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Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world.

Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H - DNA Res. (2014)

Bottom Line: Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits.Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome.Furthermore, 56 conserved synteny blocks were identified between the two species.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.

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Strategy for genome sequencing and hybrid assembly.
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DSU027F1: Strategy for genome sequencing and hybrid assembly.

Mentions: Nuclear DNA purified from the leaves of ‘Nakate-Shinkuro’ by the method of Peterson et al.26 was used for the construction of paired-end (PE; insert size of 200–300 bp) and mate-pair (MP) libraries (insert size of 2 kb) according to the standard protocol (Illumina, San Diego, CA, USA). Sequence analyses were carried out with a HiSeq 2000 sequencer (Illumina) in the PE sequencing mode (101-bases each) at Hokkaido System Science Co. Ltd, Japan. The obtained Illumina reads from PE and MP libraries were trimmed with quality scores of <10 at the 3′ termini by using fastq_quality_filter (-q 10 -p 10) and fastq_quality_trimmer (-t 10 -l 21) of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). The artefacts were removed by applying fastx_artifacts_filter of the FASTX-Toolkit. In addition, the adapter sequences in the Illumina reads were trimmed by using fastx_clipper (-M 5) of the FASTX-Toolkit. The trimmed reads of the PE and MP libraries were assembled by using SOAPdenovo v1.0527 with the default parameters. Based on the result of trial assemblies using a small fastq dataset (∼750 Mb) with various k-mer settings (i.e. k = 21, 31, 41, 45, 49, 51, 53, 55, 61, 71, and 81), k-mer size of 51 was adopted for the assembly because it resulted in the longest maximum length of scaffold. The resultant scaffolds were subjected to gap-filling with the Illumina reads by using GapCloser 1.10 (P = 31; http://soap.genomics.org.cn; Fig. 1).Figure 1.


Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world.

Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H - DNA Res. (2014)

Strategy for genome sequencing and hybrid assembly.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263298&req=5

DSU027F1: Strategy for genome sequencing and hybrid assembly.
Mentions: Nuclear DNA purified from the leaves of ‘Nakate-Shinkuro’ by the method of Peterson et al.26 was used for the construction of paired-end (PE; insert size of 200–300 bp) and mate-pair (MP) libraries (insert size of 2 kb) according to the standard protocol (Illumina, San Diego, CA, USA). Sequence analyses were carried out with a HiSeq 2000 sequencer (Illumina) in the PE sequencing mode (101-bases each) at Hokkaido System Science Co. Ltd, Japan. The obtained Illumina reads from PE and MP libraries were trimmed with quality scores of <10 at the 3′ termini by using fastq_quality_filter (-q 10 -p 10) and fastq_quality_trimmer (-t 10 -l 21) of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). The artefacts were removed by applying fastx_artifacts_filter of the FASTX-Toolkit. In addition, the adapter sequences in the Illumina reads were trimmed by using fastx_clipper (-M 5) of the FASTX-Toolkit. The trimmed reads of the PE and MP libraries were assembled by using SOAPdenovo v1.0527 with the default parameters. Based on the result of trial assemblies using a small fastq dataset (∼750 Mb) with various k-mer settings (i.e. k = 21, 31, 41, 45, 49, 51, 53, 55, 61, 71, and 81), k-mer size of 51 was adopted for the assembly because it resulted in the longest maximum length of scaffold. The resultant scaffolds were subjected to gap-filling with the Illumina reads by using GapCloser 1.10 (P = 31; http://soap.genomics.org.cn; Fig. 1).Figure 1.

Bottom Line: Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits.Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome.Furthermore, 56 conserved synteny blocks were identified between the two species.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.

Show MeSH