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De novo sequencing and comparative analysis of holy and sweet basil transcriptomes.

Rastogi S, Meena S, Bhattacharya A, Ghosh S, Shukla RK, Sangwan NS, Lal RK, Gupta MM, Lavania UC, Gupta V, Nagegowda DA, Shasany AK - BMC Genomics (2014)

Bottom Line: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively.Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism.Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, 226015 Lucknow, U,P, India. da.nagegowda@cimap.res.in.

ABSTRACT

Background: Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing.

Results: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.

Conclusion: This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.

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Related in: MedlinePlus

Distribution of transcripts encoding different transcription factors fromO. sanctumandO. basilicum. Abbreviations: basic/helix-loop-helix (bHLH), Homeodomain (HB), Zinc finger-Homeobox containing proteins (ZN-HD), MYB, APETELLA 2/Etheylene Responsive factor/Dehydration Responsive Element Binding proteins (AP2/ERF/DREB), basic leucine zipper (bZIP), WRKY, C2C2 [contains DNA binding with one finger (Dof), GATA binding proteins(GATA), Yabby, B-box, Constants-like protein (COL)], (CX2-4CX3FX5LX2HX3-5H)zinc-finger domain containing proteins (C2H2), MYB related, CCAAT binding (CCAAT), MADS- box containing (MADS), SCARECROW (GRAS), Heat Stress Factors (HSF), Auxin Regulatory Factor (ARF), calmodulin binding (CAMTA), PHD type Zinc finger protein (PHD), [TB1(teosinte branched 1), CYC (cycloidea) and PCF family genes] (TCP), Squamosa promoter binding protein (SBP), Arabidopsis Response Regulators/ B-motif (GARP-like motif) binding (ARR-B), Auxin induced factors (AUX/IAA), NLP, Growth Regulating factors (GRF/GIF), TUBBY like protein (TUB), trihelix DNA-binding domains (TRIHELIX), Basic Pentacysteine (BBR/BPC), High mobility group (HMG1/2)/ARID/BRIGHT DNA-binding domain-containing protein (HMG/ARID), Brassinosteroid (BR) repressor (BZR), Golden2-like (G2-like), Ethylene-insensitive-like (EIL), Jumonji (jmj)/zinc finger (C5HC2 type) (JUMONJI),FAR, RAV, Cys3His zinc finger domain containing protein (C3H), Vascular Plant Zinc Finger protein (VOZ), Cystein-rich polycomb-like protein (CPP), GLABROUS1 enhancer-binding protein (GeBP).
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Fig8: Distribution of transcripts encoding different transcription factors fromO. sanctumandO. basilicum. Abbreviations: basic/helix-loop-helix (bHLH), Homeodomain (HB), Zinc finger-Homeobox containing proteins (ZN-HD), MYB, APETELLA 2/Etheylene Responsive factor/Dehydration Responsive Element Binding proteins (AP2/ERF/DREB), basic leucine zipper (bZIP), WRKY, C2C2 [contains DNA binding with one finger (Dof), GATA binding proteins(GATA), Yabby, B-box, Constants-like protein (COL)], (CX2-4CX3FX5LX2HX3-5H)zinc-finger domain containing proteins (C2H2), MYB related, CCAAT binding (CCAAT), MADS- box containing (MADS), SCARECROW (GRAS), Heat Stress Factors (HSF), Auxin Regulatory Factor (ARF), calmodulin binding (CAMTA), PHD type Zinc finger protein (PHD), [TB1(teosinte branched 1), CYC (cycloidea) and PCF family genes] (TCP), Squamosa promoter binding protein (SBP), Arabidopsis Response Regulators/ B-motif (GARP-like motif) binding (ARR-B), Auxin induced factors (AUX/IAA), NLP, Growth Regulating factors (GRF/GIF), TUBBY like protein (TUB), trihelix DNA-binding domains (TRIHELIX), Basic Pentacysteine (BBR/BPC), High mobility group (HMG1/2)/ARID/BRIGHT DNA-binding domain-containing protein (HMG/ARID), Brassinosteroid (BR) repressor (BZR), Golden2-like (G2-like), Ethylene-insensitive-like (EIL), Jumonji (jmj)/zinc finger (C5HC2 type) (JUMONJI),FAR, RAV, Cys3His zinc finger domain containing protein (C3H), Vascular Plant Zinc Finger protein (VOZ), Cystein-rich polycomb-like protein (CPP), GLABROUS1 enhancer-binding protein (GeBP).

