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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

KEGG classification based on secondary metabolism categories. Bracketed numbers represent various secondary metabolic pathways abbreviated as: (1) Terpenoid backbone biosynthesis; (2) Streptomycin biosynthesis; (3) Stilbenoid, diarylheptanoid and gingerol biosynthesis; (4) Sesquiterpenoid and triterpenoid biosynthesis; (5) Polyketide sugar unit biosynthesis; (6) Phenylpropanoid biosynthesis; (7) Novobiocin biosynthesis; (8) Monoterpenoid biosynthesis; (9) Limonene and pinene degradation; (10) Isoquinoline alkaloid biosynthesis; (11) Indole alkaloid biosynthesis; (12) Glucosinolate biosynthesis; (13) Geraniol degradation; (14) Flavonoid biosynthesis; (15) Flavone and flavonol biosynthesis; (16) Diterpenoid biosynthesis; (17) Carotenoid biosynthesis; (18) Caffeine metabolism; (19) Butirosin and neomycin biosynthesis; (20) Brassinosteroid biosynthesis; (21) Biosynthesis; of siderophore group nonribosomal peptides; (22) Biosynthesis of ansamycins; (23) Betalain biosynthesis; (24) Anthocyanin biosynthesis; (25) Zeatin biosynthesis; (26) Tropane, piperidine and pyridine alkaloid biosynthesis; (27) Tetracycline biosynthesis.
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Fig3: KEGG classification based on secondary metabolism categories. Bracketed numbers represent various secondary metabolic pathways abbreviated as: (1) Terpenoid backbone biosynthesis; (2) Streptomycin biosynthesis; (3) Stilbenoid, diarylheptanoid and gingerol biosynthesis; (4) Sesquiterpenoid and triterpenoid biosynthesis; (5) Polyketide sugar unit biosynthesis; (6) Phenylpropanoid biosynthesis; (7) Novobiocin biosynthesis; (8) Monoterpenoid biosynthesis; (9) Limonene and pinene degradation; (10) Isoquinoline alkaloid biosynthesis; (11) Indole alkaloid biosynthesis; (12) Glucosinolate biosynthesis; (13) Geraniol degradation; (14) Flavonoid biosynthesis; (15) Flavone and flavonol biosynthesis; (16) Diterpenoid biosynthesis; (17) Carotenoid biosynthesis; (18) Caffeine metabolism; (19) Butirosin and neomycin biosynthesis; (20) Brassinosteroid biosynthesis; (21) Biosynthesis; of siderophore group nonribosomal peptides; (22) Biosynthesis of ansamycins; (23) Betalain biosynthesis; (24) Anthocyanin biosynthesis; (25) Zeatin biosynthesis; (26) Tropane, piperidine and pyridine alkaloid biosynthesis; (27) Tetracycline biosynthesis.

Mentions: To identify the biological pathways functional in the leaf tissues of O. sanctum and O. basilicum, 69117 and 130043 assembled transcripts from both species were mapped to the reference canonical pathways in KEGG. All transcripts were classified mainly under five categories: metabolism, cellular processes, genetic information processing, environmental information processing and others. Highest number of transcripts from both O. sanctum and O. basilicum were related to metabolism followed by others. In total, all transcripts from O. sanctum and O. basilicum were assigned to 332 KEGG pathways (Additional file4). Interestingly, 501 and 952 transcripts, respectively, from O. sanctum and O. basilicum were found to be involved in biosynthesis of various secondary metabolites. The cluster for ‘Phenylpropanoid biosynthesis [PATH: ko00940]’ and ‘Terpenoid backbone biosynthesis [PATH: ko00900]’ represented the largest group. As observed from Figure 3, the category of ‘terpenoid backbone biosynthesis’ showed highest percentage of transcripts compared to ‘phenylpropanoid biosynthesis’ in O. sanctum (20.56%) where as O. basilicum had highest percentage (17.02%) of transcripts related to ‘phenylpropanoid biosynthesis’. The list of chemicals and activities specifically in the leaf tissues of O. sanctum/tenuiflorum and O. basilicum as displayed in the Dr. Duke’s Phytochemical and Ethnobotanical database (http://sun.ars-grin.gov:8080/npgspub/xsql/duke/findsp.xsql?letter=Ocimum&p_request=Go&amt=sc) also supported the higher percentage of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. From the total compounds in Duke’s database O. sanctum showed a higher percentage of diverse terpenoids (53.1%, 34 types) where as O. basilicum was found to be rich in phenylpropanoids (65.9%, 27 types; Additional file5).Figure 3


