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Abstract Detail

Ericaceae: Systematics, Ecology and Evolution

Ortiz, Edgardo M. [1], Simpson, Beryl [2].

Phylogenomics and Comparative genomics of organelles in the Vaccinieae.

De novo assembly of organelles using short sequencing reads, is usually a tractable task in most Angiosperms. However, for a few taxa like the Ericaceae, the complete chloroplast sequence is particularly challenging to assemble due to the presence of long repeated motifs throughout the genome, mainly within the inverted repeats. We identified four types of repeated motifs ranging from ~300 bp to ~1200 bp that were present in 43 blueberry plastomes and provide some guidelines on how to use them in order to obtain better assemblies. The structural comparison of these plastomes revealed numerous rearrangements among the inverted repeats of several species as well as other interesting changes such as the extreme reduction of the small single copy region in two species through two different mechanisms. As for the comparison of gene content between the chloroplast and mitochondria of these species, we could only observe the loss of the ndhF gene in a single species. Finally, we performed several phylogenetic analyses, using the entire sequence of the chloroplast and mitochondrion as well as only their coding regions under several partitioning schemes. We detected contrasting phylogenetic signal among different chloroplast genes, suggesting that treating concatenated chloroplast markers as a single partition may not be the best approach for phylogenetic analysis in the tribe Vaccinieae.

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1 - Technical University Of Munich, Ecology & Ecosystem Management, Plant Biodiversity Research, Emil-Ramann Strasse 2, Freising, D-85354, Germany
2 - The University Of Texas At Austin, Integrative Biology, 205 West 24th St., Mail Stop C0930, Austin, TX, 78713.0, United States

de novo assembly
genomic repeats.

Presentation Type: Colloquium Presentations
Session: C07b, Ericaceae: Systematics, Ecology, and Evolution Part 2
Location: 114/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 1:45 PM
Number: C07b002
Abstract ID:964
Candidate for Awards:None


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