Evolutionary Implications of the microRNA- and piRNA Complement of
Gastrotricha
Lepidodermella squamata
Platyhelminthes
RNAi protein machinery
microRNAs
piRNAs
Journal
Non-coding RNA
ISSN: 2311-553X
Titre abrégé: Noncoding RNA
Pays: Switzerland
ID NLM: 101652294
Informations de publication
Date de publication:
22 Feb 2019
22 Feb 2019
Historique:
received:
21
12
2018
revised:
15
02
2019
accepted:
19
02
2019
entrez:
1
3
2019
pubmed:
1
3
2019
medline:
1
3
2019
Statut:
epublish
Résumé
Gastrotrichs-'hairy bellies'-are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a 'multi-omics' approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi (RNA interference) protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA, and protein data support a close relationship of gastrotrichs and flatworms.
Identifiants
pubmed: 30813358
pii: ncrna5010019
doi: 10.3390/ncrna5010019
pmc: PMC6468455
pii:
doi:
Types de publication
Journal Article
Langues
eng
Déclaration de conflit d'intérêts
The authors declare no conflict of interest.
Références
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Nature. 2010 Feb 25;463(7284):1084-8
pubmed: 20118916
Annu Rev Genet. 2015;49:213-42
pubmed: 26473382
Cell. 2018 Mar 22;173(1):20-51
pubmed: 29570994
Mol Biol Evol. 2014 Jul;31(7):1833-49
pubmed: 24748651
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85
pubmed: 26673716
Nature. 2006 Jul 13;442(7099):199-202
pubmed: 16751776
Mol Cell. 2014 Dec 4;56(5):708-16
pubmed: 25453759
Nat Methods. 2010 Nov;7(11):909-12
pubmed: 20935650
Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1513-22
pubmed: 18192183
Parasit Vectors. 2015 Feb 06;8:83
pubmed: 25656283
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
BMC Genomics. 2014 Aug 29;15:736
pubmed: 25168356
Nature. 2013 Apr 04;496(7443):57-63
pubmed: 23485966
Philos Trans R Soc Lond B Biol Sci. 2015 Dec 19;370(1684):
pubmed: 26554039
Trends Parasitol. 2014 Mar;30(3):123-9
pubmed: 24485046
EMBO J. 2010 Jun 2;29(11):1830-9
pubmed: 20436454
Curr Biol. 2015 Aug 3;25(15):2000-6
pubmed: 26212884
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Trends Genet. 2018 Mar;34(3):165-167
pubmed: 29361313
Genome Biol Evol. 2014 May;6(5):1105-17
pubmed: 24732282
Curr Biol. 2019 Jan 21;29(2):312-318.e3
pubmed: 30639106
Mol Phylogenet Evol. 2012 Apr;63(1):208-12
pubmed: 22198640
PLoS Negl Trop Dis. 2018 May 29;12(5):e0006535
pubmed: 29813122
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nucleic Acids Res. 2012 Jan;40(1):37-52
pubmed: 21911355
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Int J Parasitol. 2015 Mar;45(4):253-67
pubmed: 25659494
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Biol Rev Camb Philos Soc. 1998 Aug;73(3):203-66
pubmed: 9809012
Commun Biol. 2018 Jan 22;1:2
pubmed: 30271890
Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11546-51
pubmed: 19564616
Int J Parasitol. 2015 Dec;45(14):901-13
pubmed: 26432296
Mol Biol Evol. 2013 Nov;30(11):2369-82
pubmed: 23913097
Nature. 2006 Jul 13;442(7099):203-7
pubmed: 16751777
PLoS One. 2015 Jul 08;10(7):e0130278
pubmed: 26153694
Genes Dev. 2006 Jul 1;20(13):1709-14
pubmed: 16766680
Zoological Lett. 2016 Sep 22;2:21
pubmed: 27688902
Commun Biol. 2018 Sep 7;1:137
pubmed: 30272016
Nat Ecol Evol. 2018 Jan;2(1):174-181
pubmed: 29203920
Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3659-68
pubmed: 25071211
Cell Rep. 2015 Mar 31;10(12):2069-82
pubmed: 25818294
Cell. 2012 Jul 6;150(1):78-87
pubmed: 22738724
Int J Parasitol. 2014 Oct 1;44(11):787-93
pubmed: 24998346
Cladistics. 1998 Sep;14(3):249-285
pubmed: 34905826
Nature. 2011 Feb 10;470(7333):255-8
pubmed: 21307940
Nat Ecol Evol. 2017 Feb 21;1(3):27
pubmed: 28529980
Genome Biol. 2015 Feb 11;16:30
pubmed: 25723335
Nat Rev Genet. 2019 Feb;20(2):89-108
pubmed: 30446728
Mol Phylogenet Evol. 2012 Jul;64(1):198-203
pubmed: 22724136
Int J Parasitol. 2017 Sep;47(10-11):643-653
pubmed: 28526608
Trends Biochem Sci. 2016 Apr;41(4):324-337
pubmed: 26810602
PLoS Biol. 2015 Feb 10;13(2):e1002061
pubmed: 25668728
Nat Genet. 2019 Jan;51(1):163-174
pubmed: 30397333
Genome Biol Evol. 2018 Jun 1;10(6):1457-1470
pubmed: 29788279
Proc Biol Sci. 2015 Mar 22;282(1803):20142983
pubmed: 25694624
Annu Rev Biochem. 2015;84:405-33
pubmed: 25747396
BMC Bioinformatics. 2016 Dec 9;17(1):525
pubmed: 27938328
Parasite Immunol. 2017 Feb;39(2):
pubmed: 27809346
Curr Opin Chem Biol. 2007 Oct;11(5):569-77
pubmed: 17928262
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
BMC Bioinformatics. 2012 Jan 10;13:5
pubmed: 22233380
Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8909-E8918
pubmed: 30181261
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Genome Biol. 2018 Dec 4;19(1):213
pubmed: 30514392
Parasitology. 2007 May;134(Pt 5):609-19
pubmed: 17201997
Mol Biol Evol. 2013 Dec;30(12):2619-28
pubmed: 24025793
Biodivers Data J. 2015 Aug 14;(3):e5800
pubmed: 26379467
Parasitol Int. 2017 Dec;66(6):773-776
pubmed: 28916307
Evol Dev. 2009 Jan-Feb;11(1):50-68
pubmed: 19196333
PLoS Negl Trop Dis. 2011 Jun;5(6):e1176
pubmed: 21666793
Cell Rep. 2015 Aug 25;12(8):1234-43
pubmed: 26279574
Zoological Lett. 2017 May 29;3:6
pubmed: 28560048
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
BMC Evol Biol. 2017 Sep 11;17(1):215
pubmed: 28893179
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365