Abstract
Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.
Highlights
With the advances of sequencing technologies, genomes of many species with biological or economic importance are currently under sequencing
Several factors further complicate whole genome sequence assembly: 1) the genome size is most often large at billion base pair range; 2) most eukaryotic genomes contain repetitive elements that are either in tandem repeats or dispersed in the genome; 3) eukaryotic genomes are loaded with long tracts of simple sequence repeats that most often pose sequencing challenges because of frequent terminations at such sites [4]
The aim of this study was to determine if physical map contig-specific sequences can be generated using the nextgen sequencing, and if such sequences can bring existing small genome sequence contigs into scaffolds corresponding to the physical map contigs
Summary
With the advances of sequencing technologies, genomes of many species with biological or economic importance are currently under sequencing. Several factors further complicate whole genome sequence assembly: 1) the genome size is most often large at billion base pair range; 2) most eukaryotic genomes contain repetitive elements that are either in tandem repeats or dispersed in the genome; 3) eukaryotic genomes are loaded with long tracts of simple sequence repeats (microsatellites) that most often pose sequencing challenges because of frequent terminations at such sites [4]. All these result in segmented genome assembly. With a large genome and short contigs, the consequence is large numbers of contigs
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