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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: Systematic and functional implications of structural rearrangements in whole chloroplast genomes of Ericaceae

Authors
item Zalapa, Juan
item Kron, Kathy -
item Gillespie, Emily -
item Fajardo, Diego -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: April 8, 2013
Publication Date: April 10, 2013
Citation: Zalapa, J.E., Kron, K., Gillespie, E., Fajardo, D. 2013. Systematic and functional implications of structural rearrangements in whole chloroplast genomes of Ericaceae [abstract]. Association of Southeastern Biologists. Paper No. 117.

Technical Abstract: Sequence data from the chloroplast (cp) genome has been a standard source of data for phylogenetic studies of plants for more than two decades and structural rearrangements, such as gene order or modifications of the inverted repeat have been reported for some taxa using Sanger sequencing or restriction site data. With the development of Next Generation Sequencing (NGS), several whole cp genomes have been sequenced across the angiosperms. These studies have indicated that major structural rearrangements such as inversions and gene losses have occurred over the broad history of flowering plants. However, as of yet, there is a lack of targeted studies of cp genome structure within a particular family or order. We have investigated the cp genome structure of selected Ericaceae using NGS methods. Data for assembly and comparison was obtained from 454 sequencing (Vaccinium macrocarpon) and Ion Torrent PGM (Rhododendron mucronulatum) platforms. To detect possible cp gene rearrangements the data were analyzed and compared to other published genomes available in GenBank using Mauve v. 2.0 genome alignment software. Major structural differences were found within Ericaceae. These include gene losses (e.g., ycf in cranberry) and major differences in gene order among representatives of major clades (subfamilies) within Ericaceae.

Last Modified: 7/31/2014
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