title: Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Blakesley
authors.forename: Nancy F
authors.initials: NF
authors.lastname: Hansen
authors.forename: Jyoti
authors.initials: J
authors.lastname: Gupta
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: McDowell
authors.forename: Baishali
authors.initials: B
authors.lastname: Maskeri
authors.forename: Beatrice B
authors.initials: BB
authors.lastname: Barnabas
authors.forename: Shelise Y
authors.initials: SY
authors.lastname: Brooks
authors.forename: Holly
authors.initials: H
authors.lastname: Coleman
authors.forename: Payam
authors.initials: P
authors.lastname: Haghighi
authors.forename: Shi-Ling
authors.initials: SL
authors.lastname: Ho
authors.forename: Karen
authors.initials: K
authors.lastname: Schandler
authors.forename: Sirintorn
authors.initials: S
authors.lastname: Stantripop
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Vogt
authors.forename: Pamela J
authors.initials: PJ
authors.lastname: Thomas
authors.forename: Gerard G
authors.initials: GG
authors.lastname: Bouffard
authors.forename: Eric D
authors.initials: ED
authors.lastname: Green
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D016678:Genome; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014714:Vertebrates / Q000235:genetics*