Abstract
Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.
Highlights
Improvement in de novo assembly of large genomes is still to be desired
The degree of assembly completion in higher organisms has often not been high; the draft genome sequences of higher organisms mostly consist of large numbers of contigs/scaffolds[1,2,3,4,5,6,7,8,9], incorrect assemblies, and/ or are missing some part of the genomes[10]
Unlike the assembly of the longer read data obtained from Sanger or 454 pyrosequencing, the massive short reads from Illumina sequencers or their alternatives are usually processed by a de Bruijn graph–based algorithm
Summary
Correspondence and requests for materials should be addressed to S.A. The difficulty in assembling and scaffolding was partly due to the material for genome assembly, which was a natural heterozygous male individual To avoid these problems, our previous report suggested that complete homozygous resources would improve the quality of genome assembly[18]. The assembler fails to disentangle the branches and bubbles and cannot determine the correct sequence connections; the assembler discontinues the sequence assembly This obstruction explains why the polymorphic genomes of wild-type individuals yielded lower quality sequence results upon genome assembly. We performed another mode of assembly, mixed assembly, in which reads from other individuals were used for scaffolding with contigs formed in the non-mixed assemblies. 230-bp PE 230-bp PE 400-bp PE 2-kb MP 5-kb MP 300-bp PE 500-bp PE 230-bp PE 2-kb MP 5-kb MP 230-bp PE
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