Mentions: Transcription factors (TFs) are sequence specific DNA-binding proteins interacting with the promoter regions of target genes to modulate their expression. In plants, these proteins play a very important role in regulation of plant development, reproduction, intercellular signalling, response to environment, cell cycle and are also important in the modulation of secondary metabolites biosynthesis[38]. In recent years, many studies have been reported on the involvement of various TF families like bHLH, bZIP, Zinc fingers, MYB, ARF, HSF, WRKY, HB and NAC in regulation of secondary metabolites and plant stress responses[25, 39]. As phenylpropanoids and terpenoids are the main determinants of aroma and flavour in Ocimum, it becomes important to investigate the transcriptional regulation of the genes involved their biosynthesis, which can further be used to modulate the pathway and develop phenylpropanoid or terpenoid enriched chemotypes. A few transcription factors from other plants, eg. EMISSION OF BENZENOIDS I (EOBI), EMISSION OF BENZENOIDS II (EOBII), and ODORANT 1 (ODO 1), MYB4, members of R2R3-MYB family regulate benzenoid/phenylpropanoid volatile biosynthesis in Petunia hybrida[40, 41]. ORCA2 and AP2 family member, MYC2, a bHLH family member and WRKY1 regulate indole alkaloid and terpenoid biosynthesis pathway in Catharanthus roseus[42, 43]. Similarly, a wound inducible WRKY transcription factor from Papaver somniferum was suggested to be involved in benzylisoquinoline biosynthetic pathway[44]. Also, in Lamiaceae family plants like Salvia miltiorrhiza and Perilla frutescens, TFs belonging to bHLH family are reported to be involved in phenypropanoid biosynthesis pathway[45, 46]. In the present investigation TFs were classified according to uniprot annotation for Arabidopsis family. A total of 3489 (5.9%) and 6074 (5.8%) transcripts in O. sanctum and O. basilicum, respectively were grouped into 40 TF families (Figure 8). Those which were annotated to have sequence specific transcription factor activity but cannot be grouped among any family were included in ‘other’ TFs category, following Arabidopsis transcription factor database (http://Arabidopsis.med.ohio-state.edu/AtTFDB/) and Plant transcription factor database (http://planttfdb.cbi.pku.edu.cn/)[47] classification. A systematic analysis of these transcription factors would help in understanding differential regulation of terpenoid and phenypropanoid pathways.Figure 8


De novo sequencing and comparative analysis of holy and sweet basil transcriptomes.

Rastogi S, Meena S, Bhattacharya A, Ghosh S, Shukla RK, Sangwan NS, Lal RK, Gupta MM, Lavania UC, Gupta V, Nagegowda DA, Shasany AK - BMC Genomics (2014)

Distribution of transcripts encoding different transcription factors fromO. sanctumandO. basilicum. Abbreviations: basic/helix-loop-helix (bHLH), Homeodomain (HB), Zinc finger-Homeobox containing proteins (ZN-HD), MYB, APETELLA 2/Etheylene Responsive factor/Dehydration Responsive Element Binding proteins (AP2/ERF/DREB), basic leucine zipper (bZIP), WRKY, C2C2 [contains DNA binding with one finger (Dof), GATA binding proteins(GATA), Yabby, B-box, Constants-like protein (COL)], (CX2-4CX3FX5LX2HX3-5H)zinc-finger domain containing proteins (C2H2), MYB related, CCAAT binding (CCAAT), MADS- box containing (MADS), SCARECROW (GRAS), Heat Stress Factors (HSF), Auxin Regulatory Factor (ARF), calmodulin binding (CAMTA), PHD type Zinc finger protein (PHD), [TB1(teosinte branched 1), CYC (cycloidea) and PCF family genes] (TCP), Squamosa promoter binding protein (SBP), Arabidopsis Response Regulators/ B-motif (GARP-like motif) binding (ARR-B), Auxin induced factors (AUX/IAA), NLP, Growth Regulating factors (GRF/GIF), TUBBY like protein (TUB), trihelix DNA-binding domains (TRIHELIX), Basic Pentacysteine (BBR/BPC), High mobility group (HMG1/2)/ARID/BRIGHT DNA-binding domain-containing protein (HMG/ARID), Brassinosteroid (BR) repressor (BZR), Golden2-like (G2-like), Ethylene-insensitive-like (EIL), Jumonji (jmj)/zinc finger (C5HC2 type) (JUMONJI),FAR, RAV, Cys3His zinc finger domain containing protein (C3H), Vascular Plant Zinc Finger protein (VOZ), Cystein-rich polycomb-like protein (CPP), GLABROUS1 enhancer-binding protein (GeBP).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4125705&req=5

