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This article is part of the supplement: IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and Delivery

Open Access Poster presentation

NextGen sequence analysis of two sex-linked P. tremuloides genomic regions on chromosome 19

Matthias Fladung* and Birgit Kersten

Author Affiliations

Johann Heinrich von Thünen Institute (vTI), Institute for Forest Genetics, Sieker Landstr. 2, D-22927 Grosshansdorf, Germany

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BMC Proceedings 2011, 5(Suppl 7):P25  doi:10.1186/1753-6561-5-S7-P25


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1753-6561/5/S7/P25


Published:13 September 2011

© 2011 Fladung and Kersten; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background

Sex determination in poplars is still an open question. In the male P. tremuloides parent we identified several sex-linked SSR markers and mapped them to a central position on the male map of linkage group XIX.

Material and methods

Using DNA probes derived from these SSR markers, two BAC clones were isolated from a BAC library of the P. tremuloides male clone (Pakull B. et al., 2011, Can. J. For. Res. 41, 245-253) and further analyzed by454 sequencing (GATC Biotech AG). The generated single end reads were assembled to contigs using Newbler and Mira. The set of combined contigs (Newbler and Mira) of each BAC was subjected to scaffolding by SeqMan Pro (DNASTAR Lasergene) together with the related BAC end sequences created by Sanger sequencing (Pakull B. et al., 2011, Can. J. For. Res. 41, 245-253). The subsequent combination of the created scaffolds to BAC consensus sequences was assisted by Sanger sequencing of PCR amplified scaffold ends and connections.

Results

Mira created more contigs for both BACs than Newbler, where the N50-contig size was similar for both methods (~10,000 bp). The largest contig (38,518 bp) was assembled by Mira. Based on our strategy we already created a draft sequence of ~47,500 bp for one BAC clone. We expect a size of about 50 kb for the second BAC after finishing scaffolding.

Conclusions

Based on the final consensus sequences of both BACs, we will search for putative sex-determining regions or genes in the P. tremuloides genome and compare them with P. trichocarpa paralogs.