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

BMC Genomics

Research Article

Nancy F Hansen¹  Shelise Y Brooks²  Sirintorn Stantripop²  Jennifer C McDowell²  Shi-Ling Ho²  Baishali Maskeri²  Pamela J Thomas²  Jyoti Gupta²  Holly Coleman²  Karen Schandler²  Payam Haghighi²  Jennifer L Vogt²  Eric D Green³  Gerard G Bouffard³  Robert W Blakesley³  Beatrice B Barnabas⁴ 

[1] Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 20892, Bethesda, MD, USA;NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, 20892, Bethesda, MD, USA;NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, 20892, Bethesda, MD, USA;Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 20892, Bethesda, MD, USA;null;

关键词: Bacterial Artificial Chromosome;    Cystic Fibrosis Transmembrane Conductance Regulator;    Sequence Assembly;    Vertebrate Genome;    Finished Sequence;   

DOI  :  10.1186/1471-2164-11-21

 received in 2009-03-11, accepted in 2010-01-11,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsTo 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.ConclusionOur 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.

【 授权许可】

Unknown   
© Blakesley et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.