The draft genome of MD-2 pineapple using hybrid error correction of long reads

DNA Research

Volumn 23, Issue 5, 2016, Pages 427-439

  Redwan, Raimi M ^a   Saidin, Akzam ^b   Kumar, S V ^a  

^a UNIVERSITI MALAYSIA SABAH   (Malaysia)

^b Novocraft Technologies   (Malaysia)

Author keywords

Fruit ripening; Hybrid assembly; Pineapple; Plant genome

Indexed keywords

ETHYLENE; TRANSCRIPTOME; PLANT PROTEIN; PLANT RNA;

ARTICLE; DNA EXTRACTION; FRUIT; FRUIT RIPENING; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; PHYLOGENY; PINEAPPLE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA EXTRACTION; SEQUENCE ANALYSIS; ACCURACY; ANALYTICAL ERROR; CONTROLLED STUDY; GENE LIBRARY; GENE TECHNOLOGY; GENOME SIZE; HETEROZYGOSITY; HYBRID; PLANT GENOME; RNA SEQUENCE;

EID: 84991713156     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsw026     Document Type: Article

References (74)

1. Zanella, C. M., Janke, A., Palma-Silva, C., et al. 2012, Genetics, evolution and conservation of Bromeliaceae, Genet. Mol. Biol., 35, 1020-6.
2. Arumuganathan, K. and Earle, E. D. 1991, Nuclear DNA content of some important plant species, Plant Mol. Biol. Report., 9, 415.
3. Moore, S. 2002, Use of genomics tools to isolate key ripening genes and analyse fruit maturation in tomato, J. Exp. Bot., 53, 2023-30.
4. Cherian, S., Figueroa, C. R. and Nair, H. 2014, 'Movers and shakers' in the regulation of fruit ripening: a cross-dissection of climacteric versus non-climacteric fruit, J. Exp. Bot., 65, 4705-22.
5. Golding, J. B., Shearer, D., Wyllie, S. G. and McGlasson, W. 1998, Application of 1-MCP and propylene to identify ethylene-dependent ripening processes in mature banana fruit, Postharvest Biol. Technol., 14, 87-98.
6. Pech, J. C., Bouzayen, M. and Latché, A. 2008, Climacteric fruit ripening: ethylene-dependent and independent regulation of ripening pathways in melon fruit, Plant Sci., 175, 114-20.
7. Paul, V., Pandey, R. and Srivastava, G. C. 2012, The fading distinctions between classical patterns of ripening in climacteric and non-climacteric fruit and the ubiquity of ethylene - an overview, J. Food Sci. Technol., 49, 1-21.
8. Koia, J. H., Moyle, R. L. and Botella, J. R. 2012, Microarray analysis of gene expression profiles in ripening pineapple fruits, BMC Plant Biol., 12, 240.
9. Moyle, R., Fairbairn, D. J., Ripi, J., Crowe, M. and Botella, J. R. 2005, Developing pineapple fruit has a small transcriptome dominated by metal-lothionein, J. Exp. Bot., 56, 101-12.
10. Ong, W. D., Voo, L. Y. and Kumar, V. S. 2012, De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing, PLoS One, 7, e46937.
11. Ming, R., Van Buren, R., Wai, C. M., et al. 2015, The pineapple genome and the evolution of CAM photosynthesis, Nat. Genet., 47, 1435-42.
12. Chaisson, M. J., Huddleston, J., Dennis, M. Y., et al. 2015, Resolving the complexity of the human genome using single-molecule sequencing, Nature, 517, 608-11.
13. Hercus, C. 2015, novoLR package. Novocrarft Technology Sdn. Bhd. Kuala Lumpur, Malaysia, http://www.novocraft.com/support/download/.
14. Chan, Y. K., D'Eeckenbrugge, G. C. and Sanewski, G. M. 2003, Breeding and variety improvement. In: D. P., Bartholomew, R. E., Paull and K. G., Rohrbach, (eds), The pineapple: botany, production and uses. CAB International, Wallingford, UK, pp. 33-55.
15. Redwan, R. M., Saidin, A. and Kumar, S. V. 2015, Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae, BMC Plant Biol., 15, 196.
16. Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. and Birol, I. 2009, ABySS: a parallel assembler for short read sequence data, Genome Res., 19, 1117-23.
17. Kumar, S., Jones, M., Koutsovoulos, G., Clarke, M. and Blaxter, M. 2013, Blobology: exploring raw genome data for contaminants, symbi-onts and parasites using taxon-annotated GC-coverage plots, Front. Genet., 4, 237.
18. Price, J. C., Udall, J. A., Bodily, P. M., et al. 2012, De novo identification of 'heterotigs' towards accurate and in-phase assembly of complex plant genomes. In: Proceedings of the 2012 International Conference on Bioinformatics & Computational Biology. WORLDCOMP, pp. 144-50. Available: http://schatzlab.cshl.edu/publications/2012. Heterotig.pdf.
