Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
04 2020
04 2020
Historique:
received:
27
05
2019
accepted:
18
03
2020
pubmed:
25
3
2020
medline:
21
7
2021
entrez:
25
3
2020
Statut:
ppublish
Résumé
Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the
Identifiants
pubmed: 32205368
pii: gr.253070.119
doi: 10.1101/gr.253070.119
pmc: PMC7197479
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
647-659Informations de copyright
© 2020 Vorobev et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Bioinformatics. 2015 Mar 15;31(6):926-32
pubmed: 25398609
Microbiome. 2019 Feb 15;7(1):26
pubmed: 30770768
Environ Microbiol. 1999 Oct;1(5):431-8
pubmed: 11207763
Nature. 2010 Mar 4;464(7285):59-65
pubmed: 20203603
ISME J. 2017 Feb;11(2):512-528
pubmed: 27779617
Nat Microbiol. 2017 Nov;2(11):1533-1542
pubmed: 28894102
J Phycol. 2017 Apr;53(2):451-461
pubmed: 27992651
Heredity (Edinb). 2015 May;114(5):429-30
pubmed: 25873237
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Nat Microbiol. 2018 Jul;3(7):804-813
pubmed: 29891866
Nat Microbiol. 2017 Feb 13;2:17009
pubmed: 28191900
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Science. 2004 Apr 2;304(5667):66-74
pubmed: 15001713
Environ Microbiol. 2017 Aug;19(8):3219-3234
pubmed: 28585420
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
Science. 2012 Sep 21;337(6101):1546-50
pubmed: 22997339
Sci Data. 2018 Jan 16;5:170203
pubmed: 29337314
Environ Microbiol. 2014 Oct;16(10):3238-49
pubmed: 24761991
Science. 2015 May 22;348(6237):1261498
pubmed: 25999515
Mol Ecol. 2017 Sep;26(17):4467-4482
pubmed: 28636804
Nat Biotechnol. 2017 Nov;35(11):1026-1028
pubmed: 29035372
Nat Microbiol. 2018 Apr;3(4):430-439
pubmed: 29483657
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Bioinformatics. 2013 Oct 1;29(19):2487-9
pubmed: 23842809
Genome Biol Evol. 2019 Apr 1;11(4):1275-1292
pubmed: 30937436
Nat Ecol Evol. 2017 Apr 20;1(5):145
pubmed: 28812681
Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5
pubmed: 23509275
Front Microbiol. 2017 Apr 19;8:637
pubmed: 28469605
Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11824-11832
pubmed: 31127042
Nat Commun. 2018 Jan 25;9(1):373
pubmed: 29371626
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
ISME J. 2011 Sep;5(9):1484-93
pubmed: 21451586
Nature. 2011 May 12;473(7346):208-11
pubmed: 21562561
ISME J. 2014 Dec;8(12):2530-42
pubmed: 25226029
Science. 2015 Jun 26;348(6242):1466-9
pubmed: 26113722
Science. 1995 Mar 3;267(5202):1324-6
pubmed: 17812604
ISME J. 2009 Jan;3(1):4-12
pubmed: 19005497
PLoS Biol. 2014 Jun 24;12(6):e1001889
pubmed: 24959919
Curr Opin Chem Biol. 2016 Apr;31:58-65
pubmed: 26851513
Science. 2008 Nov 14;322(5904):1110-2
pubmed: 19008448
Genome Biol. 2009;10(8):R85
pubmed: 19698104
Ann Rev Mar Sci. 2017 Jan 3;9:413-444
pubmed: 27814033
ISME J. 2018 Apr;12(4):1094-1108
pubmed: 29348580
Genome Res. 2018 Apr;28(4):569-580
pubmed: 29496730
ISME J. 2016 Sep;10(9):2304-16
pubmed: 26882264
Bioinformatics. 2012 Apr 15;28(8):1086-92
pubmed: 22368243
Sci Data. 2017 Aug 01;4:170093
pubmed: 28763055
Science. 2015 May 22;348(6237):1261605
pubmed: 25999516
Curr Biol. 2012 Sep 11;22(17):R675-7
pubmed: 22974991
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
PLoS Biol. 2012;10(11):e1001419
pubmed: 23139639
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
Bioinformatics. 2019 May 1;35(9):1544-1552
pubmed: 30252023
Genome Res. 2013 Jan;23(1):111-20
pubmed: 22936250
Genome Res. 1999 Sep;9(9):868-77
pubmed: 10508846
Nat Biotechnol. 2014 Aug;32(8):822-8
pubmed: 24997787
PLoS One. 2012;7(6):e39648
pubmed: 22745802
Sci Data. 2015 May 26;2:150023
pubmed: 26029378
PLoS One. 2013 Dec 04;8(12):e81749
pubmed: 24324722
Ann Rev Mar Sci. 2011;3:197-225
pubmed: 21329204
Science. 2015 May 22;348(6237):1261359
pubmed: 25999513
Nature. 2010 Mar 4;464(7285):90-4
pubmed: 20173737
PeerJ. 2014 Sep 30;2:e603
pubmed: 25289188
Sci Rep. 2017 Oct 25;7(1):14019
pubmed: 29070840
Nat Microbiol. 2016 Dec 20;2:16214
pubmed: 27996008
Nat Biotechnol. 2013 Jun;31(6):533-8
pubmed: 23707974
Sci Rep. 2016 Nov 30;6:37900
pubmed: 27901108
PeerJ. 2015 Oct 08;3:e1319
pubmed: 26500826
PLoS One. 2009 Dec 22;4(12):e8407
pubmed: 20027311
Nature. 2019 Apr;568(7753):505-510
pubmed: 30867587