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Open Access Research article

An examination of targeted gene neighborhoods in strawberry

Thomas M Davis1*, Melanie E Shields2, Qian Zhang1, Denise Tombolato-Terzić5, Jeffrey L Bennetzen3, Ana C Pontaroli36, Hao Wang3, Qin Yao3, Phillip SanMiguel4 and Kevin M Folta5

Author Affiliations

1 Department of Biological Sciences, University of New Hampshire, Durham, NH 03824 USA

2 Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824 USA

3 Department of Genetics, University of Georgia, Athens, GA 30602 USA

4 Department of Horticulture and Landscape Architecture, Purdue Univ., West Lafayette, IN 47907 USA

5 Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, PO Box 110690, 1301 Fifield Hall, Gainesville, FL 32611 USA

6 Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); CC 276 (7620) Balcarce, Argentina

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BMC Plant Biology 2010, 10:81  doi:10.1186/1471-2229-10-81

Published: 4 May 2010

Abstract

Background

Strawberry (Fragaria spp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (F. vesca). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism.

Results

A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with Arabidopsis thaliana were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among ab initio predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.

Conclusions

This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.