Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plastome Sequencing and Annotation
2.2. Comparative Plastome Analysis
2.3. Tandem Repeat and Microsatellite Analysis
2.4. Phylogenetic Analysis
3. Results and Discussion
3.1. Genome Size and Features
3.2. Analysis of Microsatellites
3.3. Comparative Analysis of Genome Structure
3.4. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Taxa | R. boninensis | R. trifidus |
---|---|---|
Accession Number | MH734123 | MK465682 |
Total cpDNA size (bp)/GC content (%) | 155,807/37.1 | 155,823/37.1 |
LSC size (bp)/GC content (%) | 85,438/34.9 | 85,466/35.0 |
IR size (bp)/GC content (%) | 25,793/42.8 | 25,799/42.8 |
SSC size (bp)/GC content (%) | 18,783/31.0 | 18,759/31.0 |
Number of genes | 131 | 131 |
Number of protein-coding genes | 84 | 84 |
Number of tRNA genes | 37 | 37 |
Number of rRNA genes | 8 | 8 |
Number of duplicated genes | 17 | 17 |
Codon | Amino Acid | Count BON/TRF | RSCU BON/TRF | tRNA BON/TRF | Codon | Amino Acid | Count BON/TRF | RSCU BON/TRF | tRNA BON/TRF |
---|---|---|---|---|---|---|---|---|---|
UUU | F | 986/985 | 1.31 | UCU | S | 561/554 | 1.68/1.67 | ||
UUC | F | 514 | 0.69 | trnF-GAA | UCC | S | 343 | 1.03 | trnS-GGA |
UUA | L | 882/887 | 1.92/1.93 | trnL-UAA | UCA | S | 382/380 | 1.15 | - / trnS-UGA |
UUG | L | 550/552 | 1.2 | trnL-CAA | UCG | S | 200/204 | 0.6 | |
CUU | L | 592/590 | 1.29 | CCU | P | 408/409 | 1.5 | ||
CUC | L | 185/138 | 0.4 | CCC | P | 212/213 | 0.78 | ||
CUA | L | 356/355 | 0.78/0.77 | trnL-UAG | CCA | P | 304/300 | 1.12/1.1 | trnP-UGG |
CUG | L | 185/186 | 0.4/0.41 | CCG | P | 164 | 0.6 | ||
AUU | I | 1118/1114 | 1.48 | ACU | T | 523/525 | 1.57 | ||
AUC | I | 435 | 0.58 | trnI-GAU | ACC | T | 254 | 0.76/0.78 | trnT-GGU |
AUA | I | 711/703 | 0.94 | ACA | T | 406/407 | 1.22 | trnT-UGU | |
AUG | M | 619/620 | 1 | trnI-CAU, trnfM-CAU/trnfM-CAU | ACG | T | 148 | 0.44 | |
GUU | V | 518 | 1.45 | GCU | A | 630 | 1.8/1.81 | ||
GUC | V | 169/167 | 0.47 | trnV-GAC | GCC | A | 219 | 0.63 | |
GUA | V | 543 | 1.52 | trnV-UAC | GCA | A | 387/384 | 1.11 | trnA-UGC |
GUG | V | 202/201 | 0.56 | GCG | A | 162 | 0.46 | ||
UAU | Y | 768/767 | 1.59 | UGU | C | 229 | 1.53 | ||
UAC | Y | 196 | 0.41 | trnY-GUA | UGC | C | 71 | 0.47 | trnC-GCA |
UAA | * | 48 | 1.71/1.73 | UGA | * | 16 | 0.57/0.58 | ||
UAG | * | 20 | 0.71/0.69 | -/trnI-CAT | UGG | W | 454/452 | 1 | trnW-CCA |
CAU | H | 486/487 | 1.53 | CGU | R | 343/344 | 1.3/1.31 | trnR-ACG | |
CAC | H | 151/150 | 0.47 | trnH-GUG | CGC | R | 104 | 0.39 | |
CAA | Q | 711/713 | 1.54/1.55 | trnK-UUG - | CGA | R | 357/358 | 1.36 | |
CAG | Q | 210/209 | 0.46/0.45 | CGG | R | 116/115 | 0.44 | ||
AAU | N | 971/968 | 1.52/1.51 | AGU | S | 390/387 | 1.17/1.16 | ||
AAC | N | 310/311 | 0.48/0.49 | trnN-GUU | AGC | S | 125/126 | 0.37/0.38 | trnS-GCU |
AAA | K | 1083/1070 | 1.5/1.49 | trnK-UUU | AGA | R | 482 | 1.83 | trnR-UCU |
AAG | K | 362 | 0.5/0.51 | AGG | R | 178 | 0.68 | ||
GAU | D | 873/874 | 1.62 | GGU | G | 581/582 | 1.3 | ||
GAC | D | 203/202 | 0.38 | trnD-GUC | GGC | G | 194/193 | 0.43 | trnS-GCC |
