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The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.

Sakai H, Naito K, Ogiso-Tanaka E, Takahashi Y, Iseki K, Muto C, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Itoh T, Kaga A, Tomooka N - Sci Rep (2015)

Bottom Line: Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms.The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies.We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.

View Article: PubMed Central - PubMed

Affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.

ABSTRACT
Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.

No MeSH data available.


Related in: MedlinePlus

An overview of the azuki bean genome.The x-axis indicates the physical position in Mb in pseudomolecules of LG1, 2, and 5.
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f4: An overview of the azuki bean genome.The x-axis indicates the physical position in Mb in pseudomolecules of LG1, 2, and 5.

Mentions: Because we obtained a near-complete genome and a high-density genetic map, we could calculate the gene density, amount of repeats, and recombination frequency throughout the whole genome (Fig. 4, Supplementary Fig. 6). Overall, the recombination rate (cM/Mb) positively correlated with gene density, but negatively correlated with repeat density. We also calculated recombination per gene (cM/gene) because the interval lengths between genes are greatly different between gene-rich regions and repeat-rich regions. However, the obtained values were also higher in gene-rich regions than in repeat-rich regions, indicating that recombination is highly suppressed in the putative centromeric and pericentromeric regions (Fig. 4, Supplementary Fig. 6). There were also several regions with no recombination, other than the centromeric regions, suggesting some structural variation such as inversions between the azuki bean and V. nepalensis (Fig. 4, Supplementary Fig. 6).


The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.

Sakai H, Naito K, Ogiso-Tanaka E, Takahashi Y, Iseki K, Muto C, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Itoh T, Kaga A, Tomooka N - Sci Rep (2015)

An overview of the azuki bean genome.The x-axis indicates the physical position in Mb in pseudomolecules of LG1, 2, and 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663752&req=5

f4: An overview of the azuki bean genome.The x-axis indicates the physical position in Mb in pseudomolecules of LG1, 2, and 5.
Mentions: Because we obtained a near-complete genome and a high-density genetic map, we could calculate the gene density, amount of repeats, and recombination frequency throughout the whole genome (Fig. 4, Supplementary Fig. 6). Overall, the recombination rate (cM/Mb) positively correlated with gene density, but negatively correlated with repeat density. We also calculated recombination per gene (cM/gene) because the interval lengths between genes are greatly different between gene-rich regions and repeat-rich regions. However, the obtained values were also higher in gene-rich regions than in repeat-rich regions, indicating that recombination is highly suppressed in the putative centromeric and pericentromeric regions (Fig. 4, Supplementary Fig. 6). There were also several regions with no recombination, other than the centromeric regions, suggesting some structural variation such as inversions between the azuki bean and V. nepalensis (Fig. 4, Supplementary Fig. 6).

Bottom Line: Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms.The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies.We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.

View Article: PubMed Central - PubMed

Affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.

ABSTRACT
Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.

No MeSH data available.


Related in: MedlinePlus