Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Species Collection and Taxonomic Identification
2.2. DNA Extraction and Sequencing
2.3. Genome Assembly, Annotation, and Analysis
2.4. Phylogenetic Analyses
3. Results
3.1. Genome Organization and Composition
3.2. PCGs and Codon Usage
3.3. Ribosomal RNA and Transfer RNA Genes
3.4. Overlapping and Intergenic Spacer Regions
3.5. AT-Rich Region
3.6. Phylogenetic Relationships
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | B. flavus | B. fanjingensis | Y. strigatus | Y. erythrus | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Size | Anticodons | Int. | Size | Anticodons | Int. | Size | Anticodons | Int. | Size | Anticodons | Int. | |
Start/Stop | Start/Stop | Start/Stop | Start/Stop | |||||||||
trnI | 67 | ATC | 67 | ATC | 65 | ATC | 65 | ATC | ||||
trnQ | 69 | CAA | 7 | 69 | CAA | 9 | 69 | CAA | 7 | 69 | CAA | 7 |
trnM | 67 | ATG | 13 | 66 | ATG | 20 | 64 | ATG | −1 | 64 | ATG | −1 |
nad2 | 966 | ATT/TAA | 0 | 966 | ATT/TAA | 0 | 966 | ATT/TAA | 0 | 966 | ATT/TAA | 0 |
trnW | 65 | TGA | −1 | 63 | TGA | 0 | 68 | TGA | −1 | 68 | TGA | −1 |
trnC | 74 | TGC | −8 | 73 | TGC | −8 | 57 | TGC | −8 | 58 | TGC | −8 |
trnY | 67 | TAC | 12 | 66 | TAC | 15 | 63 | TAC | 4 | 62 | TAC | 6 |
cox1 | 1539 | ATG/TAA | 23 | 1536 | ATG/TAA | 23 | 1534 | ATG/T | 9 | 1534 | ATG/T | 10 |
trnL2 | 70 | TTA | 1 | 70 | TTA | 8 | 66 | TTA | 0 | 68 | TTA | 0 |
cox2 | 675 | ATT/TAA | 0 | 675 | ATT/TAA | 0 | 675 | ATA/TAA | 0 | 675 | ATA/TAA | 0 |
trnK | 70 | AAG | 20 | 71 | AAG | 40 | 71 | AAG | 20 | 71 | AAG | 8 |
trnD | 69 | GAC | 2 | 70 | GAC | 0 | 66 | GAC | 0 | 65 | GAC | 0 |
atp8 | 134 | ATT/TAA | 0 | 119 | ATT/TAA | 2 | 156 | ATT/TAA | 0 | 156 | ATT/TAA | 0 |
atp6 | 652 | ATA/T | −7 | 655 | ATA/T | −7 | 652 | ATG/T | −7 | 652 | ATG/T | −7 |
cox3 | 783 | ATG/TAA | 0 | 783 | ATG/TAA | 0 | 781 | ATG/T | 0 | 781 | ATG/T | 0 |
trnG | 65 | GGA | 7 | 66 | GGA | 26 | 66 | GGA | 0 | 63 | GGA | −1 |
nad3 | 348 | ATA/TAA | 0 | 348 | ATA/TAA | 0 | 348 | ATT/TAG | 0 | 348 | ATT/TAA | −1 |
trnA | 69 | GCA | −1 | 68 | GCA | 6 | 64 | GCA | −2 | 64 | GCG | 0 |
trnR | 66 | CGA | 3 | 65 | CGA | 12 | 63 | CGA | 3 | 59 | CGA | 4 |
trnN | 71 | AAC | 23 | 71 | AAC | 3 | 67 | AAC | 4 | 67 | AAC | 8 |
trnS1 | 60 | AGC | −1 | 61 | AGC | −1 | 59 | AGC | −1 | 58 | AGC | −1 |
trnE | 67 | GAA | 18 | 71 | GAA | 10 | 62 | GAA | −1 | 62 | GAA | −1 |
trnF | 65 | TTC | 37 | 62 | TTC | 34 | 63 | TTC | 0 | 64 | TTC | 0 |
nad5 | 1713 | GTG/TAA | 48 | 1671 | GTG/TAA | 58 | 1678 | GTG/T | 4 | 1654 | ATG/T | 3 |
trnH | 72 | CAC | 0 | 70 | CAC | 0 | 60 | CAC | 0 | 62 | CAC | 0 |
nad4 | 1366 | ATG/T | 1 | 1321 | ATG/T | 1 | 1317 | ATG/TAA | 21 | 1308 | ATA/TAG | 27 |
nad4l | 270 | ATG/TAA | −7 | 270 | ATG/TAA | −7 | 273 | ATG/TAA | −7 | 273 | ATG/TAA | 1 |
trnT | 69 | ACA | 2 | 69 | ACA | 38 | 67 | ACA | 2 | 67 | ACA | 2 |
trnP | 63 | CCA | 4 | 66 | CCA | 26 | 63 | CCA | 9 | 66 | CCA | 4 |
nad6 | 504 | ATA/TAA | 1 | 501 | ATA/TAA | 1 | 492 | ATA/TAA | 1 | 492 | ATA/TAA | 1 |
cob | 1140 | ATG/TAA | 32 | 1134 | ATG/TAA | 33 | 1119 | ATG/TAA | −8 | 1117 | ATG/T | −8 |
