Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition.
BACKGROUND
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. Albeit the 4th most important food crop in the world, other than a collection of approximately 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.


RESULTS
In 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.


CONCLUSIONS
Genomic 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.
Zhu
Wei
W
Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA. zhuw@medimmune.com
Ouyang
Shu
S
Iovene
Marina
M
O'Brien
Kimberly
K
Vuong
Hue
H
Jiang
Jiming
J
Buell
C Robin
CR
D001482:Base Composition; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D017124:Conserved Sequence; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D023061:Gene Order; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D018551:Solanum lycopersicum / Q000235:genetics*; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D011198:Solanum tuberosum / Q000235:genetics*; D013045:Species Specificity; D016615:Telomere / Q000235:genetics
D018744:DNA, Plant