Abstract
BackgroundRice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data.ResultsTo facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies.ConclusionAnalysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences revealed by optical maps constructed from a broad range of rice subspecies and varieties.
Highlights
Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops
We show that a high-resolution physical map based on the direct analysis of genomic DNA, spans existing sequence physical gaps, validates the genome sequence assembly, characterizes gaps, corrects sequence misassemblies, and creates a physical scaffold for sequence finishing
The assembly step used for each bin produces a group of "consensus maps," or restriction maps comprising all significant restriction enzyme cleavage sites found within their respective contigs
Summary
Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Several genome centres have established very effective "pipelines" for the sequencing of entire genomes, often using a mixed strategy drawing data from mapped clones and whole genome shotgun efforts [1]. Such pipelines are rapidly evolving through the incorporation of new, high-throughput sequencing platforms, that obviate conventional clone libraries, or Sanger sequencing chemistries [2,3], but yield sequence reads of limited length. The main issues will likely center on the validation of "strategically" unfinished genome sequences and comprehensive description of genome structure These issues become acute when sequenced genomes are selected from nascently described organisms lacking genetic resources or an associated scientific community. Future comparative studies could suffer from sequencing errors, and not fully discern structural variation – a major feature of genome evolution and a source of disease genotypes
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