Fig8: Distribution of transcripts encoding different transcription factors fromO. sanctumandO. basilicum. Abbreviations: basic/helix-loop-helix (bHLH), Homeodomain (HB), Zinc finger-Homeobox containing proteins (ZN-HD), MYB, APETELLA 2/Etheylene Responsive factor/Dehydration Responsive Element Binding proteins (AP2/ERF/DREB), basic leucine zipper (bZIP), WRKY, C2C2 [contains DNA binding with one finger (Dof), GATA binding proteins(GATA), Yabby, B-box, Constants-like protein (COL)], (CX2-4CX3FX5LX2HX3-5H)zinc-finger domain containing proteins (C2H2), MYB related, CCAAT binding (CCAAT), MADS- box containing (MADS), SCARECROW (GRAS), Heat Stress Factors (HSF), Auxin Regulatory Factor (ARF), calmodulin binding (CAMTA), PHD type Zinc finger protein (PHD), [TB1(teosinte branched 1), CYC (cycloidea) and PCF family genes] (TCP), Squamosa promoter binding protein (SBP), Arabidopsis Response Regulators/ B-motif (GARP-like motif) binding (ARR-B), Auxin induced factors (AUX/IAA), NLP, Growth Regulating factors (GRF/GIF), TUBBY like protein (TUB), trihelix DNA-binding domains (TRIHELIX), Basic Pentacysteine (BBR/BPC), High mobility group (HMG1/2)/ARID/BRIGHT DNA-binding domain-containing protein (HMG/ARID), Brassinosteroid (BR) repressor (BZR), Golden2-like (G2-like), Ethylene-insensitive-like (EIL), Jumonji (jmj)/zinc finger (C5HC2 type) (JUMONJI),FAR, RAV, Cys3His zinc finger domain containing protein (C3H), Vascular Plant Zinc Finger protein (VOZ), Cystein-rich polycomb-like protein (CPP), GLABROUS1 enhancer-binding protein (GeBP).
Mentions: Transcription factors (TFs) are sequence specific DNA-binding proteins interacting with the promoter regions of target genes to modulate their expression. In plants, these proteins play a very important role in regulation of plant development, reproduction, intercellular signalling, response to environment, cell cycle and are also important in the modulation of secondary metabolites biosynthesis[38]. In recent years, many studies have been reported on the involvement of various TF families like bHLH, bZIP, Zinc fingers, MYB, ARF, HSF, WRKY, HB and NAC in regulation of secondary metabolites and plant stress responses[25, 39]. As phenylpropanoids and terpenoids are the main determinants of aroma and flavour in Ocimum, it becomes important to investigate the transcriptional regulation of the genes involved their biosynthesis, which can further be used to modulate the pathway and develop phenylpropanoid or terpenoid enriched chemotypes. A few transcription factors from other plants, eg. EMISSION OF BENZENOIDS I (EOBI), EMISSION OF BENZENOIDS II (EOBII), and ODORANT 1 (ODO 1), MYB4, members of R2R3-MYB family regulate benzenoid/phenylpropanoid volatile biosynthesis in Petunia hybrida[40, 41]. ORCA2 and AP2 family member, MYC2, a bHLH family member and WRKY1 regulate indole alkaloid and terpenoid biosynthesis pathway in Catharanthus roseus[42, 43]. Similarly, a wound inducible WRKY transcription factor from Papaver somniferum was suggested to be involved in benzylisoquinoline biosynthetic pathway[44]. Also, in Lamiaceae family plants like Salvia miltiorrhiza and Perilla frutescens, TFs belonging to bHLH family are reported to be involved in phenypropanoid biosynthesis pathway[45, 46]. In the present investigation TFs were classified according to uniprot annotation for Arabidopsis family. A total of 3489 (5.9%) and 6074 (5.8%) transcripts in O. sanctum and O. basilicum, respectively were grouped into 40 TF families (Figure 8). Those which were annotated to have sequence specific transcription factor activity but cannot be grouped among any family were included in ‘other’ TFs category, following Arabidopsis transcription factor database (http://Arabidopsis.med.ohio-state.edu/AtTFDB/) and Plant transcription factor database (http://planttfdb.cbi.pku.edu.cn/)[47] classification. A systematic analysis of these transcription factors would help in understanding differential regulation of terpenoid and phenypropanoid pathways.Figure 8

Bottom Line: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively.Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism.Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Divison, CSIR-Central Institute of Medicinal and Aromatic Plants, P,O, CIMAP, 226015 Lucknow, U,P, India. da.nagegowda@cimap.res.in.

ABSTRACT

Background: Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing.

Results: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism. Also SSR and SNP markers were identified in the transcriptomes of both species with many SSRs linked to phenylpropanoid and terpenoid pathway genes.

Conclusion: This is the first report of a comparative transcriptome analysis of Ocimum species and can be utilized to characterize genes related to secondary metabolism, their regulation, and breeding special chemotypes with unique essential oil composition in Ocimum.

Show MeSH
Related in: MedlinePlus