Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship
Abstract
:1. Introduction
2. Results
2.1. General Features and Organization of Chloroplast Genomes
2.2. SSR Analysis and Repeats, an Insight into the Genome
2.3. Comparative Analysis and Sequence Divergence Analyses
2.4. Boundaries between Inverted Repeat and Single Copy Regions
2.5. Phylogenetic Relationships
3. Discussion
4. Methodology
4.1. Sample Collection
4.2. DNA Extraction and Genome Sequencing
4.3. Chloroplast Reference-Based Genome Assembly
4.4. Prosopis Species Genome Annotation
4.5. Repeat Identification
4.6. Chloroplast Genome Divergence and Phylogenetic Relationship
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
BI | Bayesian inference |
IR | Inverted repeat |
LSC | Large single copy |
ML | maximum likelihood |
MP | Maximum parsimony |
NGS | Next generation sequencing |
rRNA | Ribosomal RNA |
SSC | Short single copy |
SSRs | Simple sequence repeats |
tRNA | Transfer RNA |
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P. Cineraria | P. Juliflora | P. Glandulosa | A. Microsperma | P. Javanica | |
---|---|---|---|---|---|
Size (bp) | 163,677 | 163,237 | 163,040 | 159,389 | 161,681 |
Overall GC contents | 35.9 | 35.9 | 35.9 | 36.5 | 35.9 |
LSC size (bp) | 92,937 | 92,495 | 92,310 | 88,577 | 91,093 |
SSC size (bp) | 18,878 | 18,880 | 19,132 | 18,756 | 18,574 |
IR size (bp) | 25,931 | 25,931 | 25,931 | 26,028 | 26,007 |
Protein coding regions (bp) | 78,883 | 78,421 | 78,039 | 78,030 | 78,075 |
tRNA size (bp) | 2868 | 2927 | 2810 | 2793 | 2794 |
rRNA size (bp) | 9052 | 9052 | 9052 | 9052 | 9052 |
Number of genes | 131 | 132 | 128 | 128 | 130 |
Number of protein coding genes | 85 | 85 | 83 | 83 | 83 |
Number of rRNAs | 8 | 8 | 8 | 8 | 8 |
Number of tRNA s | 38 | 39 | 37 | 37 | 37 |
Genes with introns | 21 | 21 | 23 | 22 | 23 |
Gene | Location | Exon I (bp) | Intron 1 (bp) | Exon II (bp) | Intron II (bp) | Exon III (bp) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | ||
atpF | LSC | 145 | 145 | 145 | 744 | 726 | 727 | 389 | 407 | 407 | ||||||
petB | LSC | 6 | 6 | 6 | 815 | 815 | 815 | 642 | 642 | 642 | ||||||
petD | LSC | 8 | 8 | 8 | 720 | 720 | 720 | 475 | 475 | 475 | ||||||
rpl2 a | IR | 391 | 393 | 393 | 665 | 662 | 662 | 434 | 435 | 435 | ||||||
rpl16 | LSC | 9 | 9 | 9 | 1173 | 1173 | 1173 | 399 | 399 | 399 | ||||||
rps16 | LSC | 40 | 40 | 40 | 884 | 883 | 883 | 245 | 245 | 245 | ||||||
rpoC1 | LSC | 432 | 432 | 432 | 842 | 802 | 802 | 1578 | 1617 | 1617 | ||||||
rps12 * | LSC-IR | 114 | 114 | 114 | 232 | 232 | 232 | 540 | 540 | 540 | 26 | 26 | ||||
clpP | LSC | 69 | 69 | 69 | 789 | 790 | 789 | 291 | 291 | 291 | 642 | 642 | 642 | 228 | 228 | 228 |
ndhA | SSC | 552 | 553 | 552 | 1449 | 1452 | 1457 | 540 | 539 | 540 | ||||||
ndhB a | IR | 777 | 777 | 777 | 685 | 684 | 685 | 756 | 756 | 756 | ||||||
ycf3 | LSC | 126 | 126 | 126 | 729 | 729 | 728 | 228 | 228 | 228 | 738 | 738 | 738 | 153 | 153 | 153 |
trnA-UGC a | IR | 38 | 38 | 38 | 802 | 794 | 802 | 35 | 35 | 35 | ||||||
trnI –GAUa | IR | 42 | 42 | 42 | 948 | 948 | 948 | 35 | 35 | 35 | ||||||
trnL-UAA | LSC | 37 | 37 | 37 | 536 | 536 | 536 | 50 | 50 | 50 | ||||||
