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Open Access Research article

Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

Pei Xu1, Xiaohua Wu1, Jie Luo2, Baogen Wang1, Yonghua Liu1, Jeffrey D Ehlers3, Sha Wang1, Zhongfu Lu1 and Guojing Li1*

Author affiliations

1 Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China

2 Institute of Digital Agricultural Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China

3 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124 USA

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Citation and License

BMC Genomics 2011, 12:467  doi:10.1186/1471-2164-12-467

Published: 27 September 2011

Abstract

Background

Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far.

Results

We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (Cucumis sativus) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster.

Conclusions

This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired traits.