Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Jervine Quantification
2.3. Representational Difference Analysis and Library Construction
2.4. De Novo Assembly and Functional Annotation
3. Results and Discussion
3.1. Jervine Concentration
3.2. Sequence De Novo Assembly
3.3. Functional Annotation
3.4. Identification of Genes Involved in Terpenoid Backbone and Cholesterol Biosynthesis
3.5. Identification of the Genes in Later Stages of Jervine Biosynthesis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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CHL-RDA | MeJ-RDA | SQ-RDA | |
---|---|---|---|
Total number of contigs | 3547 | 3712 | 4789 |
Total bases in contigs (bp) | 988,613 | 1,047,608 | 1,339,219 |
Min length of contigs (bp) | 74 | 34 | 60 |
Max length of contigs (bp) | 922 | 1003 | 886 |
Average length of contigs (bp) | 279 | 282 | 280 |
GC content (%) | 49.5 | 48.3 | 47.1 |
N75 (bp) | 233 | 235 | 234 |
N50 (bp) | 275 | 279 | 279 |
N25 (bp) | 339 | 343 | 339 |
Number of contigs <500 bp | 3480 | 3621 | 4708 |
Number of contigs ≥500 bp | 67 | 91 | 81 |
Database | RDA Library | ||
---|---|---|---|
CHL | MeJ | SQ | |
NT | 3175 | 3474 | 4379 |
NR | 3005 | 3308 | 4188 |
KOG | 1648 | 1721 | 2193 |
Pfam | 1801 | 1858 | 2383 |
KEGG | 1415 | 1438 | 1845 |
GO | 2082 | 2647 | 3308 |
Total | 3528 | 3662 | 4701 |
Unigenes ID | Function | Reference Gene | Blastx E-Value |
---|---|---|---|
CHL-RDA_contig_1929 | C-22 hydroxylation | PGA2 (Solanum tuberosum) | 2.90 × 10−12 |
CHL-RDA_contig_1930 | C-22 hydroxylation | PGA2 (Solanum tuberosum) | 2.40 × 10−12 |
CHL-RDA_contig_3050 | C-26 hydroxylation | CYP94N1v2 (Veratrum californicum) | 9.27 × 10−15 |
MeJ-RDA_contig_1334 | C-26 hydroxylation | CYP734A7 (Solanum lycopersicum) | 3.00 × 10−38 |
MeJ-RDA_contig_1251 | transamination | GABAT2 (Veratrum californicum) | 2.51 × 10−44 |
CHL-RDA_contig_648 | C-11 hydroxylation | CYP88D6 (Glycyrrhiza glabra) | 2.59 × 10−16 |
SQ-RDA_contig_3964 | C-16 hydroxylation | CYP86A2 (Arabidopsis thaliana) | 1.05 × 10−33 |
MeJ-RDA_contig_2593 | C-16 hydroxylation | 16DOX (Solanum lycopersicum) | 5.60 × 10−26 |
MeJ-RDA_contig_81 | C-16 hydroxylation | 16DOX (Solanum lycopersicum) | 5.55 × 10−12 |
SQ-RDA_contig_2664 | reduction of heterocycles | PYCR (Medicago truncatula) | 2.00×10−55 |
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Szeliga, M.; Ciura, J.; Tyrka, M. Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis. Life 2020, 10, 88. https://doi.org/10.3390/life10060088
Szeliga M, Ciura J, Tyrka M. Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis. Life. 2020; 10(6):88. https://doi.org/10.3390/life10060088
Chicago/Turabian StyleSzeliga, Magdalena, Joanna Ciura, and Mirosław Tyrka. 2020. "Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis" Life 10, no. 6: 88. https://doi.org/10.3390/life10060088