Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities
Abstract
:1. Introduction
2. Results
2.1. The Number of FMO Genes Varies in Wild and Cultivated Species of Rice
2.2. The Distribution of FMO Genes on Chromosomes Reveals the Presence of Gene Clusters
2.3. Phylogenetic Analysis Shows Conservation among FMO Family and the Majority of Them Belongs to the S-Oxygenating Clade in Different Oryza Species
2.4. Protein Motif Analysis Reveals Five Conserved Motifs in FMO Members from Different Oryza Species
2.5. Analysis of Gene Architecture Depicts Conservation among Orthologs from Different Oryza Species
2.6. Domain Assessment Reveals Loss of Extra Copies of FAD Domain during the Course of Domestication
2.7. Developmental and Stress-Mediated Expression Profiling of FMO Genes Reveals Tissue Specificity and Perturbations in a Subset of Genes in Different Abiotic Stresses
3. Discussion
4. Materials and Methods
4.1. Identification of the FMO Family Members in Rice
4.2. Phylogenetic Analysis
4.3. Motif Analysis
4.4. Evaluation of Domain Architecture of the FMO Family Proteins
4.5. Evaluation of the Gene Structure
4.6. Developmental and Stress-Mediated Expression Profiling of the FMO Encoding Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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(A) Chromosome | O. brachyantha | O. punctata | O. meridionalis | O. glumaepatula | O. glaberrima |
1 | ObrFMO1 (OB01G18060) | OpFMO1 (OPUNC01G07650) | OmFMO1(OMERI01G07820) | OgFMO1 (OGLUM01G08960) | OglFMO1 (ORGLA01G0069900) |
ObrFMO2 (OB01G21130) | OpFMO2 (OPUNC01G10840) | OmFMO2 (OMERI01G13920) | OgFMO2 (OGLUM01G12480) | OglFMO2 (ORGLA01G0126800) | |
ObrFMO3 (OB01G33700) | OpFMO3 (OPUNC01G16290) | OmFMO3 (OMERI01G14340) | OgFMO3 (OGLUM01G17290) | OglFMO3 (ORGLA01G0197300) | |
ObrFMO4 (OB01G38810) | OpFMO4 (OPUNC01G24520) | OmFMO4 (OMERI01G24550) | OgFMO4 (OGLUM01G17860) | OglFMO4 (ORGLA01G0245000) | |
OpFMO5 (OPUNC01G29760) | OmFMO5 (OMERI01G27380) | OgFMO5 (OGLUM01G28330) | |||
OgFMO6 (OGLUM01G33960) | |||||
2 | ObrFMO5 (OB02G29400) | OpFMO6 (OPUNC02G19680) | OmFMO6 (OMERI02G00100) | OgFMO7 (OGLUM02G22140) | OglFMO5 (ORGLA02G0106500) |
OmFMO7 (OMERI02G12510) | OglFMO6 (ORGLA02G0187600) | ||||
OmFMO8 (OMERI02G12660) | |||||
3 | ObrFMO6 (OB03G14710) | OpFMO7 (OPUNC03G04320) | OmFMO9 (OMERI03G04440) | OgFMO8 (OGLUM03G04490) | OglFMO7 (ORGLA03G0044100) |
