Author Correction: Rapid de novo assembly of the European eel genome from nanopore sequencing reads (Scientific Reports, (2017), 7, 1, (7213), 10.1038/s41598-017-07650-6);Rapid de novo assembly of the European eel genome from nanopore sequencing reads

Scientific Reports

Volumn 7, Issue 1, 2017, Pages

  Jansen, Hans J ^a   Liem, Michael ^b   Jong Raadsen, Susanne A ^a   Dufour, Sylvie ^c   Weltzien, Finn Arne ^d   Swinkels, William ^e   Koelewijn, Alex ^e   Palstra, Arjan P ^f   Pelster, Bernd ^g   Spaink, Herman P ^b   Thillart, Guido E Van Den ^a   Dirks, Ron P ^a   Henkel, Christiaan V ^b,h,i  

^a ZF screens BV ^*  (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c SORBONNE UNIVERSITÉ   (France)

^d NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^e DUPAN Foundation   (Netherlands)

^f WAGENINGEN UNIVERSITY   (Netherlands)

^g UNIVERSITY OF INNSBRUCK   (Austria)

^h UNIVERSITY OF APPLIED SCIENCES LEIDEN   (Netherlands)

ⁱ Generade Centre of Expertise in Genomics   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGY; DNA SEQUENCE; EEL; GENETICS; GENOME; GENOME SIZE; GENOMICS; HIGH THROUGHPUT SEQUENCING; NANOPORE; PROCEDURES;

ANIMALS; COMPUTATIONAL BIOLOGY; EELS; GENOME; GENOME SIZE; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NANOPORES; SEQUENCE ANALYSIS, DNA;

EID: 85026912929     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-019-44275-3     Document Type: Erratum

References (52)

