The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions.
Gastrodia
Genome evolution
Mycoheterotrophy
Mycorrhizal roots
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
07 Apr 2022
07 Apr 2022
Historique:
received:
13
01
2022
accepted:
01
04
2022
entrez:
8
4
2022
pubmed:
9
4
2022
medline:
12
4
2022
Statut:
epublish
Résumé
To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia. Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species. Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.
Sections du résumé
BACKGROUND
BACKGROUND
To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia.
RESULTS
RESULTS
Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species.
CONCLUSION
CONCLUSIONS
Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.
Identifiants
pubmed: 35392808
doi: 10.1186/s12870-022-03573-1
pii: 10.1186/s12870-022-03573-1
pmc: PMC8988336
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
179Subventions
Organisme : National Natural Science Foundation of China
ID : 31870195; 31670194
Informations de copyright
© 2022. The Author(s).
Références
BMC Evol Biol. 2019 Feb 26;19(1):63
pubmed: 30808310
Bioinformatics. 2009 May 1;25(9):1105-11
pubmed: 19289445
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
New Phytol. 2020 Apr;226(2):541-554
pubmed: 31863481
Nature. 2007 Sep 27;449(7161):463-7
pubmed: 17721507
Bot Stud. 2017 Dec;58(1):33
pubmed: 28779349
Science. 2013 Dec 20;342(6165):1241089
pubmed: 24357323
Science. 2001 Aug 10;293(5532):1129-33
pubmed: 11498589
Biotechnol Adv. 2020 Nov 1;43:107553
pubmed: 32439576
New Phytol. 1994 Jun;127(2):171-216
pubmed: 33874520
Mol Ecol. 2017 Mar;26(6):1652-1669
pubmed: 28099773
Mol Biol Evol. 2019 Sep 1;36(9):1884-1901
pubmed: 31058965
New Phytol. 2014 Apr;202(2):594-605
pubmed: 24494717
Science. 2017 Jun 16;356(6343):1172-1175
pubmed: 28596307
Mol Plant. 2012 Nov;5(6):1263-80
pubmed: 22933714
Biochem Biophys Res Commun. 2018 Jan 1;495(1):280-285
pubmed: 29097201
Plant Methods. 2016 Feb 15;12:15
pubmed: 26884807
New Phytol. 2017 Jan;213(1):365-379
pubmed: 27859287
Bioinformatics. 2014 Oct 15;30(20):2843-51
pubmed: 24974202
Mol Plant. 2019 Dec 2;12(12):1561-1576
pubmed: 31706032
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Plant J. 2021 Dec;108(6):1609-1623
pubmed: 34647389
Planta. 2019 Jan;249(1):21-30
pubmed: 30187155
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
Genomics. 2006 Dec;88(6):745-751
pubmed: 16857340
Nature. 2010 Jan 14;463(7278):178-83
pubmed: 20075913
Nucleic Acids Res. 2007 Jan;35(Database issue):D883-7
pubmed: 17145706
Plant Methods. 2019 May 21;15:50
pubmed: 31139240
Am J Bot. 2012 Sep;99(9):1513-23
pubmed: 22935364
FEMS Microbiol Lett. 1997 Sep 15;154(2):165-71
pubmed: 9311112
Nature. 2005 Jun 9;435(7043):824-7
pubmed: 15944706
Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5
pubmed: 18940856
Plant J. 2007 Oct;52(1):105-13
pubmed: 17672842
Mol Plant. 2015 Jun;8(6):922-34
pubmed: 25825286
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
New Phytol. 2017 Jan;213(1):10-12
pubmed: 27891646
Nature. 2002 Sep 26;419(6905):389-92
pubmed: 12353033
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
New Phytol. 2015 Oct;208(1):79-87
pubmed: 25982949
New Phytol. 2017 Jun;214(4):1631-1645
pubmed: 28380681
Plant Cell Physiol. 2011 Sep;52(9):1628-40
pubmed: 21784786
Genome Biol. 2010;11(2):R14
pubmed: 20132535
Plant Cell. 2017 Oct;29(10):2319-2335
pubmed: 28855333
Cell. 1999 Nov 12;99(4):367-76
pubmed: 10571179
