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Open Access Research article

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

Robert W Blakesley12, Nancy F Hansen2, Jyoti Gupta1, Jennifer C McDowell1, Baishali Maskeri1, Beatrice B Barnabas, Shelise Y Brooks1, Holly Coleman1, Payam Haghighi1, Shi-Ling Ho1, Karen Schandler1, Sirintorn Stantripop1, Jennifer L Vogt1, Pamela J Thomas1, NISC Comparative Sequencing Program12, Gerard G Bouffard12 and Eric D Green12*

Author affiliations

1 NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

2 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

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Citation and License

BMC Genomics 2010, 11:21  doi:10.1186/1471-2164-11-21

Published: 11 January 2010

Abstract

Background

The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.

Results

To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.

Conclusion

Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.