ObrFMO7 (OB03G16080) | OpFMO8 (OPUNC03G05820) | OmFMO10 (OMERI03G05840) | OgFMO9 (OGLUM03G06010) | OglFMO8 (ORGLA03G0058000) | |
4 | ObrFMO8 (OB04G11140) | OpFMO9 (OPUNC04G01360) | OmFMO11 (OMERI04G01170) | OgFMO10 (OGLUM04G03890) | OglFMO9 (ORGLA04G0010900 |
ObrFMO9 (OB04G13610) | OpFMO10 (OPUNC04G04050) | OmFMO12 (OMERI04G04660) | OgFMO11 (OGLUM04G03900) | OglFMO10 (ORGLA04G0035200) | |
OmFMO13 (OMERI04G04670) | OgFMO12 (OGLUM04G03920) | OglFMO11 (ORGLA04G0035300) | |||
OmFMO14 (OMERI04G04680) | |||||
5 | OmFMO15 (OMERI05G21010) | OgFMO13 (OGLUM05G24890) | |||
OmFMO16 (OMERI05G09400) | |||||
6 | ObrFMO10 (OB06G16030) | OpFMO11 (OPUNC06G06240) | OmFMO17 (OMERI06G03520) | OgFMO14 (OGLUM06G06900) | OglFMO12 (ORGLA06G0061000) |
OpFMO12 (OPUNC06G15440) | OmFMO18 (OMERI06G03530) | OgFMO15 (OGLUM06G06910) | OglFMO13 (ORGLA06G0060800) | ||
OmFMO19 (OMERI06G03580) | OgFMO16 (OGLUM06G14980) | OglFMO14 (ORGLA06G0141900) | |||
OmFMO20 (OMERI06G07480) | OgFMO17 (OGLUM06G18150) | ||||
OmFMO21 (OMERI06G07660) | |||||
7 | ObrFMO11 (OB07G10720) | OpFMO13 (OPUNC07G00810) | OmFMO22 (OMERI07G09890) | OgFMO18 (OGLUM07G00790) | OglFMO15 (ORGLA07G0007100) |
ObrFMO12 (OB07G10730) | OpFMO14 (OPUNC07G00820) | OgFMO19 (OGLUM07G00830) | OglFMO16 (ORGLA07G0007200) | ||
ObrFMO13 (OB07G10740) | OpFMO15 (OPUNC07G00840) | OgFMO20 (OGLUM07G11860) | OglFMO17 (ORGLA07G0104200) | ||
ObrFMO14 (OB07G10800) | OpFMO16 (OPUNC07G11050) | ||||
ObrFMO15 (OB07G18620) | |||||
8 | ObrFMO16 (OB08G20080) | ||||
9 | ObrFMO17 (OB09G25280) | OpFMO17 (OPUNC09G17070) | OgFMO21 (OGLUM09G00600) | OglFMO18 (ORGLA09G0148600) | |
ObrFMO18 (OB09G25420) | OgFMO22 (OGLUM09G19160) | OglFMO19 (ORGLA09G0148800) | |||
ObrFMO19 (OB09G25300) | OgFMO23 (OGLUM09G19180) | OglFMO20 (ORGLA09G0149000) | |||
OgFMO24 (OGLUM09G19210) | |||||
10 | ObrFMO20 (OB10G25150) | OpFMO18 (OPUNC10G16400) | OmFMO23 (OMERI10G14540) | OgFMO25 (OGLUM10G04710) | OglFMO21 (ORGLA10G0131800) |
ObrFMO21 (OB10G25220) | OpFMO19 (OPUNC10G16470) | OmFMO24 (OMERI10G14600) | OgFMO26 (OGLUM10G18140) | OglFMO22 (ORGLA10G0132300) | |
OgFMO27 (OGLUM10G18190) | |||||
11 | ObrFMO22 (OB11G13490) | OpFMO20 (OPUNC11G06230) | OmFMO25 (OMERI11G05170) | OgFMO28 (OGLUM11G05950) | OglFMO23 (ORGLA11G0056800) |
ObrFMO23 (OB11G14940) | OpFMO21 (OPUNC11G14790) | OmFMO26 (OMERI11G08970) | OgFMO29 (OGLUM11G06000) | ||
12 | ObrFMO24 (OB12G14990) | OpFMO22 (OPUNC12G05050) | OmFMO27 (OMERI12G03610) | OgFMO30 (OGLUM12G06000) | OglFMO24 (ORGLA12G0049500) |
ObrFMO25 (OB12G21170) | |||||