19. Wu, T. D. and Watanabe, C. K. 2005, GMAP: a genomic mapping and alignment program for mRNA and EST sequences, Bioinformatics, 21, 1859-75.
20. Chaisson, M. J. and Tesler, G. 2012, Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory, BMC Bioinformatics, 13, 1-18.
21. Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J. and Arvestad, L. 2014, BESST - efficient scaffolding of large fragmented assemblies, BMC Bioinformatics, 15, 1-11.
22. Boetzer, M. and Pirovano, W. 2014, SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information, BMC Bioinformatics, 15, 1-9.
23. Xue, W., Li, J. T., Zhu, Y. P., et al. 2013, L-RNA-scaffolder: scaffolding genomes with transcripts, BMC Genomics, 14, 1-14.
24. Parra, G., Bradnam, K. and Korf, I. 2007, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, 23, 1061-7.
25. Chagné, D., Crowhurst, R. N., Pindo, M., et al. 2014, The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'), PLoS One, 9, e92644.
26. Kang, Y. J., Satyawan, D., Shim, S., et al. 2015, Draft genome sequence of adzuki bean, Vigna angularis, Sci. Rep., 5, 8069.
27. Al-Dous, E. K., George, B., Al-Mahmoud, M. E., et al. 2011, De novo genome sequencing and comparative genomics of date palm (Phoenix dacty-lifera), Nat. Biotechnol., 29, 521-7.
28. Kielbasa, S. M., Wan, R., Sato, K., Kiebasa, S. M., Horton, P. and Frith, M. C. 2011, Adaptive seeds tame genomic sequence comparison. Genome Res., 21, 487-93.
29. Fass, J. 2014, COMPASS-scripts to COMpare a DNA sequence ASSembly to a trusted reference sequence, p. https://github.com/jfass/compass, last accessed in 9th June 2016.
30. De Wit, P., Pespeni, M. H., Ladner, J. T., et al. 2012, The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis, Mol. Ecol. Resour., 12, 1058-67.
31. Campbell, M. S., Law, M., Holt, C., et al. 2014, MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations, Plant Physiol., 164, 513-24.
32. Han, Y. and Wessler, S. R. 2010, MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences, Nucleic Acids Res., 38, e199.
33. Ellinghaus, D., Kurtz, S. and Willhoeft, U. 2008, LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, 9, 1-14.
34. Korf, I. 2004, Gene finding in novel genomes, BMC Bioinformatics, 5, 1-9.
35. Stanke, M., Steinkamp, R., Waack, S. and Morgenstern, B. 2004, AUGUSTUS: a web server for gene finding in eukaryotes, Nucleic Acids Res., 32, W309-12.
36. Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y. O. and Borodovsky, M. 2008, Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training, Genome Res., 18, 1979-90.
37. Pertea, G., Huang, X., Liang, F., et al. 2003, TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets, Bioinformatics, 19, 651-2.
38. Schattner, P., Brooks, A. N. and Lowe, T. M. 2005, The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucleic Acids Res., 33, W686-9.
39. Bairoch, A. and Apweiler, R. 2000, The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000, Nucleic Acids Res., 28, 45-8.
40. Zdobnov, E. M. and Apweiler, R. 2001, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, 17, 847-8.
41. Gremme, G., Steinbiss, S. and Kurtz, S. 2013, GenomeTools: a comprehensive software library for efficient processing of structured genome annotations, IEEE/ACM Trans. Comput. Biol. Bioinform., 10, 645-56.
42. Li, L., Stoeckert, C. J. Jr. and Roos, D. S. 2003, OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res., 13, 2178-89.
43. Nawrocki, E. P., Kolbe, D. L. and Eddy, S. R. 2009, Infernal 1.0: inference of RNA alignments, Bioinformatics, 25, 1335-7.
44. Nawrocki, E. P., Burge, S. W., Bateman, A., et al. 2015, Rfam 12.0: updates to the RNA families database, Nucleic Acids Res., 43, D130-7.
45. Katoh, K. and Standley, D. M. 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772-80.
46. Stamatakis, A. 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312-3.
47. Ptitsyn, A. and Moroz, L. L. 2012, Computational workflow for analysis of gain and loss of genes in distantly related genomes. In: Proceedings of the Ninth Annual MCBIOS Conference. BioMed Central Ltd., London, UK, pp. 1-6
48. The International Brachypodium Initiative. 2010, Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature, 463, 763-8.
49. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J. and Van De Peer, Y. 2002, The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice, Genome Res., 12, 1792-801.