New Phytol. 2003 Oct;160(1):209-223
pubmed: 33873535
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
New Phytol. 2015 Aug;207(3):669-82
pubmed: 25865500
Nat Commun. 2018 Jul 11;9(1):2683
pubmed: 29992948
Nat Commun. 2010 Jul 27;1:48
pubmed: 20975705
Cell Surf. 2019 Mar 21;5:100022
pubmed: 32743138
New Phytol. 2017 Apr;214(1):48-55
pubmed: 28067952
Mol Biol Evol. 2015 May;32(5):1284-95
pubmed: 25637935
New Phytol. 2018 Dec;220(4):1031-1046
pubmed: 29806959
Plant Cell. 2018 Jan;30(1):101-116
pubmed: 29321188
Mol Phylogenet Evol. 2019 Oct;139:106540
pubmed: 31252068
Nucleic Acids Res. 2007;35(11):3823-35
pubmed: 17526529
Science. 2019 Nov 22;366(6468):1021-1023
pubmed: 31754003
G3 (Bethesda). 2022 Mar 4;12(3):
pubmed: 35100375
Genome Biol. 2010;11(10):R106
pubmed: 20979621
Nature. 2017 Sep 21;549(7672):379-383
pubmed: 28902843
Proc Biol Sci. 2015 Sep 7;282(1814):
pubmed: 26311671
BMC Genomics. 2006 Dec 28;7:327
pubmed: 17194304
Plant Cell Environ. 2021 Jan;44(1):17-19
pubmed: 33047320
Front Plant Sci. 2021 Dec 09;12:793876
pubmed: 34956293
Plant Cell. 1995 Jul;7(7):921-34
pubmed: 7640526
Plant Cell Environ. 2021 Jan;44(1):20-33
pubmed: 32583877
Nucleic Acids Res. 2000 Jan 1;28(1):263-6
pubmed: 10592242
Nat Commun. 2018 Dec 21;9(1):5451
pubmed: 30575731
Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4126-33
pubmed: 9539701
Plant Physiol. 2008 Sep;148(1):402-13
pubmed: 18614712
Plant Cell. 2006 Apr;18(4):893-906
pubmed: 16517759
Curr Protoc Bioinformatics. 2018 Dec;64(1):e56
pubmed: 30332532
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Genome Res. 2014 Dec;24(12):2041-9
pubmed: 25327137
Bioinformatics. 2005 Oct 1;21(19):3787-93
pubmed: 15817693
Plant Cell. 2012 Oct;24(10):4236-51
pubmed: 23073651
New Phytol. 2015 Oct;208(1):26-38
pubmed: 25989832
Nat Genet. 2010 Mar;42(3):264-7
pubmed: 20139979
Nat Commun. 2018 Apr 24;9(1):1615
pubmed: 29691383
Plant Sci. 2017 Oct;263:39-45
pubmed: 28818382
Genome Biol Evol. 2016 Aug 03;8(7):2164-75
pubmed: 27412609
Nat Genet. 2015 Jan;47(1):65-72
pubmed: 25420146
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Nat Biotechnol. 2013 Dec;31(12):1119-25
pubmed: 24185095
Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10
pubmed: 22140109
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80
pubmed: 14681412
Mol Biol Evol. 2013 Aug;30(8):1987-97
pubmed: 23709260
New Phytol. 2020 Sep;227(5):1519-1529
pubmed: 31985062
Nat Methods. 2013 Jun;10(6):563-9
pubmed: 23644548
New Phytol. 2016 Jul;211(1):11-5
pubmed: 26832994
Bioinformatics. 2009 May 15;25(10):1335-7
pubmed: 19307242
Trends Plant Sci. 2014 Jul;19(7):426-31
pubmed: 24513255
Trends Plant Sci. 2021 Mar;26(3):272-287
pubmed: 33277186
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12
pubmed: 15215400
Plant Signal Behav. 2011 Oct;6(10):1436-9
pubmed: 21904115
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4
pubmed: 15608160
New Phytol. 2016 Sep;211(4):1338-51
pubmed: 27110912
Bioinformatics. 2004 Nov 1;20(16):2878-9
pubmed: 15145805
Nat Commun. 2017 Nov 2;8(1):1279
pubmed: 29093472
Curr Biol. 2011 Sep 27;21(18):1559-64
pubmed: 21924907
Mol Biol Evol. 2011 Jul;28(7):2077-86
pubmed: 21289370
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
J Biosci. 2002 Feb;27(1 Suppl 1):7-14
pubmed: 11927773
Ann Bot. 2015 Sep;116(3):391-402
pubmed: 26271118
New Phytol. 2010 Feb;185(3):605-9
pubmed: 20356335
Front Plant Sci. 2019 Nov 01;10:1359
pubmed: 31736999
Nat Genet. 2019 Oct;51(10):1549-1558
pubmed: 31570895