Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
07 07 2023
07 07 2023
Historique:
received:
13
10
2022
accepted:
31
05
2023
medline:
10
7
2023
pubmed:
8
7
2023
entrez:
7
7
2023
Statut:
epublish
Résumé
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
Identifiants
pubmed: 37420035
doi: 10.1038/s42003-023-05002-x
pii: 10.1038/s42003-023-05002-x
pmc: PMC10328945
doi:
Substances chimiques
Silicon Dioxide
7631-86-9
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
697Informations de copyright
© 2023. The Author(s).
Références
Sci Rep. 2018 Jul 19;8(1):10916
pubmed: 30026492
Science. 2006 Sep 1;313(5791):1261-6
pubmed: 16946064
Nature. 2003 Feb 20;421(6925):841-3
pubmed: 12594512
Ann Rev Mar Sci. 2011;3:291-315
pubmed: 21329207
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Bioinformatics. 2015 Mar 15;31(6):926-32
pubmed: 25398609
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Syst Biol. 2020 Mar 1;69(2):265-279
pubmed: 31364707
Sci Rep. 2020 Oct 7;10(1):16687
pubmed: 33028894
Ecol Lett. 2007 Dec;10(12):1170-81
pubmed: 17927770
Math Biosci. 2005 Feb;193(2):159-82
pubmed: 15748728
Nat Ecol Evol. 2018 Apr;2(4):697-704
pubmed: 29459706
mSystems. 2022 Feb 22;7(1):e0120321
pubmed: 35089068
Curr Genet. 2016 Nov;62(4):887-896
pubmed: 27091756
New Phytol. 2018 Jul;219(1):462-473
pubmed: 29624698
ISME J. 2022 Jun;16(6):1557-1569
pubmed: 35145244
Nat Commun. 2017 Nov 3;8(1):1292
pubmed: 29101388
Plant J. 2015 Feb;81(3):519-28
pubmed: 25438865
Viruses. 2016 Mar 01;8(3):66
pubmed: 26938550
J Phycol. 2014 Dec;50(6):977-83
pubmed: 26988780
J Eukaryot Microbiol. 2013 Jul-Aug;60(4):414-20
pubmed: 23710621
PLoS One. 2015 Jun 08;10(6):e0129081
pubmed: 26052941
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Cell Mol Life Sci. 2008 Jul;65(13):1957-76
pubmed: 18322649
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Nat Rev Genet. 2010 Feb;11(2):97-108
pubmed: 20051986
Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6943-8
pubmed: 23569277
Nucleic Acids Res. 2001 Jun 15;29(12):2607-18
pubmed: 11410670
J Cell Sci. 2005 Jul 1;118(Pt 13):2791-801
pubmed: 15976441
J Biol Chem. 2016 Mar 4;291(10):4982-97
pubmed: 26710847
Can J Microbiol. 1962 Apr;8:229-39
pubmed: 13902807
Science. 2004 Oct 1;306(5693):79-86
pubmed: 15459382
J Phycol. 2011 Feb;47(1):144-51
pubmed: 27021720
PLoS One. 2014 Oct 22;9(10):e111069
pubmed: 25338000
Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4352-7
pubmed: 21368207
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
BMC Bioinformatics. 2005 Feb 15;6:31
pubmed: 15713233
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Mol Cell Proteomics. 2015 Apr;14(4):1113-26
pubmed: 25670805
Commun Biol. 2019 Jun 28;2:245
pubmed: 31286062
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
J Phycol. 2016 Oct;52(5):716-731
pubmed: 27335204
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654
pubmed: 34320186
Protist. 2009 May;160(2):285-300
pubmed: 19231282
Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10438-43
pubmed: 18653757
Curr Biol. 2015 Feb 2;25(3):364-371
pubmed: 25557662
Nat Commun. 2018 Jan 25;9(1):373
pubmed: 29371626
Int Rev Cytol. 2004;237:91-154
pubmed: 15380667
Curr Biol. 2019 May 6;29(9):1503-1511.e6
pubmed: 31006567
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Microbiol Resour Announc. 2020 Aug 13;9(33):
pubmed: 32817146
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457
pubmed: 32300014
Angew Chem Int Ed Engl. 2008;47(9):1729-32
pubmed: 18203228
Nature. 2006 May 18;441(7091):341-4
pubmed: 16572122
Protoplasma. 2017 Jan;254(1):461-471
pubmed: 27048177
iScience. 2020 Aug 21;23(8):101424
pubmed: 32798972
Plant Cell. 2017 Aug;29(8):2047-2070
pubmed: 28765511
Ann Rev Mar Sci. 2017 Jan 3;9:311-335
pubmed: 27483121
BMC Biol. 2017 Jul 24;15(1):65
pubmed: 28738898
PLoS Biol. 2014 Jun 24;12(6):e1001889
pubmed: 24959919
mSystems. 2020 Oct 27;5(5):
pubmed: 33109753
J Cell Biol. 1996 Jan;132(1-2):49-61
pubmed: 8567729
Biochem J. 2004 Jun 1;380(Pt 2):487-96
pubmed: 14992688
Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14237-14242
pubmed: 27911777
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Semin Cell Dev Biol. 2004 Dec;15(6):679-89
pubmed: 15561587
Sci Adv. 2018 May 16;4(5):eaar4536
pubmed: 29774236
Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):E5906-E5915
pubmed: 27647881
BMC Bioinformatics. 2017 Dec 28;18(Suppl 16):571
pubmed: 29297295
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Environ Microbiol. 2009 Feb;11(2):512-25
pubmed: 19196281
Nat Commun. 2019 Oct 7;10(1):4552
pubmed: 31591397
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14
pubmed: 19274634
J Cell Sci. 2001 Mar;114(Pt 6):1061-77
pubmed: 11228151
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Bioinformatics. 2014 May 1;30(9):1290-1
pubmed: 24395753
New Phytol. 2021 Apr;230(1):155-170
pubmed: 33486789
PLoS One. 2009;4(3):e4966
pubmed: 19305505
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Nature. 2008 Nov 13;456(7219):239-44
pubmed: 18923393
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Genome Biol. 2012 Jul 26;13(7):R66
pubmed: 22835381
New Phytol. 2017 Jul;215(1):140-156
pubmed: 28429538
Nature. 2017 Jan 26;541(7638):536-540
pubmed: 28092920
J Biol Chem. 2004 Oct 8;279(41):42993-9
pubmed: 15304518
Am Nat. 2005 Sep;166(3):E45-61
pubmed: 16224684
ISME J. 2016 Oct;10(10):2419-34
pubmed: 27003244
PLoS Genet. 2013 Jun;9(6):e1003272
pubmed: 23785293
Microbiol Mol Biol Rev. 2010 Mar;74(1):42-57
pubmed: 20197498
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Nature. 2009 Sep 17;461(7262):393-8
pubmed: 19741609
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Nat Commun. 2022 Feb 10;13(1):799
pubmed: 35145076
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604
Genome Res. 2014 Aug;24(8):1384-95
pubmed: 24755901
Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3175-80
pubmed: 21300899
Nature. 2010 Jun 3;465(7298):617-21
pubmed: 20520714
Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14133-8
pubmed: 11106386
Life Sci Alliance. 2019 Sep 30;2(5):
pubmed: 31570514
Lipids. 2006 Dec;41(12):1073-88
pubmed: 17269553
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
PLoS One. 2017 Jul 7;12(7):e0181098
pubmed: 28686696
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Science. 2007 Feb 2;315(5812):612-7
pubmed: 17272712
Am Nat. 2011 Jul;178(1):98-112
pubmed: 21670581