(B) Chromosome | O. barthii | O. nivara | O. indica | O. rufipogon | O. japonica |
1 | ObaFMO1 (OBART01G07810) | OnFMO1 (ONIVA01G10070) | OsIFMO1 (BGIOSGA001676) | OrFMO1 (ORUFI01G08580) | OsJFMO1 (Os01g0224700) |
ObaFMO2 (OBART01G15500) | OnFMO2 (ONIVA01G17610) | OsIFMO2 (BGIOSGA003035) | OrFMO2 (ORUFI01G17290) | OsJFMO2 (Os01g0368000) | |
ObaFMO3 (OBART01G24440) | OnFMO3 (ONIVA01G27650) | OsIFMO3 (BGIOSGA003523) | OrFMO3 (ORUFI01G27360) | OsJFMO3 (Os01g0645400) | |
ObaFMO4 (OBART01G29910) | OnFMO4 (ONIVA01G34190) | OsIFMO4 (BGIOSGA004101) | OrFMO4 (ORUFI01G33000) | OsJFMO4 (Os01g0732700) | |
OsIFMO5 (BGIOSGA004401) | |||||
OsIFMO6 (BGIOSGA007947) | |||||
2 | ObaFMO5 (OBART02G11820) | OnFMO5 (ONIVA02G24200) | OsIFMO7 (BGIOSGA008498) | OrFMO5 (ORUFI02G11880) | OsJFMO5 (Os02g0272200) |
ObaFMO6 (OBART02G21940) | OrFMO6 (ORUFI02G23020) | OsJFMO6 (Os02g0580600) | |||
3 | ObaFMO7 (OBART03G04640) | OnFMO6 (ONIVA03G04410) | OsIFMO8 (BGIOSGA011917) | OrFMO7 (ORUFI03G04340) | OsJFMO7 (Os03g0162000) |
ObaFMO8 (OBART03G06010) | OnFMO7 (ONIVA03G06000) | OsIFMO9 (BGIOSGA011989) | OrFMO8 (ORUFI03G05830) | OsJFMO8 (Os03g0182000) | |
4 | ObaFMO9 (OBART04G01320) | OnFMO8 (ONIVA04G01060) | OsIFMO10 (BGIOSGA015543) | OrFMO9 (ORUFI04G01570) | OsJFMO9 (Os04g0128900) |
ObaFMO10 (OBART04G04730) | OsIFMO11 (BGIOSGA015544) | OrFMO10 (ORUFI04G05470) | OsJFMO10 (Os04g0223500) | ||
ObaFMO11 (OBART04G04740) | OsIFMO12 (BGIOSGA015545) | OsJFMO11 (Os04g0223901) | |||
OsIFMO13 (BGIOSGA015673) | |||||
5 | ObaFMO12 (OBART05G23490) | OsIFMO14 (BGIOSGA017689) | OrFMO11 (ORUFI05G24980) | OsJFMO12 (Os05g0528600) | |
6 | ObaFMO13 (OBART06G06490) | OnFMO9 (ONIVA06G07560) | OsIFMO15 (BGIOSGA021117) | OrFMO12 (ORUFI06G06790) | OsJFMO13 (Os06g0203200) |
ObaFMO14 (OBART06G14000) | OnFMO10 (ONIVA06G07670) | OsIFMO16 (BGIOSGA021291) | OrFMO13 (ORUFI06G14920) | OsJFMO14 (Os06g0203400) | |
ObaFMO15 (OBART06G17060) | OnFMO11 (ONIVA06G07680) | OsIFMO17 (BGIOSGA021706) | OrFMO14 (ORUFI06G18060) | OsJFMO15 (Os06g0528700) | |
OnFMO12 (ONIVA06G20350) | OsIFMO18 (BGIOSGA021707) | ||||
7 | ObaFMO16 (OBART07G00890) | OnFMO13 (ONIVA07G10070) | OsIFMO19 (BGIOSGA024391) | OrFMO15 (ORUFI07G00810) | OsJFMO16 (Os07g0111700) |
OsIFMO20 (BGIOSGA025032) | OrFMO16 (ORUFI07G00820) | OsJFMO17 (Os07g0111900) | |||
OsIFMO21 (BGIOSGA025033) | OrFMO17 (ORUFI07G12500) | OsJFMO18 (Os07g0112000) | |||
OsIFMO22 (BGIOSGA025034) | OsJFMO19 (Os07g0112100) | ||||