1. Coppe, A. et al. Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics 11, 635 (2010).
2. Henkel, C. V. et al. Primitive duplicate Hox clusters in the European eel's genome. PLoS One 7, e32231 (2012).
3. Pujolar, J. M. et al. Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel. BMC Genomics 13, 507 (2012).
4. Minegishi, Y., Henkel, C. V., Dirks, R. P. & van den Thillart, G. E. Genomics in eels - towards aquaculture and biology. Mar Biotechnol (NY) 14, 583-590 (2012).
5. IUCN Red List. doi: 10.2305/IUCN.UK.2014-1.RLTS.T60344A45833138.en (2014).
6. Ager-Wick, E. et al. The pituitary gland of the European eel reveals massive expression of genes involved in the melanocortin system. PLoS One 8, e77396 (2013).
7. Dirks, R. P. et al. Identification of molecular markers in pectoral fin to predict artificial maturation of female European eels (Anguilla anguilla). Gen Comp Endocrinol 204, 267-276 (2014).
8. Churcher, A. M. et al. Deep sequencing of the olfactory epithelium reveals specific chemosensory receptors are expressed at sexual maturity in the European eel Anguilla anguilla. Mol Ecol 24, 822-834 (2015).
9. Burgerhout, E. et al. Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel (Anguilla anguilla); biomarkers for broodstock selection. Gen Comp Endocrinol 225, 185-196 (2016).
10. Pelster, B., Schneebauer, G. & Dirks, R. P. Anguillicola crassus infection significantly affects the silvering related modifications in steady state mRNA levels in gas gland tissue of the European eel. Front Physiol 7, 175 (2016).
11. Pujolar, J. M. et al. A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel. Mol Ecol Resour 13, 706-714 (2013).
12. Pasquier, J. et al. Multiple kisspeptin receptors in early osteichthyans provide new insights into the evolution of this receptor family. PLoS One 7, e48931 (2012).
13. Maugars, G. & Dufour, S. Demonstration of the coexistence of duplicated LH receptors in teleosts, and their origin in ancestral actinopterygians. PLoS One 10, e0135184 (2015).
14. Morini, M. et al. Duplicated leptin receptors in two species of eel bring new insights into the evolution of the leptin system in vertebrates. PLoS One 10, e0126008 (2015).
15. Jacobsen, M. W. et al. Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata). Mol Ecol 23, 4785-4798 (2014).
16. Pujolar, J. M. et al. Genome-wide single-generation signatures of local selection in the panmictic European eel. Mol Ecol 23, 2514-2528 (2014).
17. Ip, C. L. et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res 4, 1075 (2015).
18. Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17, 239 (2016).
19. Tyson, J. R. et al. Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomics rearrangements using the MinION sequencing device. BioRxiv, doi: 10.1101/099143 (2017).
20. Weirather, J. L. et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis [version 1; referees: 2 approved with reservations]. F1000Res 6, 100 (2017).
21. Koren, S. et al. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 14, R101 (2013).
22. Loman, N. J., Quick, J. & Simpson, J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12, 733-735 (2015).
23. Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737-746 (2017).
24. Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13, 1050-1054 (2016).
25. Koren, S., Walenz, B. P., Berlin, K., Miller, J. R. & Phillippy, A. M. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27, 722-736 (2017).
26. Kamath, G. M., Shomorony, I., Xia, F., Courtade, T. A. & Tse, D. N. HINGE: long-read assembly achieves optimal repeat resolution. Genome Res 27, 747-756 (2017).
27. Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103-2110 (2016).
28. Ye, C., Hill, C. M., Wu, S., Ruan, J. & Ma, Z. DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci Rep 6, 31900 (2016).
29. Keinath, M. C. et al. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep 5, 16413 (2015).
30. Biscotti, M. A. et al. The lungfish transcriptome: a glimpse into molecular evolution events at the transition from water to land. Sci Rep 6, 21571 (2016).
31. Zonneveld, B. J. The systematic value of nuclear genome size for all species of Tulipa L. (Liliacaeae). Plant Syst Evol 281, 217-245 (2009).
32. Li, X. & Waterman, M. S. Estimating the repeat structure and length of DNA sequences using l-tuples. Genome Res 13, 1916-1922 (2003).
33. Vuture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics, doi: 10.1093/bioinformatics/btx153 (2017).
34. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-Assembled contigs using SSPACE. Bioinformatics 27, 578-579 (2011).
35. Henkel, C. V. et al. First draft genome sequence of the Japanese eel. Anguilla japonica. Gene 511, 195-201 (2012).
36. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212 (2015).
37. Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).
38. Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25, 1-7 (2015).
39. Pavey, S. A. et al. Draft genome of the American eel (Anguilla rostrata). Mol Ecol Resour, doi: 10.1111/1755-0998.12608 (2016).
40. Albert, V., Jónsson, B. & Bernatchez, L. Natural hybrids in Atlantic eels (Anguilla anguilla, A. rostrata): evidence for successful reproduction and fluctuating abundance in space and time. Mol Ecol 15, 1903-1916 (2006).
41. Hunt, M., Newbold, C., Berriman, M. & Otto, T. D. A comprehensive evaluation of assembly scaffolding tools. Genome Biol 15, R42 (2014).
42. Chapman, J. A. et al. A whole-genome shotgun approach for assembling and anchoring the hexaploidy bread wheat genome. Genome Biol 16, 26 (2015).
43. Urban, J. M., Bliss, J., Lawrence, C. E. & Gerbi, S. A. Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. BioRxiv, doi: 10.1101/019281 (2015).
44. Datema, E. et al. The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only. BioRxiv, doi: 10.1101/084772 (2016).
45. Mostovoy, Y. et al. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 13, 587-590 (2016).
46. Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764-770 (2011).
47. Magoc, T. & Salzberg, S. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
48. Watson, M. et al. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics 31, 114-115 (2015).
49. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-95 (2010).
50. Sović, I. et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat Commun 7, 11307 (2016).
51. Lee, C. Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics 19, 999-1008 (2003).
52. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol 5, R12 (2004).