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)

KEGG classification based on secondary metabolism categories. Bracketed numbers represent various secondary metabolic pathways abbreviated as: (1) Terpenoid backbone biosynthesis; (2) Streptomycin biosynthesis; (3) Stilbenoid, diarylheptanoid and gingerol biosynthesis; (4) Sesquiterpenoid and triterpenoid biosynthesis; (5) Polyketide sugar unit biosynthesis; (6) Phenylpropanoid biosynthesis; (7) Novobiocin biosynthesis; (8) Monoterpenoid biosynthesis; (9) Limonene and pinene degradation; (10) Isoquinoline alkaloid biosynthesis; (11) Indole alkaloid biosynthesis; (12) Glucosinolate biosynthesis; (13) Geraniol degradation; (14) Flavonoid biosynthesis; (15) Flavone and flavonol biosynthesis; (16) Diterpenoid biosynthesis; (17) Carotenoid biosynthesis; (18) Caffeine metabolism; (19) Butirosin and neomycin biosynthesis; (20) Brassinosteroid biosynthesis; (21) Biosynthesis; of siderophore group nonribosomal peptides; (22) Biosynthesis of ansamycins; (23) Betalain biosynthesis; (24) Anthocyanin biosynthesis; (25) Zeatin biosynthesis; (26) Tropane, piperidine and pyridine alkaloid biosynthesis; (27) Tetracycline biosynthesis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: KEGG classification based on secondary metabolism categories. Bracketed numbers represent various secondary metabolic pathways abbreviated as: (1) Terpenoid backbone biosynthesis; (2) Streptomycin biosynthesis; (3) Stilbenoid, diarylheptanoid and gingerol biosynthesis; (4) Sesquiterpenoid and triterpenoid biosynthesis; (5) Polyketide sugar unit biosynthesis; (6) Phenylpropanoid biosynthesis; (7) Novobiocin biosynthesis; (8) Monoterpenoid biosynthesis; (9) Limonene and pinene degradation; (10) Isoquinoline alkaloid biosynthesis; (11) Indole alkaloid biosynthesis; (12) Glucosinolate biosynthesis; (13) Geraniol degradation; (14) Flavonoid biosynthesis; (15) Flavone and flavonol biosynthesis; (16) Diterpenoid biosynthesis; (17) Carotenoid biosynthesis; (18) Caffeine metabolism; (19) Butirosin and neomycin biosynthesis; (20) Brassinosteroid biosynthesis; (21) Biosynthesis; of siderophore group nonribosomal peptides; (22) Biosynthesis of ansamycins; (23) Betalain biosynthesis; (24) Anthocyanin biosynthesis; (25) Zeatin biosynthesis; (26) Tropane, piperidine and pyridine alkaloid biosynthesis; (27) Tetracycline biosynthesis.
Mentions: To identify the biological pathways functional in the leaf tissues of O. sanctum and O. basilicum, 69117 and 130043 assembled transcripts from both species were mapped to the reference canonical pathways in KEGG. All transcripts were classified mainly under five categories: metabolism, cellular processes, genetic information processing, environmental information processing and others. Highest number of transcripts from both O. sanctum and O. basilicum were related to metabolism followed by others. In total, all transcripts from O. sanctum and O. basilicum were assigned to 332 KEGG pathways (Additional file4). Interestingly, 501 and 952 transcripts, respectively, from O. sanctum and O. basilicum were found to be involved in biosynthesis of various secondary metabolites. The cluster for ‘Phenylpropanoid biosynthesis [PATH: ko00940]’ and ‘Terpenoid backbone biosynthesis [PATH: ko00900]’ represented the largest group. As observed from Figure 3, the category of ‘terpenoid backbone biosynthesis’ showed highest percentage of transcripts compared to ‘phenylpropanoid biosynthesis’ in O. sanctum (20.56%) where as O. basilicum had highest percentage (17.02%) of transcripts related to ‘phenylpropanoid biosynthesis’. The list of chemicals and activities specifically in the leaf tissues of O. sanctum/tenuiflorum and O. basilicum as displayed in the Dr. Duke’s Phytochemical and Ethnobotanical database (http://sun.ars-grin.gov:8080/npgspub/xsql/duke/findsp.xsql?letter=Ocimum&p_request=Go&amt=sc) also supported the higher percentage of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. From the total compounds in Duke’s database O. sanctum showed a higher percentage of diverse terpenoids (53.1%, 34 types) where as O. basilicum was found to be rich in phenylpropanoids (65.9%, 27 types; Additional file5).Figure 3

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