A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis.
Praesagittifera naikaiensis
acoel
draft nuclear genome
Journal
GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872
Informations de publication
Date de publication:
01 04 2019
01 04 2019
Historique:
received:
17
09
2018
revised:
10
01
2019
accepted:
18
02
2019
entrez:
7
4
2019
pubmed:
7
4
2019
medline:
18
12
2019
Statut:
ppublish
Résumé
Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis. To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules. Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Sections du résumé
BACKGROUND
Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.
FINDINGS
To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.
CONCLUSIONS
Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Identifiants
pubmed: 30953569
pii: 5429687
doi: 10.1093/gigascience/giz023
pmc: PMC6451197
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Science. 1999 Mar 19;283(5409):1919-23
pubmed: 10082465
Bioinformatics. 2016 Jul 1;32(13):1925-32
pubmed: 27153683
Bioinformatics. 2014 Feb 15;30(4):566-8
pubmed: 24297520
Nature. 2011 Feb 10;470(7333):255-8
pubmed: 21307940
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Bioinformatics. 2013 Nov 1;29(21):2669-77
pubmed: 23990416
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
BMC Genomics. 2013 Sep 08;14:604
pubmed: 24010822
BMC Bioinformatics. 2005 Feb 15;6:31
pubmed: 15713233
Curr Biol. 2014 May 19;24(10):1107-13
pubmed: 24768051
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66
pubmed: 14500829
Sci Rep. 2017 May 12;7(1):1847
pubmed: 28500313
Bioinformatics. 2005 May 1;21(9):1859-75
pubmed: 15728110
Genome Res. 2009 Sep;19(9):1630-8
pubmed: 19570905
Gigascience. 2015 Aug 04;4:35
pubmed: 26244089
BMC Bioinformatics. 2012 Sep 19;13:238
pubmed: 22988817
Nucleic Acids Res. 2016 Jul 8;44(12):e113
pubmed: 27131372
PLoS One. 2012;7(11):e47768
pubmed: 23185243
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
BMC Evol Biol. 2010 Oct 13;10:309
pubmed: 20942955
Gigascience. 2019 Apr 1;8(4):
pubmed: 30953569
Mol Phylogenet Evol. 2004 Nov;33(2):321-32
pubmed: 15336667
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
Nature. 2016 Feb 4;530(7588):89-93
pubmed: 26842059
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500