Genome sequencing from a single nematode using whole genome amplification

• Project/Area Number: 24780044
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Plant pathology
• Research Institution: University of Miyazaki
• Principal Investigator: Kikuchi Taisei 宮崎大学, 医学部, 准教授 (20353659)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 寄生虫 / ゲノム / ゲノム増幅 / 全ゲノム増幅 / 一塩基多型 / 線虫

Outline of Final Research Achievements

Genome sequencing of uncultivable parasitic nematodes is difficult because of limited amount of DNA from isolated individuals. In this study we aimed to develop a novel and efficient method to sequence genome from a single nematode using whole genome amplification (WGA) and a Next generation sequencer (NGS). Based on evaluation of existing results of WGA samples we have designed three new methods of WGA-NGS. We evaluated the three methods in terms of amplification uniformity, SNP distribution and generation of chimera DNA. We found all the methods are useful for SNP detection, but they are different in chimeric DNA generation and a combination of multiple methods can help to achieve better quality of assembly.

Research Products

• [Journal Article] Development and validation of SSR markers for the plant-parasitic nematode Subanguina moxae using genome assembly of Illumina pair-end reads (2015)
  • Author(s): T Takeuchi, M Yamaguchi, R Tanaka, M Dayi, N Ogura, T Kikuchi
  • Journal Title: Nematology Volume: -
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. (2015)
  • Author(s): Atsushi Iguchi, Sunao Iyoda, Taisei Kikuchi, Yoshitoshi Ogura, Keisuke Katsura, Makoto Ohnishi, Tetsuya Hayashi, Nicholas R Thomson
  • Journal Title: DNA Res Volume: 22 Issue: 1 Pages: 101-107
  • DOI: 10.1093/dnares/dsu043
  • Peer Reviewed / Open Access
• [Journal Article] Karyotype and reproduction mode of the rodent parasite Strongyloides venezuelensis. (2014)
  • Author(s): Hino A, Tanaka T, Takaishi M, Fujii Y, Palomares-Rius JE, Hasegawa K, Maruyama H, Kikuchi T
  • Journal Title: Parasitology Volume: 141 Issue: 13 Pages: 1736-1745
  • DOI: 10.1017/s0031182014001036
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Signatures of adaptation to plant parasitism in nematode genomes. (2014)
  • Author(s): Bird, D.M., Jones, J.T., Opperman, C.H., Kikuchi, T., and Danchin, E.G.
  • Journal Title: Parasitology Volume: 無し Issue: S1 Pages: 1-14
  • DOI: 10.1017/s0031182013002163
  • Peer Reviewed
• [Journal Article] K Daigo, T Takeuchi, T Kikuchi, N Ogura (2014)
  • Author(s): The nucleotide sequence analysis of ITS1-5.8SrDNA-ITS2 region of Subanguina moxae collected in Japan.
  • Journal Title: Nematological Research Volume: 44 Pages: 49-53
  • Peer Reviewed / Open Access
• [Journal Article] Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics (2014)
  • Author(s): Ryusei Tanaka, Akina Hino, Isheng J. Tsai, Juan Emilio Palomares-Rius1, Ayako Yoshida,Yoshitoshi Ogura, Tetsuya Hayashi, Haruhiko Maruyama, Taisei Kikuchi
  • Journal Title: PLOS ONE Volume: 9 Issue: 10 Pages: e110769-e110769
  • DOI: 10.1371/journal.pone.0110769
  • Peer Reviewed / Open Access
• [Journal Article] Comparative genomics of Taphrina fungi causing varying degrees of tumourous deformity in plants. (2014)
  • Author(s): Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T.
  • Journal Title: Genome Biology and Evolution Volume: (printing) Issue: 4 Pages: 861-872
  • DOI: 10.1093/gbe/evu067
  • Peer Reviewed / Open Access
• [Journal Article] Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi (2014)
  • Author(s): Juan E Palomares-Rius, Yuuri Hirooka, Isheng J Tsai, Hayato Masuya, Akina Hino, Natsumi Kanzaki, John T Jones, Taisei Kikuchi
  • Journal Title: BMC evolutionary biology Volume: 14 Issue: 1 Pages: 69-69
  • DOI: 10.1186/1471-2148-14-69
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. (2014)
  • Author(s): Cotton J, Lilley C, Jones L, Kikuchi T, Reid A, Thorpe P, Tsai I, Beasley H, Blok V, Cock P, et al :
  • Journal Title: Genome Biol Volume: 15(3) Issue: 3 Pages: R43-R43
  • DOI: 10.1186/gb-2014-15-3-r43
  • Peer Reviewed
• [Journal Article] Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase. (2014)
  • Author(s): Kikuchi, T., Helder, J., Cock, P.J., and Jones, J.T.
  • Journal Title: Nematology Volume: 16 Pages: 99-107
  • Peer Reviewed
• [Journal Article] Summrizing Specific Profiles in Illumina Sequencing from Whole-Genome Amplified DNA (2013)
  • Author(s): Tsai, I.J., Hunt, M., Holroyd, N., Huckvale, T., Berriman, M., and Kikuchi, T.
  • Journal Title: DNA Research Volume: in press Issue: 3 Pages: 243-254
  • DOI: 10.1093/dnares/dst054
  • Peer Reviewed
• [Journal Article] REAPR: a universal tool for genome assembly evaluation. (2013)
  • Author(s): Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., and Otto, T.D
  • Journal Title: Genome Biol Volume: 14 Issue: 5 Pages: R47-R47
  • DOI: 10.1186/gb-2013-14-5-r47
  • Peer Reviewed
• [Journal Article] Top 10 plant-parasitic nematodes in molecular plant pathology. (2013)
  • Author(s): Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jone s MGK, Kikuchi T, Manzanilla-Lopez R, Palomares-Rius JE, Wesemael WML, et al :
  • Journal Title: Mol Plant Pathol Volume: 14(9) Issue: 9 Pages: 946-961
  • DOI: 10.1111/mpp.12057
  • Peer Reviewed
• [Journal Article] The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. (2013)
  • Author(s): Laing, R., Kikuchi, T., Martinelli, A., Tsai, I., Beech, R., Redman, E., Holroyd, N., Bartley, D., Beasley, H., Britton, C., et al.
  • Journal Title: Genome Biol Volume: 14 Issue: 8 Pages: R88-R88
  • DOI: 10.1186/gb-2013-14-8-r88
  • Peer Reviewed
• [Journal Article] Omics fields of study related to plant-parasitic nematodes. (2013)
  • Author(s): Palomares-Rius, J.E., and Kikuchi, T.
  • Journal Title: Journal of Integrated OMICS Volume: 3 Pages: 1-10
  • Peer Reviewed
• [Journal Article] Secretome Analysis of the Pine Wood Nematode Bursaphelenchus xylophilus Reveals the Tangled Roots of Parasitism and Its Potential for Molecular Mimicry (2013)
  • Author(s): Shinya R, Morisaka H, Kikuchi T, Takeuchi Y, Ueda M, Futai K
  • Journal Title: PLoS ONE Volume: なし Issue: 6 Pages: e67377-e67377
  • DOI: 10.1371/journal.pone.0067377
  • Peer Reviewed / Open Access / Acknowledgement Compliant