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United States Department of Agriculture

Agricultural Research Service

Research Project: CRANBERRY GENETIC IMPROVEMENT AND INSECT PEST MANAGEMENT

Location: Vegetable Crops Research Unit

Title: Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes

Authors
item Steffan, Shawn
item Senalik, Douglas
item Polashock, James
item Vorsa, Nicholi -
item Fajardo, Diego -
item Harbut, Rebecca -
item Zalapa, Juan

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: April 12, 2012
Publication Date: July 7, 2012
Citation: Steffan, S.A., Senalik, D.A., Polashock, J.J., Vorsa, N., Fajardo, D., Harbut, R., Zalapa, J.E. 2012. Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes [abstract]. Botany 2012 - The Next Generation. Paper. No. 1043.

Technical Abstract: The mitochondria genome of the American cranberry (Vaccinium macrocarpon Ait.) cultivar “HyRed” is being reconstructed using sequence 454 shotgun data and in silico procedures. We previously reconstructed and annotated a putative plastid cranberry genome with an approximate length of 176kb. The reliability of the sequence data was investigated by a phylogenetic analysis including 30 species outside the order Ericales (with 54 plastid genes), which placed V. macrocarpon inside the Asterids clade, as reported in other studies using single genes. The aligned putative plastid genome contained numerous rearrangements in comparison with other Asterid chloroplast genomes. Currently, we have performed homology comparisons of our cranberry 454 sequence data against all previously published plant mitochondrial genomes. We have assembled a set of eight scaffolds using 57 contigs spanning a total length of 468kb. Additionally, we are using Illumina organelle data to close gaps and confirm our putative mitochondrial genome. Cranberry organellar sequencing will be useful as a reference for further sequencing efforts in Vaccinium and related species and for future evolutionary and phylogentic studies.

Last Modified: 7/28/2014