Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
03 12 2019
03 12 2019
Historique:
received:
29
04
2019
accepted:
04
11
2019
entrez:
5
12
2019
pubmed:
5
12
2019
medline:
10
10
2020
Statut:
epublish
Résumé
Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.
Identifiants
pubmed: 31796747
doi: 10.1038/s41597-019-0311-3
pii: 10.1038/s41597-019-0311-3
pmc: PMC6890685
doi:
Types de publication
Dataset
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
302Commentaires et corrections
Type : ErratumIn
Références
Genome Res. 2017 May;27(5):768-777
pubmed: 28232478
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Nat Methods. 2016 Jul;13(7):587-90
pubmed: 27159086
Int J Mol Sci. 2018 Aug 17;19(8):
pubmed: 30126154
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Nat Genet. 2019 Jan;51(1):163-174
pubmed: 30397333
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
pubmed: 22127870
Bioinformatics. 2010 Oct 15;26(20):2620-1
pubmed: 20736339
Biomed Res Int. 2019 Apr 11;2019:7847064
pubmed: 31111066
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9
pubmed: 16845043
Curr Protoc Bioinformatics. 2004 May;Chapter 4:Unit 4.10
pubmed: 18428725
Nature. 2013 Apr 04;496(7443):57-63
pubmed: 23485966
Acta Trop. 2019 Jan;189:1-5
pubmed: 30248315
Parasit Vectors. 2018 May 30;11(1):324
pubmed: 29848351
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Gigascience. 2018 Mar 1;7(3):1-6
pubmed: 29342277
BMC Bioinformatics. 2018 Jul 18;19(1):273
pubmed: 30021513
Bioinformatics. 2013 Oct 1;29(19):2487-9
pubmed: 23842809
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Cytogenet Genome Res. 2005;110(1-4):462-7
pubmed: 16093699
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Parasitology. 2018 May;145(6):807-813
pubmed: 29173204
Acta Parasitol. 2016 Mar;61(2):429-42
pubmed: 27078671
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Sci Data. 2019 Dec 3;6(1):302
pubmed: 31796747
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14
pubmed: 19274634
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Bioinformatics. 2015 Jun 15;31(12):2035-7
pubmed: 25661542
Cell Rep. 2017 Jan 17;18(3):762-776
pubmed: 28099853
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
Nat Genet. 2013 Oct;45(10):1168-75
pubmed: 24013640
Gigascience. 2015 Aug 04;4:35
pubmed: 26244089
Gigascience. 2018 Apr 1;7(4):1-5
pubmed: 29635297
Worm. 2012 Jan 1;1(1):15-21
pubmed: 24058818
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9
pubmed: 27098042
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Mol Biol Evol. 2001 May;18(5):721-30
pubmed: 11319256
Parasitology. 2014 May;141(6):826-36
pubmed: 24709293
Front Microbiol. 2018 Jan 15;8:2672
pubmed: 29379475
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Exp Parasitol. 2011 Oct;129(2):158-63
pubmed: 21782814
Mol Biol Evol. 2019 Sep 1;36(9):1931-1941
pubmed: 31077328
Mol Biochem Parasitol. 2017 Jul;215:2-10
pubmed: 27899279
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365
Methods Mol Biol. 2017;1611:59-73
pubmed: 28451972
Parasit Vectors. 2017 Jun 27;10(1):314
pubmed: 28655342