| Abstract Detail
Bryological and Lichenological Section/ABLS Forrest, Laura L. [1], Wickett, Norman J. [2], Goffinet, Bernard [1]. Liverwort chloroplasts – into the next generation. Next generation DNA sequencing generates vast amounts of data using massively parallel sequencing technology. We have applied this technique to total genomic DNA for a range of liverworts using the Roche 454 Titanium platform in order to recover entire chloroplast genomes. Data have so far been obtained for thalloid liverworts Haplomitrium, Treubia, Blasia, Moerckia, Fossombronia and Metzgeria, and leafy liverworts Pleurozia, Ptilidium and Scapania. Sequence data for Metzgeria and Ptilidium were generated from GS FLX Titanium traditional shotgun General Libraries, while the other 7 used the newly released Rapid Library shotgun MID protocol (which has the advantage of requiring vastly less input DNA – 5 ng instead of 5 μg). The proportion of chloroplast to non-chloroplast data varied taxon by taxon, with 3.1% of total reads BLASTing to chloroplast genes in Ptilidium but only 0.5% in Treubia. Average read lengths also varied substantially, with a mean of 334 bases in Treubia, and 424 in Scapania. Genomes have been assembled for Haplomitrium, Metzgeria and Ptilidium; of these, the annotation for Ptilidium is closest to completion. Ptilidium’s chloroplast genome consists of ca. 119,000 bases, and contains 92 protein-coding genes (including 4 rRNAs) and 30 tRNAs. Initial results suggest all the newly-assembled genomes are colinear with the previously-assembled Marchantia chloroplast, revealing a lack of chloroplast rearrangement despite considerable morphological innovation and time – for example, the divergence of Haplomitrium from the rest of the liverwort lineage has been dated back ca. 400 million years (Wikström et al. 2009, pp 146-152, The Timetree of Life, eds. Hedges & Kumar, OUP). Broader Impacts:
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1 - University of Connecticut, Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT, 06269-3043, USA
2 - Pennsylvania State University, Department of Biology, 403 Life Sciences Building, University Park, Pennsylvania, 16802, USA
Keywords:
chloroplast genome
Marchantiophyta
liverwort
Roche 454.
Presentation Type: Oral Paper:Papers for Sections
Session: 19
Location: 554A/Convention Center
Date: Monday, August 2nd, 2010
Time: 3:15 PM
Number: 19005
Abstract ID:358 |