GAA | E | 1020/1022 | 1.48/1.49 | trnE-UUC | GGA | G | 701/699 | 1.57 | trnG-UCC |
GAG | E | 358/354 | 0.52/0.51 | GGG | G | 313/312 | 0.7 |
Codon | Amino Acid | Count CRA/TAK | RSCU CRA/TAK | tRNA CRA/TAK | Codon | Amino Acid | Count CRA/TAK | RSCU CRA/TAK | tRNA CRA/TAK |
---|---|---|---|---|---|---|---|---|---|
UUU | F | 980/979 | 1.31 | UCU | S | 557 | 1.68 | ||
UUC | F | 514 | 0.69 | trnF-GAA | UCC | S | 345 | 1.04 | trnS-GGA |
UUA | L | 886/887 | 1.93 | trnL-UAA | UCA | S | 383 | 1.15 | trnS-UGA |
UUG | L | 557/555 | 1.21 | trnL-CAA | UCG | S | 198 | 0.6 | |
CUU | L | 593/592 | 1.29 | CCU | P | 412 | 1.52 | ||
CUC | L | 181 | 0.39 | CCC | P | 211 | 0.78 | ||
CUA | L | 363/361 | 0.79 | trnL-UAG | CCA | P | 303 | 1.11 | trnP-UGG |
CUG | L | 181/182 | 0.39/0.4 | CCG | P | 161 | 0.59 | ||
AUU | I | 1105/1105 | 1.48 | ACU | T | 525/523 | 1.57 | ||
AUC | I | 442 | 0.59 | trnI-GAU | ACC | T | 251 | 0.75 | trnT-GGU |
AUA | I | 693 | 0.93 | ACA | T | 406/408 | 1.22 | trnT-UGU | |
AUG | M | 617 | 1 | trnI-CAU, trnfM-CAU, trnM-CAU | ACG | T | 152/151 | 0.46/0.45 | |
GUU | V | 519 | 1.45 | GCU | A | 634 | 1.82 | ||
GUC | V | 172 | 0.48 | trnV-GAC | GCC | A | 218 | 0.63 | |
GUA | V | 536/538 | 1.5/1.51 | trnV-UAC | GCA | A | 377/376 | 1.08 | trnA-UGC |
GUG | V | 201/200 | 0.56 | GCG | A | 163/164 | 0.47 | ||
UAU | Y | 766 | 1.59 | UGU | C | 229 | 1.53 | ||
UAC | Y | 195 | 0.41 | trnY-GUA | UGC | C | 70 | 0.47 | trnC-GCA |
UAA | * | 47 | 1.68 | UGA | * | 14 | 0.5 | ||
UAG | * | 23 | 0.82 | UGG | W | 451 | 1 | trnW-CCA | |
CAU | H | 479/477 | 1.52/1.51 | CGU | R | 341 | 1.29 | trnR-ACG | |
CAC | H | 152/154 | 0.48/0.49 | trnH-GUG | CGC | R | 105/104 | 0.49/0.39 | |
CAA | Q | 714 | 1.54 | trnQ-UUG | CGA | R | 362/360 | 1.36 | |
CAG | Q | 211 | 0.46 | CGG | R | 116/117 | 0.44 | ||
AAU | N | 969 | 1.52 | AGU | S | 388/387 | 1.17/1.16 | ||
AAC | N | 307 | 0.48 | trnN-GUU | AGC | S | 124/125 | 0.37 | trnS-GCU |
AAA | K | 1065/1066 | 1.5 | trnK-UUU | AGA | R | 486/488 | 1.83/1.84 | trnR-UCU |
AAG | K | 353/352 | 0.5 | AGG | R | 182 | 0.69 | ||
GAU | D | 867 | 1.62 | GGU | G | 576/577 | 1.29 | ||
GAC | D | 204/205 | 0.38 | trnD-GUC | GGC | G | 198/197 | 0.44 | trnS-GCC |
GAA | E | 1017 | 1.48 | trnE-UUC | GGA | G | 700/697 | 1.57 | trnG-UCC |
GAG | E | 358 | 0.52 | GGG | G | 311/313 | 0.7 |
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Yang, J.; Takayama, K.; Pak, J.-H.; Kim, S.-C. Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes 2019, 10, 774. https://doi.org/10.3390/genes10100774
Yang J, Takayama K, Pak J-H, Kim S-C. Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes. 2019; 10(10):774. https://doi.org/10.3390/genes10100774
Chicago/Turabian StyleYang, JiYoung, Koji Takayama, Jae-Hong Pak, and Seung-Chul Kim. 2019. "Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula" Genes 10, no. 10: 774. https://doi.org/10.3390/genes10100774
APA StyleYang, J., Takayama, K., Pak, J. -H., & Kim, S. -C. (2019). Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes, 10(10), 774. https://doi.org/10.3390/genes10100774