Limits...
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

NG graphs of the three assemblies in scaffold length (a) and contig length (b). The y-axis indicates the calculated NG contig/scaffold length (NG1 through NG100, see text for detail) in each assembled genome. The vertical line indicates the NG50 contig/scaffold length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4663752&req=5

f1: NG graphs of the three assemblies in scaffold length (a) and contig length (b). The y-axis indicates the calculated NG contig/scaffold length (NG1 through NG100, see text for detail) in each assembled genome. The vertical line indicates the NG50 contig/scaffold length.

Mentions: In addition to N50 values, we calculated NG values (NG1 through NG100) where NG50, for example, is determined by taking the last-counted contig/scaffold size over the sum of all contig/scaffold sizes, from the longest to the shortest, until the sum reaches 50% of the estimated genome size21. The resulting “NG graph” can visualize differences in contig/scaffold lengths and coverage between the assemblies21 (Fig. 1).


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)

NG graphs of the three assemblies in scaffold length (a) and contig length (b). The y-axis indicates the calculated NG contig/scaffold length (NG1 through NG100, see text for detail) in each assembled genome. The vertical line indicates the NG50 contig/scaffold length.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: NG graphs of the three assemblies in scaffold length (a) and contig length (b). The y-axis indicates the calculated NG contig/scaffold length (NG1 through NG100, see text for detail) in each assembled genome. The vertical line indicates the NG50 contig/scaffold length.
Mentions: In addition to N50 values, we calculated NG values (NG1 through NG100) where NG50, for example, is determined by taking the last-counted contig/scaffold size over the sum of all contig/scaffold sizes, from the longest to the shortest, until the sum reaches 50% of the estimated genome size21. The resulting “NG graph” can visualize differences in contig/scaffold lengths and coverage between the assemblies21 (Fig. 1).

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