50. Li, J. H., Tang, C. H., Song, C. Y., Chen, M. J., Feng, Z. Y. and Pan, Y. J. 2006, A simple, rapid and effective method for total RNA extraction from Lentinula edodes, Biotechnol. Lett., 28, 1193-7.
51. Smeds, L. and Künstner, A. 2011, CONDETRI - a content dependent read trimmer for Illumina data, PLoS One, 6, e26314.
52. Trapnell, C., Roberts, A., Goff, L., et al. 2014, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat. Protoc., 7, 562-78.
53. Myers, E. W., Sutton, G. G., Delcher, A. L., et al. 2000, A whole-genome assembly of Drosophila, Science, 287, 2196-204.
54. Ye, C., Hill, C., Ruan, J. and Ma, Z. S. 2015, DBG2OLC: Efficient Assembly of Large Genomes Using the Compressed Overlap Graph, arXiv, 1410.2801, 1-20.
55. Yan, L., Wang, X., Liu, H., et al. 2015, The genome of Dendrobium offi-cinale illuminates the biology of the important traditional Chinese orchid herb, Mol. Plant, 8, 922-34.
56. Birol, I., Raymond, A., Jackman, S. D., et al. 2013, Assembling the 20Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data, Bioinformatics, 29, 1492-7.
57. Natsume, S., Takagi, H., Shiraishi, A., et al. 2015, The draft genome of hop (Humulus lupulus), an essence for brewing, Plant Cell Physiol., 56, 428-41.
58. Peng, Y., Lai, Z., Lane, T., et al. 2014, De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms, Plant Physiol., 166, 1241-54.
59. Zhang, G., Liu, X., Quan, Z., et al. 2012, Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential, Nat. Biotechnol., 30, 549-54.
60. Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. 2013, REAPR: a universal tool for genome assembly evaluation, Genome Biol., 14, R47.
61. International Rice Genome Sequencing Project. 2005, The map-based sequence of the rice genome, Nature, 436, 793-800.
62. Al-Mssallem, I. S., Hu, S., Zhang, X., et al. 2013, Genome sequence of the date palm Phoenix dactylifera L., Nat. Commun., 4, 1-9.
63. Davey, M. W., Gudimella, R., Harikrishna, J. A., Sin, L. W., Khalid, N. and Keulemans, J. 2013, A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids, BMC Genomics, 14, 683.
64. Paterson, A. H., Bowers, J. E., Bruggmann, R., et al. 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551-6.
65. Baumgarten, A., Cannon, S., Spangler, R. and May, G. 2003, Genome-level evolution of resistance genes in Arabidopsis thaliana, Genetics, 165, 309-19.
66. Bremer, B., Bremer, K., Chase, M. W., et al. 2009, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III, Bot. J. Linn. Soc., 161, 105-21.
67. D'Hont, A., Denoeud, F., Aury, J. M., et al. 2012, The banana (Musa acu-minata) genome and the evolution of monocotyledonous plants, Nature, 488, 213-7.
68. Tang, H., Bowers, J. E., Wang, X. and Paterson, A. H. 2010, Angiosperm genome comparisons reveal early polyploidy in the monocot lineage, Proc. Natl. Acad. Sci. U. S. A., 107, 472-7.
69. Hertweck, K. L., Kinney, M. S., Stuart, S. A., et al. 2015, Phylogenetics, divergence times and diversification from three genomic partitions in mono-cots, Bot. J. Linn. Soc., 178, 375-93.
70. Trainotti, L., Pavanello, A., Casadoro, G., Colombo, V. G. and Padova, I. 2005, Different ethylene receptors show an increased expression during the ripening of strawberries: does such an increment imply a role for ethylene in the ripening of these non-climacteric fruits? J. Exp. Bot., 56, 2037-46.
71. Fortes, A. M., Agudelo-Romero, P., Silva, M. S., Ali, K., Sousa, L. and Maltese, F. 2011, Transcript and metabolite analysis in Trincadeira culti-var reveals novel information regarding the dynamics of grape ripening, BMC Plant Biol., 11, 1-34.
72. Huang, G., Li, T., Li, X., et al. 2014, Comparative transcriptome analysis of climacteric fruit of Chinese pear (Pyrus ussuriensis) reveals new insights into fruit ripening, PLoS One, 9, e107562.
73. Périn, C., Gomez-Jimenez, M., Hagen, L., et al. 2002, Molecular and genetic characterization of a non-climacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit, Plant Physiol., 129, 300-9.
74. Aizat, W. M., Able, J. A., Stangoulis, J. C. R. and Able, A. J. 2013, Characterisation of ethylene pathway components in non-climacteric capsicum, BMC Plant Biol., 13, 191.