OsJFMO20 (Os07g0437000) | |||||
8 | OnFMO14 (ONIVA08G22170) | ||||
9 | ObaFMO17 (OBART09G18660) | OnFMO15 (ONIVA09G19750) | OsIFMO23 (BGIOSGA029321) | OrFMO18 (ORUFI09G20190) | OsJFMO21 (Os09g0548400) |
ObaFMO18 (OBART09G18680) | OnFMO16 (ONIVA09G19770) | OsIFMO24 (BGIOSGA029325) | OrFMO19 (ORUFI09G20260) | OsJFMO22 (Os09g0548700) | |
ObaFMO19 (OBART09G18710) | OnFMO17 (ONIVA09G19830) | OsIFMO25 (BGIOSGA029326) | OsJFMO23 (Os09g0549300) | ||
OnFMO18 (ONIVA10G13930) | |||||
10 | ObaFMO20 (OBART10G18040) | OnFMO19 (ONIVA10G14730) | OsIFMO26 (BGIOSGA031436) | OrFMO20 (ORUFI10G19230) | OsJFMO24 (Os10g0553800) |
ObaFMO21 (OBART10G18090) | OnFMO20 (ONIVA10G14740) | OsIFMO27 (BGIOSGA031433) | OrFMO21 (ORUFI10G19280) | OsJFMO25 (Os10g0554300) | |
OnFMO21 (ONIVA10G20590) | |||||
OnFMO22 (ONIVA10G20640) | |||||
11 | ObaFMO22 (OBART11G06190) | OnFMO23 (ONIVA11G06260) | OsIFMO28 (BGIOSGA034995) | OrFMO22 (ORUFI11G06350) | OsJFMO26 (Os11g0207700) |
ObaFMO23 (OBART11G06210) | OrFMO23 (ORUFI11G06380) | OsJFMO27 (Os11g0207900) | |||
12 | ObaFMO24 (OBART12G05080) | OnFMO24 (ONIVA12G04710) | OsIFMO29 (BGIOSGA036502) | OrFMO24 (ORUFI12G05850) | OsJFMO28 (Os12g0189500) |
ObaFMO25 (OBART12G13520) |
Chromosome | O. brachyantha | O. punctata | O. meridionalis | O. glumaepatula | O. glaberrima | O. barthii | O. nivara | O. indica | O. rufipogon | O. japonica |
---|---|---|---|---|---|---|---|---|---|---|
1 | ObrFMO1 | OpFMO1 | OmFMO1 | OgFMO1 | OglFMO1 | ObaFMO1 | OnFMO1 | OsIFMO2 | OrFMO1 | OsJFMO1 |
ObrFMO2 | OpFMO2 | OgFMO2 | ||||||||
OpFMO3 | OmFMO3 | OgFMO4 | OglFMO2 | ObaFMO2 | OsIFMO3 | OrFMO2 | OsJFMO2 | |||
ObrFMO3 | OpFMO4 | OmFMO4 | OgFMO5 | OglFMO3 | ObaFMO3 | OnFMO3 | OsIFMO4 | OrFMO3 | OsJFMO3 | |
ObrFMO4 | OpFMO5 | OmFMO5 | OgFMO6 | OglFMO4 | ObaFMO4 | OnFMO4 | OsIFMO5 | OrFMO4 | OsJFMO4 | |
2 | OmFMO8 | OglFMO5 | ObaFMO5 | OsIFMO6 | OrFMO5 | OsJFMO5 | ||||
ObrFMO5 | OpFMO6 | OmFMO6, OmFMO16 * | OgFMO7 | OglFMO6 | ObaFMO6 | OnFMO5 | OsIFMO7 | OrFMO6 | OsJFMO6 | |
3 | ObrFMO6 | OpFMO7 | OmFMO9 | OgFMO8 | OglFMO7 | ObaFMO7 | OnFMO6 | OsIFMO8 | OrFMO7 | OsJFMO7 |
ObrFMO7 | OpFMO8 | OmFMO10 | OgFMO9 | OglFMO8 | ObaFMO8 | OnFMO7 | OsIFMO9 | OrFMO8 | OsJFMO8 | |
4 | ObrFMO8 | OpFMO9 | OmFMO11, OmFMO2 * | OgFMO21 *, OgFMO3 | OglFMO9 | ObaFMO9 | OnFMO8, OnFMO2 * | OsIFMO1, OsIFMO13 | OrFMO9 | OsJFMO9 |
ObrFMO9 | OpFMO10 | OmFMO13 | OgFMO11 | OglFMO10 | ObaFMO10 | OnFMO19 * | OsIFMO11, OsIFMO12 | OsJFMO10 | ||
