The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing
Abstract
:1. Introduction
2. Results and Discussion
2.1. Chloroplast Genome Assembly
2.2. Features of the C. annuum var. glabriusculum Chloroplast Genome
Features | Chloroplast |
---|---|
Genome size (bp) | 156,817 |
GC content (%) | 37.7 |
Total number of genes | 132 |
Protein coding genes | 87 |
No. of rRNA genes | 8 |
No. of tRNA genes | 37 |
No. of gene duplicated in IR regions | 7 |
Total introns | 12 |
Single intron (gene) | 9 |
Double introns (gene) | 3 |
Single intron (tRNA) | 6 |
2.3. Discovery of SSRs and SNPs
2.4. Discussion
Gene Products of Capsicum annuum var. glabriusculum | |
---|---|
Photosystem I | psaA, B, C, I, J, ycf3 2, ycf4 |
Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z |
Cytochrome b6/f | petA, B 1, D 1, G, L, N |
ATP synthase | atpA, B, E, F 1, H, I |
Rubisco | rbcL |
NADH oxidoreductase | ndhA 1, B 1,3, C, D, E, F, G, H, I, J, K |
Large subunit ribosomal proteins | rpl2 1,3, 14, 16 1, 20, 22, 23 3, 32, 33, 36 |
Small subunit ribosomal proteins | rps2, 3, 4, 7 3, 8, 11, 12 2,3,4, 14, 15, 16 1, 18, 19 |
RNA polymerase | rpoA, B, C1 1, C2 |
Unknown function protein coding gene | ycf1 3, 2 3, 15 3 |
Other genes | accD, ccsA, cemA, clpP 2, matK |
rRNAs | rrn16 3, 23 3, 4.5 3, 5 3 |
tRNAs | trnA-UGC 1,3, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC 1, trnG-GCC, trnH-GUG, trnI-CAU 3, trnI-GAU 1,3, trnK-UUU 1, trnL-UAA 1, trnL-UAG, trnL-CAA 3, trnfM-CAU, trnM-CAU, trnN-GUU 3, trnP-UGG, trnQ-UUG, trnR-ACG 3, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-UAC 1, trnV-GAC 3, trnW-CCA, trnY-GUA |
3. Experimental Section
3.1. Sampling and DNA Extraction
3.2. Library Preparation and Sequencing
3.3. Chloroplast Genome Assembly
3.4. Gene Annotation
3.5. Discovery of SNPs and SSRs
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Raveendar, S.; Na, Y.-W.; Lee, J.-R.; Shim, D.; Ma, K.-H.; Lee, S.-Y.; Chung, J.-W. The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing. Molecules 2015, 20, 13080-13088. https://doi.org/10.3390/molecules200713080
Raveendar S, Na Y-W, Lee J-R, Shim D, Ma K-H, Lee S-Y, Chung J-W. The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing. Molecules. 2015; 20(7):13080-13088. https://doi.org/10.3390/molecules200713080
Chicago/Turabian StyleRaveendar, Sebastin, Young-Wang Na, Jung-Ro Lee, Donghwan Shim, Kyung-Ho Ma, Sok-Young Lee, and Jong-Wook Chung. 2015. "The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing" Molecules 20, no. 7: 13080-13088. https://doi.org/10.3390/molecules200713080