한국패류학회지 (The Korean Journal of Malacology)

한국패류학회 (The Malacological Society of Korea)
권호 표지
DOI QR코드

DOI QR Code

Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks

  • Kang, Se Won (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • Park, So Young (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • Patnaik, Bharat Bhusan (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • Hwang, Hee Ju (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • Kim, Changmu (National Institute of Biological Resources) ;
  • Kim, Soonok (National Institute of Biological Resources) ;
  • Lee, Jun Sang (Institute of Environmental Research, Kangwon National University) ;
  • Han, Yeon Soo (College of Agriculture and Life Science, Chonnam National University) ;
  • Lee, Yong Seok (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
  • 투고 : 2015.09.20
  • 심사 : 2015.09.30
  • 발행 : 2015.09.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

키워드

참고문헌

  1. Baker, M. (2010) Next-generation sequencing: adjusting to data overload. Nature Methods, 7: 495-499. https://doi.org/10.1038/nmeth0710-495
  2. Bao, H., Guo, H., Wang, J., Zhou, R., Lu, X. and Shi, S. (2009) MapView: visualization of short reads alignment on a desktop computer. Bioinformatics, 25: 1554-1555. https://doi.org/10.1093/bioinformatics/btp255
  3. Harrison, N. and Kidner, C.A. (2011) Next-generation sequencing and systematics: What can a billion base pairs of DNA sequences data do to you? Taxon, 60: 1552-1566.
  4. Jeong, J.E., Kang, S.W., Hwang, H.J., Chae, S-H., Patnaik, B.B., Han, Y.S., Lee, J.B., Jo, Y.H., Lee, B.L., Seog, D-H. and Lee, Y.S. (2013) Expressed sequence tags (ESTs) analysis of Tenebrio molitor larvae. Entomological Research, 43: 168-176. https://doi.org/10.1111/1748-5967.12019
  5. Jeong, J.E., Patnaik, B.B., Kang, S.W., Hwang, H-J., Park, S.Y., Wang, T.H., Park, E.B., Lee, J.B., Nam, M-M., Jo, Y.H., Han, Y.S., Lee, J-S., Park, H.S. and Lee, Y.S. (2015) Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure. Genes and Genomics. doi:10.1007/s13258-015-0334-x.
  6. Kang, S.W., Hwang, H.J., Park, S.Y., Wang, T.H., Park, E.B., Lee, T.H., Hwang, U.W., Lee, J.S., Park, H.S., Han, Y.S., Lim, C.E., Kim, S. and Lee, Y.S. (2014) Mollusks sequence database: Version II. Korean Journal of Malacology, 30: 429-431. https://doi.org/10.9710/kjm.2014.30.4.429
  7. Kim, K.M., Park, J-H., Bhattacharya, D. and Yoon, H.S. (2014) Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology, 64: 333-345. https://doi.org/10.1099/ijs.0.054221-0
  8. Lee, Y-S., Jo, Y-H., Kim, D-S., Kim, D-W., Kim, M-Y., Choi, S-H., Yon, J-O., Byun, I-S., Kang, B-R., Jeong, K-H. and Park, H-S. (2004) Construction of BLAST server for Mollusks. Korean Journal of Malacology, 20: 165-169.
  9. Mardis, E.R. (2013) Next-Generation Sequencing Platforms. Annual Review of Analytical Chemistry, 6: 287-303. https://doi.org/10.1146/annurev-anchem-062012-092628
  10. Riesgo, A., Andrade, S.C.S., Sharma, P.P., Novo, M., Perez-Porro, A.R., Vahtera, V., Gonzalez, V.L., Kawauchi, G.Y. and Giribet, G. (2012) Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Frontiers in Zoology, 9: 33. https://doi.org/10.1186/1742-9994-9-33
  11. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of National Academy of Sciences, USA, 74: 5463-5467. https://doi.org/10.1073/pnas.74.12.5463
  12. Tsiliki, G., Tsaramirsis, K. and Kossida, S. (2014) AmalgamScope: Merging annotations data across the Human genome. BioMed Research International, Article ID 893501.
  13. Zhu, Z., Niu, B., Chen, J., Wu, S., Sun, S. and Li, W. (2013) MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics, 29: 122-123. https://doi.org/10.1093/bioinformatics/bts567

피인용 문헌

  1. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery vol.11, pp.2, 2016, https://doi.org/10.1371/journal.pone.0148622
  2. Assembly, Functional Annotation, and Discovery of SSR Markers vol.2016, pp.2314-4378, 2016, https://doi.org/10.1155/2016/4169587
  3. Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers vol.291, pp.5, 2016, https://doi.org/10.1007/s00438-016-1233-9
  4. Classification and Phylogenetic Studies of Cephalopods from four countries of South-East Asia vol.32, pp.1, 2016, https://doi.org/10.9710/kjm.2016.32.1.55
  5. A Mitochondiral Cytochrome Oxidase I gene based identification of Corbicula ssp. commercially available in South Korea vol.32, pp.2, 2016, https://doi.org/10.9710/kjm.2016.32.2.127
  6. Felder, 1862 vol.46, pp.2, 2016, https://doi.org/10.1111/1748-5967.12164
  7. Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery vol.7, pp.10, 2016, https://doi.org/10.3390/genes7070035
  8. Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery vol.7, pp.12, 2016, https://doi.org/10.3390/genes7120114
  9. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing vol.16, pp.12, 2015, https://doi.org/10.3390/ijms161226213
  10. De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology vol.17, pp.3, 2016, https://doi.org/10.3390/ijms17030379
  11. Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics vol.10, pp.2, 2018, https://doi.org/10.1093/gbe/evy019
  12. ) using the Illumina platform vol.48, pp.1, 2018, https://doi.org/10.1111/1748-5967.12292
  13. Transcriptome analysis of air-breathing land slug, Incilaria fruhstorferi reveals functional insights into growth, immunity, and reproduction vol.20, pp.1, 2019, https://doi.org/10.1186/s12864-019-5526-3
  14. 연체동물 NGS 데이터 분석을 위한 PANM 데이터베이스 업데이트 (Version II) vol.32, pp.3, 2015, https://doi.org/10.9710/kjm.2016.32.3.185
  15. Transcriptome studies of the floodwater mosquito, AEDES VEXANS (Diptera: Culicidae) with potential as secondary vectors using Illumina HiSeq 4,000 sequencing vol.50, pp.12, 2015, https://doi.org/10.1111/1748-5967.12440