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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.

Show MeSH
Histogram of gene ontology classification. The results are summarized in three main categories: biological process, cellular component and molecular function. Bars represent assignments of O. basilicum and O. sanctum transcripts (percent) with BLAST matches in the uniprot database (Arabidopsis) to each GO term.
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Fig2: Histogram of gene ontology classification. The results are summarized in three main categories: biological process, cellular component and molecular function. Bars represent assignments of O. basilicum and O. sanctum transcripts (percent) with BLAST matches in the uniprot database (Arabidopsis) to each GO term.

Mentions: Gene Ontology (GO) is an international standardized gene functional classification system offering an updated and a strictly defined concept to comprehensively describe the properties of genes and gene products in any organism[24]. In order to assign putative functions, transcripts from O. sanctum and O. basilicum were compared against the NR protein sequences of Arabidopsis, rice and lamiaceae family available at uniprot database using blastx algorithm. The associated hits were searched for their respective GO. Based on sequence homology, 59380 sequences from O. sanctum and 104856 sequences from O. basilicum were categorized into 51 functional groups under three main categories: biological process (BP), cellular component (CC) and molecular function (MF) (Figure 2). Highest percentages of genes were classified under ‘unknown groups’ in all the three GO catagories, followed by ‘binding activity’ (42.18% in O. sanctum and 43.12% in O. basilicum), ‘membranes’ (24.03% in O. sanctum and 24.55% in O. basilicum), ‘other biological processes’ (21.62% in O. sanctum and 20.45% in O. basilicum), ‘nucleus’ (13.98% in O. sanctum and 13.23% in O. basilicum) and ‘hydrolase activity’ (11.99% in O. sanctum and 12.94% in O. basilicum) were observed. Reports on Salvia miltiorrhiza transcriptome, a member of the same family, also represents the ‘binding activity’ of the transcripts in MF category to be with maximum percentage with an anomaly in CC and BP categories[25]. Higher number of genes represented in ‘binding and hydrolase activity’ indicates dominance of gene regulation, signal transduction and enzymatically active processes. Extremely low percentage of genes were classified in terms of ‘antioxidant’ (0.02% both in O. sanctum and O. basilicum), ‘transcriptional regulation activity’ (0.1% in O. sanctum and 0.09% in O. basilicum) and ‘localization’ (0.09% in O. sanctum and 0.07% in O. basilicum) categories (Figure 2). Both the libraries showed similar type of distribution pattern of unigenes under different GO terms. This study suggests the existence of huge potential for new gene identification, as a large number of unigenes from O. sanctum and O. basilicum were classified to ‘unknown’ subgroups of the three main categories.Figure 2


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)

Histogram of gene ontology classification. The results are summarized in three main categories: biological process, cellular component and molecular function. Bars represent assignments of O. basilicum and O. sanctum transcripts (percent) with BLAST matches in the uniprot database (Arabidopsis) to each GO term.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Histogram of gene ontology classification. The results are summarized in three main categories: biological process, cellular component and molecular function. Bars represent assignments of O. basilicum and O. sanctum transcripts (percent) with BLAST matches in the uniprot database (Arabidopsis) to each GO term.
Mentions: Gene Ontology (GO) is an international standardized gene functional classification system offering an updated and a strictly defined concept to comprehensively describe the properties of genes and gene products in any organism[24]. In order to assign putative functions, transcripts from O. sanctum and O. basilicum were compared against the NR protein sequences of Arabidopsis, rice and lamiaceae family available at uniprot database using blastx algorithm. The associated hits were searched for their respective GO. Based on sequence homology, 59380 sequences from O. sanctum and 104856 sequences from O. basilicum were categorized into 51 functional groups under three main categories: biological process (BP), cellular component (CC) and molecular function (MF) (Figure 2). Highest percentages of genes were classified under ‘unknown groups’ in all the three GO catagories, followed by ‘binding activity’ (42.18% in O. sanctum and 43.12% in O. basilicum), ‘membranes’ (24.03% in O. sanctum and 24.55% in O. basilicum), ‘other biological processes’ (21.62% in O. sanctum and 20.45% in O. basilicum), ‘nucleus’ (13.98% in O. sanctum and 13.23% in O. basilicum) and ‘hydrolase activity’ (11.99% in O. sanctum and 12.94% in O. basilicum) were observed. Reports on Salvia miltiorrhiza transcriptome, a member of the same family, also represents the ‘binding activity’ of the transcripts in MF category to be with maximum percentage with an anomaly in CC and BP categories[25]. Higher number of genes represented in ‘binding and hydrolase activity’ indicates dominance of gene regulation, signal transduction and enzymatically active processes. Extremely low percentage of genes were classified in terms of ‘antioxidant’ (0.02% both in O. sanctum and O. basilicum), ‘transcriptional regulation activity’ (0.1% in O. sanctum and 0.09% in O. basilicum) and ‘localization’ (0.09% in O. sanctum and 0.07% in O. basilicum) categories (Figure 2). Both the libraries showed similar type of distribution pattern of unigenes under different GO terms. This study suggests the existence of huge potential for new gene identification, as a large number of unigenes from O. sanctum and O. basilicum were classified to ‘unknown’ subgroups of the three main categories.Figure 2

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