Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)
Abstract
:1. Introduction
2. Results and Discussion
2.1. Chloroplast Database Mapping
2.2. Chloroplast Assembly and Annotation
2.3. Phylogenomic Analysis
2.4. Chloroplast Genome Comparison
2.5. Phylogenetic Analysis
2.6. Simple Sequence Repeats (SSR) Analysis
2.7. Single Nucleotide Polymorphism (SNP) Analysis
3. Materials and Methods
3.1. Samples
3.2. Genomic DNA Extraction, Quantification and Quality Assessment
3.3. DNA Library Preparation and NGS
3.4. Chloroplast Assembly and Annotation
3.5. Phylogenomics, Phylogenetics and SSR Search
3.6. Single Nucleotide Polymorphism (SNP) Search and Characterization
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Species | Raw Data Reads | Alignment Percentage | Aligned Reads | Average Coverage | GC Content | Size (bp) |
---|---|---|---|---|---|---|
ST1 | 48,875,452 | 4.28% | 2,093,045 | 3549.43 | 36.48% | 154,450 |
ST2 | 65,161,387 | 5.26% | 3,424,884 | 5881.42 | 36.46% | 154,473 |
ST-hyb1 | 47,916,209 | 5.39% | 2,581,423 | 4440.65 | 36.48% | 154,239 |
ST-hyb2 | 42,444,815 | 7.67% | 3,253,301 | 5613.72 | 36.49% | 154,325 |
SM | 46,355,472 | 4.97% | 2,301,647 | 3920.12 | 36.43% | 154,426 |
Specie | rRNA | tRNA | CDS | Duplicated Genes | Total Genes | LSC (bp) | IR (bp) | SSC (bp) |
---|---|---|---|---|---|---|---|---|
ST1 | 4 | 32 | 78 | 17 | 131 | 85,769 | 24,773 | 19,135 |
ST2 | 4 | 32 | 78 | 17 | 131 | 85,735 | 24,804 | 19,130 |
ST-hyb1 | 4 | 32 | 78 | 17 | 131 | 85,600 | 24,774 | 19,091 |
ST-hyb2 | 4 | 32 | 78 | 17 | 131 | 85,590 | 24,767 | 19,201 |
SM | 4 | 32 | 78 | 17 | 131 | 85,690 | 24,800 | 19,136 |
Gene Category | Gene Functional Group | Name |
---|---|---|
Photosynthesis related | ATP synthase | atpA, atpB, atpE, atpF ★, atpH, atpI |
Cytochrome b/f complex | petA, petB, petD, petG, petL, petN | |
Cytochrome c synthesis | ccsA | |
NADPH dehydrogenase | ndhA ★, ndhB ★, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Photosystem I | psaA, psaB, psaC, psaI, psaJ | |
Photosystem I stability | ycf3 ★, ycf4 | |
Photosystem II | psbA, psbB (x2), psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN (pbf1), psbT, psbZ | |
Rubisco | rbcL | |
Transcription and translation related | Ribosomal proteins | rps2, rps3, rps4, rps7 (x2), rps8, rps11, rps12 ★ (x2), rps14, rps15, rps16 ★, rps18, rps19, rpl2 ★ (x2), rpl14, rpl16, rpl20, rpl22, rpl23 (x2), rpl32, rpl33, rpl36 |
Transcription | rpoA, rpoB, rpoC1 ★, rpoC2 | |
RNA | Ribosomal RNA | rrn4.5 (x2), rrn5 (x2), rrn16 (x2), rrn23 (x2) |
Transfer RNA | trnA-UGC ★ (x2), trnC-GCA, trnD-GUC, trnE-UUC ★, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU (x2), trnI-GAU (x2), trnK-UUU ★, trnL-CAA (x2), trnL-UAA ★, trnL-UAG, trnM-CAU, trnN-GUU (x2), trnP-GGG, trnP-UGG, trnQ-UUG, trnR-ACG (x2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-CGU ★, trnT-GGU, trnT-UGU, trnV-GAC (x2), trnV-UAC ★, trnW-CCA, trnY-GUA | |
Others | Carbon metabolism | cemA |
Fatty acid synthesis | accD | |
Proteolysis | clpP ★ | |
RNA processing | matK | |
Unknown function | Conserved reading frames | yfc1, ycf2 (x2) |
Species | 1x | 2x | 3x | 4x | 5x | 6x | Total | CDS | IGS | Intron | IRa | IRb | SSC | LSC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ST1 | 100 | 11 | 11 | 7 | 1 | 1 | 131 | 21 | 89 | 21 | 6 | 5 | 24 | 96 |
ST2 | 100 | 11 | 12 | 8 | 2 | 1 | 134 | 23 | 90 | 21 | 6 | 6 | 26 | 96 |
ST-hyb1 | 101 | 10 | 11 | 8 | 1 | 1 | 132 | 21 | 92 | 19 | 6 | 5 | 25 | 96 |
ST-hyb2 | 98 | 12 | 11 | 7 | 1 | 1 | 130 | 20 | 91 | 19 | 6 | 6 | 25 | 93 |
SM | 113 | 10 | 11 | 7 | 1 | 1 | 143 | 22 | 103 | 18 | 6 | 6 | 29 | 102 |
SNP Shared | ST1 | ST2 | ST-hyb1 | ST-hyb2 | SM |
---|---|---|---|---|---|
ST1 | - | 9 | 18 | 2 | 8 |
ST2 | 9 | - | 8 | 2 | 4 |
ST-hyb1 | 18 | 8 | - | 4 | 5 |
ST-hyb2 | 2 | 2 | 4 | - | 29 |
SM | 8 | 4 | 5 | 29 | - |
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Pezoa, I.; Villacreses, J.; Rubilar, M.; Pizarro, C.; Galleguillos, M.J.; Ejsmentewicz, T.; Fonseca, B.; Espejo, J.; Polanco, V.; Sánchez, C. Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island). Plants 2021, 10, 342. https://doi.org/10.3390/plants10020342
Pezoa I, Villacreses J, Rubilar M, Pizarro C, Galleguillos MJ, Ejsmentewicz T, Fonseca B, Espejo J, Polanco V, Sánchez C. Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island). Plants. 2021; 10(2):342. https://doi.org/10.3390/plants10020342
Chicago/Turabian StylePezoa, Ignacio, Javier Villacreses, Miguel Rubilar, Carolina Pizarro, María Jesús Galleguillos, Troy Ejsmentewicz, Beatriz Fonseca, Jaime Espejo, Víctor Polanco, and Carolina Sánchez. 2021. "Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)" Plants 10, no. 2: 342. https://doi.org/10.3390/plants10020342