OmFMO12 OmFMO14 | OgFMO10, OgFMO12 | OglFMO11 | ObaFMO11 | OnFMO20 * | OsIFMO10 | OrFMO10 | OsJFMO11 | |||
OmFMO15 | OgFMO13 | ObaFMO12 | OnFMO14 * | OsIFMO14 | OrFMO11 | OsJFMO12 | ||||
5 | ObrFMO10 | OmFMO20, OmFMO21 | OgFMO14 | OglFMO12 | ObaFMO13 | OnFMO9 | OsIFMO18 | OsJFMO13 | ||
6 | OnFMO10 | |||||||||
OpFMO11 | OgFMO15 | OglFMO13 | OnFMO11 | OsIFMO17 | OrFMO12 | OsJFMO14 | ||||
OpFMO12 | OgFMO17 | OglFMO14 | ObaFMO15 | OnFMO12 | OsIFMO15 | OrFMO14 | OsJFMO15 | |||
OmFMO26 * | OgFMO25, OgFMO16 * | ObaFMO14 | OsIFMO16, OsIFMO22 | OrFMO13 | OsJFMO18 * | |||||
7 | ObrFMO11, ObrFMO12, ObrFMO13 | OpFMO13 | OgFMO18 | ObaFMO16 | OnFMO18 * | OsIFMO20 | OrFMO15 | OsJFMO16, OsJFMO17 | ||
ObrFMO14, ObrFMO22, ObrFMO16 * | OpFMO14, OpFMO15 | OmFMO7 * | OgFMO19 | OglFMO15, OglFMO16 | OsIFMO21 | OrFMO16 | OsJFMO19 | |||
ObrFMO15 | OpFMO16 | OmFMO22 | OgFMO20 | OglFMO17 | OnFMO13 | OsIFMO19 | OrFMO17 | OsJFMO20 | ||
9 | ObrFMO17 | OpFMO17 | OmFMO17 * | OgFMO22 | OglFMO18 | ObaFMO17 | OnFMO15 | OsIFMO25 | OrFMO18 | OsJFMO21 |
ObrFMO19 | OmFMO18 * | OgFMO23 | OglFMO19 | ObaFMO18 | OnFMO16 | OsIFMO24 | - | OsJFMO22 | ||
ObrFMO18 | OmFMO19 * | OgFMO24 | OglFMO20 | ObaFMO19 | OnFMO17 | OsIFMO23 | OrFMO19 | OsJFMO23 | ||
10 | ObrFMO20 | OpFMO18 | OmFMO23 | OgFMO26 | OglFMO21 | ObaFMO20 | OnFMO21 | OsIFMO26 | OrFMO20 | OsJFMO24 |
ObrFMO21 | OpFMO19 | OmFMO24 | OgFMO27 | OglFMO22 | ObaFMO21 | OnFMO22 | OsIFMO27 | OrFMO21 | OsJFMO25 | |
11 | OpFMO20 | OmFMO25 | OgFMO28 | OglFMO23 | ObaFMO22 | OrFMO22, OrFMO23 | OsJFMO26 | |||
ObrFMO23 | OpFMO21 | OgFMO29 | ObaFMO23 | OnFMO23 | OsIFMO28 | OsJFMO27 | ||||
12 | ObrFMO24 | OpFMO22 | OmFMO27 | OgFMO30 | OglFMO24 | ObaFMO24 | OnFMO24 | OsIFMO29 | OrFMO24 | OsJFMO28 |
ObrFMO25 | ObaFMO25 | - |
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Gaba, Y.; Bhowal, B.; Pareek, A.; Singla-Pareek, S.L. Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities. Int. J. Mol. Sci. 2023, 24, 4190. https://doi.org/10.3390/ijms24044190
Gaba Y, Bhowal B, Pareek A, Singla-Pareek SL. Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities. International Journal of Molecular Sciences. 2023; 24(4):4190. https://doi.org/10.3390/ijms24044190
Chicago/Turabian StyleGaba, Yashika, Bidisha Bhowal, Ashwani Pareek, and Sneh Lata Singla-Pareek. 2023. "Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities" International Journal of Molecular Sciences 24, no. 4: 4190. https://doi.org/10.3390/ijms24044190