Dataset Information

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.

SUBMITTER: Jackman SD

PROVIDER: S-EPMC4758241 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

Jackman Shaun D SD Warren René L RL Gibb Ewan A EA Vandervalk Benjamin P BP Mohamadi Hamid H Chu Justin J Raymond Anthony A Pleasance Stephen S Coope Robin R Wildung Mark R MR Ritland Carol E CE Bousquet Jean J Jones Steven J M SJ Bohlmann Joerg J Birol Inanç I

Genome biology and evolution 20151208 1

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 co ...[more]

PMID: 26645680

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Project description:Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits and the levels of several hormones and expression of gibberellin-related genes in apical internodes were also determined. Over the first 2-years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination, but in some cases, open-pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and δ13C) and more accumulation of zeatin and isopentenyladenosine. In conclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs.

Dataset Information

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

Publications

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

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