trnS2 | 68 | TCA | 48 | 70 | TCA | 11 | 62 | TCA | 2 | 64 | TCA | 0 |
nad1 | 949 | ATG/T | −4 | 963 | ATG/TAA | 16 | 942 | ATG/TAA | 6 | 945 | ATG/TAA | −1 |
trnL1 | 67 | CTA | 3 | 63 | CTA | 1 | 65 | CTA | 1 | 64 | CTA | 1 |
rrnL | 1227 | - | 0 | 1221 | - | 0 | 1222 | - | 0 | 1222 | - | 0 |
trnV | 56 | GTA | 0 | 61 | GTA | 0 | 58 | GTA | 0 | 56 | GTA | 0 |
rrnS | 717 | - | 0 | 738 | - | 0 | 732 | - | 0 | 732 | - | 0 |
CR | 1318 | 0 | 1230 | 0 | 2288 | 0 | 1609 | 0 | ||||
Total | 16053 | 15979 | 16640 | 15922 |
Regions | Size (bp) | T(U) | C | A | G | A+T (%) | G+C (%) | AT Skewness | GC Skewness |
---|---|---|---|---|---|---|---|---|---|
Full Genome | |||||||||
B. flavus | 16053 | 32 | 13.2 | 47.5 | 7.2 | 79.5 | 20.4 | 0.194 | −0.293 |
B. fanjingensis | 15979 | 32.2 | 12.6 | 48.1 | 7 | 80.3 | 19.6 | 0.197 | −0.288 |
Y. strigatus | 16640 | 33 | 12.5 | 46.8 | 7.7 | 79.8 | 20.2 | 0.173 | −0.238 |
Y. erythrus | 15922 | 33.3 | 12.7 | 46.4 | 7.6 | 79.7 | 20.3 | 0.164 | −0.251 |
13 PCGs | |||||||||
B. flavus | 11039 | 44.5 | 11.2 | 33.9 | 10.3 | 78.4 | 21.5 | −0.135 | −0.042 |
B. fanjingensis | 10942 | 44.5 | 11.2 | 34.3 | 9.9 | 78.8 | 21.1 | −0.129 | −0.062 |
Y. strigatus | 10933 | 43.9 | 11.1 | 35.2 | 9.8 | 79.1 | 20.9 | −0.11 | −0.062 |
Y. erythrus | 10901 | 44.4 | 11.0 | 34.6 | 10.0 | 79 | 21 | −0.124 | −0.048 |
2 rRNAs | |||||||||
B. flavus | 1944 | 47.7 | 6.6 | 32.8 | 12.9 | 80.5 | 19.5 | −0.185 | 0.323 |
B. fanjingensis | 1959 | 46.7 | 6.5 | 34 | 12.8 | 80.7 | 19.3 | −0.157 | 0.328 |
Y. strigatus | 1954 | 48.7 | 6.7 | 32.2 | 12.4 | 80.9 | 19.1 | −0.203 | 0.298 |
Y. erythrus | 1954 | 47.5 | 6.9 | 33.5 | 12.1 | 81 | 19 | −0.172 | 0.278 |
22 tRNAs | |||||||||
B. flavus | 1476 | 37.8 | 9.1 | 42.1 | 11.0 | 79.9 | 20.1 | 0.054 | 0.095 |
B. fanjingensis | 1478 | 37.1 | 8.9 | 43.4 | 10.7 | 80.5 | 19.6 | 0.078 | 0.092 |
Y. strigatus | 1408 | 37.4 | 8.8 | 42.0 | 11.8 | 79.4 | 20.6 | 0.058 | 0.146 |
Y. erythrus | 1406 | 38.0 | 8.6 | 41.1 | 12.3 | 79.1 | 20.9 | 0.039 | 0.177 |
AT-rich regions | |||||||||
B. flavus | 1318 | 39.3 | 11.1 | 44.9 | 4.7 | 84.2 | 15.8 | 0.067 | −0.405 |
B. fanjingensis | 1230 | 41.5 | 7.4 | 47.6 | 3.5 | 89.1 | 10.9 | 0.068 | −0.358 |
Y. strigatus | 2288 | 38.8 | 10.3 | 43.5 | 7.3 | 82.3 | 17.7 | 0.057 | −0.169 |
Y. erythrus | 1609 | 40.9 | 11.5 | 41.8 | 5.8 | 82.7 | 17.3 | 0.011 | −0.329 |
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Gong, N.; Yang, L.; Chen, X.-S. Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha). Int. J. Mol. Sci. 2021, 22, 1348. https://doi.org/10.3390/ijms22031348
Gong N, Yang L, Chen X-S. Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha). International Journal of Molecular Sciences. 2021; 22(3):1348. https://doi.org/10.3390/ijms22031348
Chicago/Turabian StyleGong, Nian, Lin Yang, and Xiang-Sheng Chen. 2021. "Structural Features and Phylogenetic Implications of Four New Mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha)" International Journal of Molecular Sciences 22, no. 3: 1348. https://doi.org/10.3390/ijms22031348