Abstract
BackgroundThe Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses.ResultsIn this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed.ConclusionGenomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.
Highlights
The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber
For low quality and vector sequences, 140,259 sequences were generated with an average read length of 621 nucleotides representing a total of 87.14 Mb of potato genome sequence (Table 1)
We report on a large set of genomic sequences representing 10.2% of the potato genome
Summary
The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. The tuber is primarily composed of starch, it contains high levels of proteins and due to its importance as a food source, a prime focus in potato research has been tuber quality [1,2,3,4,5,6] Another key focus in potato research is disease resistance as potato is susceptible to several pathogens including Phytophthora infestans, the causal agent of late blight of potato. Genomic resources for potato have been developed including Expressed Sequence Tag (ESTs; [12,13,14]), bacterial artificial chromosome (BAC) clone libraries [15,16], microarray platforms [2,17], and a dense genetic map [18]. The PGSC is enabled by the availability of two resources, a dense genetic map for potato [18] and an anchored Amplified Fragment Length Polymorphism-fingerprinted BAC library [28]
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