Abstract Detail

Phylogenomics

Sanderson, Michael [1], Copetti, Dario [2], Burquez, Alberto [3], Bustamante, Enriquena [4], Charboneau, Joseph [5], Eguiarte, Luis E. [6], Kumar, Sudhir [7], McMahon, Michelle [8], Steele, Kelly [9], Wing, Rod [2], Yang, Tae-Jin [10], Lee, Hyun Oh [11], Lee, Junki [10], Zwickl, Derrick [12], Wojciechowski, Martin [13].

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea, Cactaceae).

We used high throughput sequencing to assemble and annotate the plastid genome of saguaro cactus, Carnegiea gigantea (Engelm.) Britton & Rose, an icon of the Sonoran Desert and exemplar of the diverse radiation of Cactaceae. Five independent assemblies using three protocols and two plant accessions agreed to very high resolution on the structure of the genome. Saguaro's plastid genome is 113,064 nt in length, making it the smallest known plastid genome in angiosperms that are still photosynthetic. This reduction in size is due to the loss of the ancestral large inverted repeat commonly found in plants and the complete deletion of nine of 11 plastid ndh genes (and partial loss of the remaining two). One small inversion is present in the ancestral large single copy region, and the remaining differences in gene order and content can be explained by a single additional large inversion, together with multiple deletions of ndh genes. Key structural features were verified by targeted PCR and sequencing. A concatenated analysis of 42 plastid genes from saguaro and other representatives of Cactineae places saguaro in its expected phylogenetic position in Core Cactoideae I. We probed our draft nuclear and mitochondrial assemblies for copies of ndh genes and found ~100 copies, none of which are likely to be functional. Focusing just on ndhF, we inferred from read coverage mapping that most of its homologs are in the nuclear genome. A phylogenetic analysis of nuclear ndhF sequences and plastid homologs found elsewhere in Cactineae places the copies squarely within crown group Cactaceae, on long branches suggestive of typically higher nuclear substitution rates.

1 - University of Arizona, Ecology and Evolutionary Biology, Tucson, AZ, 85749, USA
2 - University of Arizona, School of Plant Sciences, Tucson, AZ, 85721, USA
3 - Universidad Nacional Autonoma De Mexico, Ecologia De La Biodiversidad, Apartado Postal 1354, Hermosillo, Sonora, 83000, Mexico
4 - UNAM, Instituto de Ecologia, Hermosillo, Sonora, Mexico
5 - University of Arizona, Ecology and Evolutionary Biology, Tucson, AZ, 85721, USA
6 - Universidad Nacional Autonoma De Mexico, UNAM, Apartado Postal 70-275, C.U., Coyoacán, México, N/A, C.P. 04510, Mexico
7 - Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA, 19122, USA
8 - University Of Arizona, Department. Of Plant Sciences, Forbes 303, PO Box 210036, Tucson, AZ, 85721, USA
9 - Arizona State University , Faculty of Science and Mathematics, College of Letters and Sciences, Mesa, AZ, 85212, USA
10 - Seoul National University, Department of Plant Science, Seoul, 151-921, Korea
11 - Phyzen Genomics Institute, Seoul, 151-836, Korea
12 - University of Arizona, Ecology and Evolutionary Biology, Tucson, AZ, 85721, US
13 - Arizona State University, School of Life Sciences, Tempe, AZ, 85287, USA

Keywords:
plastid genome
Cactaceae
phylogenomics.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PPY003
Abstract ID:799
Candidate for Awards:None