trnK-UUU | LSC | 29 | 29 | 29 | 2492 | 2491 | 2491 | 37 | 37 | 37 | ||||||
trnG-GCC | LSC | 23 | 702 | 49 | ||||||||||||
trnV-UAC | LSC | 37 | 37 | 37 | 619 | 619 | 619 | 39 | 39 | 39 |
Category | Group of Genes | Name of Genes |
---|---|---|
Self-replication | Large subunit of ribosomal proteins | rpl2, 14, 16, 20, 23, 32, 33, 36 |
Small subunit of ribosomal proteins | rps2, 3, 4, 7, 8, 11, 12, 14, 15, 16, 18, 19 | |
DNA dependent RNA polymerase | rpoA, B, C1, C2 | |
rRNA genes | rrn4.5, rrn5, rrn16, rrn23 | |
tRNA genes | trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC trnF-GAA, trnfM-CAU, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA, trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU, trnP-GGG, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA | |
Photosynthesis | Photosystem I | psaA, B, C, I, |
Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z | |
Cytochrome b6/f complex | petA, B, D, G, L, N | |
ATP synthase | atpA, B, E, F, H, I | |
Rubisco | rbcL | |
Maturase | matK | |
Protease | clpP | |
Envelop membrane protein | cemA | |
Subunit Acetyl- CoA-Carboxylate | accD | |
c-type cytochrome synthesis gene | ccsA | |
Unknown | Conserved Open reading frames | ycf1, 2, 3, 4 |
T/U | C | A | G | Length (bp) | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | P. j | P. c | P. g | |
Genome | 32.5 | 32.5 | 32.5 | 18.3 | 18.3 | 18.3 | 31.6 | 31.6 | 31.7 | 17.6 | 17.6 | 17.6 | 163,237 | 163,677 | 163,040 |
LSC | 34.2 | 34.2 | 34.2 | 17.0 | 17.0 | 17.0 | 32.6 | 32.6 | 32.6 | 16.1 | 16.2 | 16.1 | 92,495 | 92,937 | 92,310 |
SSC | 34.9 | 34.9 | 34.6 | 15.9 | 16.0 | 15.7 | 34.7 | 34.6 | 35.2 | 14.5 | 14.5 | 14.4 | 18,880 | 18,878 | 19,132 |
IR | 28.8 | 28.8 | 28.5 | 20.6 | 20.6 | 22.1 | 28.5 | 28.5 | 28.8 | 22.1 | 22.1 | 20.6 | 25,931 | 25,931 | 25,931 |
tRNA | 25.1 | 24.9 | 24.8 | 23.4 | 23.5 | 23.8 | 22.1 | 22.0 | 21.9 | 29.4 | 29.6 | 29.5 | 2927 | 2868 | 2810 |
rRNA | 18.9 | 18.9 | 18.8 | 23.7 | 23.7 | 23.6 | 25.7 | 25.7 | 25.7 | 31.7 | 31.7 | 31.9 | 9052 | 9052 | 9052 |
Protein coding genes | 31.7 | 31.7 | 31.7 | 17.4 | 17.4 | 17.4 | 30.9 | 30.8 | 30.8 | 20.0 | 20.1 | 20.1 | 78,421 | 78,883 | 78,039 |
1st position | 32.6 | 33.0 | 32.4 | 17.9 | 18.14 | 18.2 | 31.4 | 31.5 | 31.7 | 17.9 | 17.5 | 17.5 | 54,412 | 54,559 | 54,347 |
2nd position | 32.4 | 32.33 | 32.7 | 18.5 | 18.4 | 17.7 | 31.5 | 31.3 | 32.1 | 17.4 | 17.8 | 17.5 | 54,412 | 54,559 | 54,347 |
3rd position | 32.3 | 32.44 | 32.4 | 20.9 | 18.1 | 18.8 | 32.0 | 31.9 | 31 | 17.4 | 17.3 | 17.7 | 54,412 | 54,559 | 54,347 |
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Asaf, S.; Khan, A.L.; Khan, A.; Al-Harrasi, A. Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. Int. J. Mol. Sci. 2020, 21, 3280. https://doi.org/10.3390/ijms21093280
Asaf S, Khan AL, Khan A, Al-Harrasi A. Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. International Journal of Molecular Sciences. 2020; 21(9):3280. https://doi.org/10.3390/ijms21093280
Chicago/Turabian StyleAsaf, Sajjad, Abdul Latif Khan, Arif Khan, and Ahmed Al-Harrasi. 2020. "Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship" International Journal of Molecular Sciences 21, no. 9: 3280. https://doi.org/10.3390/ijms21093280