, J., Birol, I. (2016) Organellar genomes of white spruce (Picea glauca): assembly and annotation. Genome Biology and Evolution, 8(1):29-41. (URL )

Résumé

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.

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@ARTICLE { JackmanWarrenGibbEtAl2016,
    AUTHOR = { Jackman, S.D. and Warren, R.L. and Gibb, E.A. and Vandervalk, B.P. and Mohamadi, H. and Chu, J. and Raymond, A. and Pleasance, S. and Coope, R. and Wildung, M.R. and Ritland, C.E. and Bousquet, J. and Jones, S.J.M. and Bohlmann, J. and Birol, I. },
    TITLE = { Organellar genomes of white spruce (Picea glauca): assembly and annotation },
    JOURNAL = { Genome Biology and Evolution },
    YEAR = { 2016 },
    VOLUME = { 8 },
    PAGES = { 29-41 },
    NUMBER = { 1 },
    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. },
    DOI = { 10.1093/gbe/evv244 },
    OWNER = { nafon9 },
    TIMESTAMP = { 2016.02.09 },
    URL = { http://gbe.oxfordjournals.org/content/8/1/29.abstract },
}

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