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Abstract Detail



Phylogenomics

Carlsen, Monica Maria [1].

How much plastome data is enough to resolve the backbone of a phylogeny in a rapid radiation of species? The genus Anthurium (Araceae) as a case study.

Anthurium is an extremely diverse and strictly neotropical genus of Araceae that includes ca. 900 species. The most recent molecular phylogeny of the genus, generated using chloroplast (trnG intron, trnH-psbA and trnC-ycf6 intergenic spacers) and nuclear (CHS first intron) DNA regions, was able to distinguish 18 highly supported clades within the genus. However, relationships among these major clades were not supported, and the backbone of the phylogeny was still unresolved. In this study, we used a genome skimming technique to generate complete chloroplast genomes for 39 Anthurium species and 5 outgroups representing all major clades in the previous phylogeny, in order to investigate the amount of plastome data necessary to improve phylogenetic resolution within the genus. The chloroplast genome structure in Anthurium is relatively conserved, including a large single copy region (LSC; ca. 85-90,000 bps long), a small single copy region (SSC; ca. 20-25,000 bps long) and two identical inverted repeats (IR; ca. 20,000 bps long each), with no major inversions or rearrangements beside the split of trnH gene at the IR boundary. As expected, the use of full chloroplast genome alignments greatly increased the number of informative sites and phylogenetic support in deeper nodes of the phylogeny. However, some areas of the plastomes were identified as providing a higher number of informative characters, for example, intergenic spacers located within the LSC region, regions in close proximity to trn- coding genes, and areas associated with flanking regions of mono- or bi-nucleotide repeats. In general, genes located in the LSC region had a higher substitution rate than all other regions of the chloroplast genome. A resampling analysis of entire plastomes showed that, in the case of Anthurium, sampling of only coding regions requires a higher number of loci to resolve the genus phylogeny, compared to sampling ca. 14-20 intergenic spacers which should give enough power to do so. Therefore, sampling just a smaller number of these regions instead of whole plastomes should be sufficient to recover highly supported phylogenetic estimates.


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1 - Smithsonian Institution - National Museum of Natural History, Botany, P.O.Box 37012, Washington, DC, 20013, USA

Keywords:
Anthurium
Araceae
Genome skimming
High-throughput Sequencing
plastomes
phylogenomics.

Presentation Type: Oral Paper:Papers for Topics
Session: 73
Location: Salon 9/The Shaw Conference Centre
Date: Wednesday, July 29th, 2015
Time: 4:30 PM
Number: 73011
Abstract ID:1291
Candidate for Awards:None


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