The Complete Mitochondrial Genomes of Aelia sibirica and A. fieberi (Hemiptera, Pentatomidae), and Phylogenetic Implications
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling, DNA Extraction, and Sequencing
2.2. Genome Annotations and Sequence Analyses
2.3. Phylogenetic Analysis
3. Results
3.1. Genomic Features
3.2. Nucleotide Composition and Codon Usage
3.3. PCGs
3.4. Ribosomal and Transfer RNA Genes
3.5. Control Region
3.6. Phylogenetic Analyses
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Placement | Species | GenBank Accession Number | ||
---|---|---|---|---|
Acanthosomatidae | Sastragala esakii | NC_058975 | ||
Pentatomidae | Phyllocephalinae | Gonopsis affinis | NC_036745 | |
Dalsira scabrata | KX505855 | |||
Asopinae | Arma chinensis | MW355500 | ||
Cazira horvathi | MF497718 | |||
Dinorhynchus dybowskyi | NC_037724 | |||
Eocanthecona furcellata | MZ440302 | |||
Stiretrus anchorago | BK059217 | |||
Zicrona caerulea | MW847250 | |||
Podopinae | Deroploa parva | MW679032 | ||
Graphosoma rubrolineatum | KX267740 | |||
Scotinophara lurida | MF497733 | |||
Pentatominae | Aeliini | Aelia fieberi | ON059969 | |
Aelia sibirica | NC_067883 | |||
Antestiini | Plautia crossota | MK757497 | ||
Sephelini | Brachymna tenuis | MF497711 | ||
Eysarcorini | Carbula sinica | NC_037741 | ||
Caystrini | Caystrus obscurus | MF497717 | ||
Carpocorini | Dolycoris baccarum | JQ743672 | ||
Halyini | Erthesina fullo | MK374364 | ||
Strachiini | Eurydema dominulus | MG584833 | ||
Cappaeini | Halyomorpha halys | LC579925 | ||
Hoplistoderini | Hoplistodera incisa | MF620037 | ||
Menidini | Menida violacea | MF497728 | ||
Nezarini | Nezara viridula | NC_011755 | ||
Chinavia impicticornis | MG253262 | |||
Pentatomini | Pentatoma semiannulata | MT985377 | ||
Placosternum urus | MF497730 |
Gene | Size (bp) | Position | IGS (bp) | Anti- Codon | Start Codon | Stop Codon | |
---|---|---|---|---|---|---|---|
Start | Stop | ||||||
trnI | 66/66 | 1/1 | 66/66 | 0/8 | GAU | — | — |
trnQ | 69/69 | 64/75 | 132/143 | −3/−3 | UUG | — | — |
trnM | 66/66 | 152/150 | 217/215 | 19/6 | CAU | — | — |
nad2 | 987/987 | 218/216 | 1204/1202 | 0/0 | — | ATC | TAA |
trnW | 66/66 | 1211/1221 | 1276/1286 | 6/18 | UCA | — | — |
trnC | 62/66 | 1269/1279 | 1330/1344 | −8/−8 | GCA | — | — |
trnY | 65/65 | 1334/1348 | 1398/1412 | 3/3 | GUA | — | — |
cox1 | 1542/1542 | 1408/1422 | 2949/2963 | 9/9 | — | TTG | TAA |
trnL2UUR | 65/66 | 2945/2959 | 3009/3024 | −5/−5 | UAA | — | — |
cox2 | 679/679 | 3010/3025 | 3688/3703 | −5/0 | — | ATA | T |
trnK | 71/70 | 3689/3704 | 3759/3773 | 0/0 | CUU | — | — |
trnD | 66/66 | 3774/3770 | 3839/3835 | 14/−4 | GUC | — | — |
atp8 | 159/159 | 3840/3836 | 3998/3994 | 0/0 | — | TTG/GTG | TAA |
atp6 | 675/675 | 3992/3988 | 4666/4662 | −7/3 | — | ATG | TAA |
cox3 | 789/789 | 4669/4665 | 5457/5453 | 2/2 | — | ATG | TAA |
trnG | 63/63 | 5464/5458 | 5526/5520 | 6/4 | UCC | — | — |
nad3 | 352/377 | 5527/5521 | 5878/5897 | 0/0 | — | ATA | TAG/T |
trnA | 64/66 | 5879/5898 | 5942/5963 | 0/0 | UGC | — | — |
trnR | 64/61 | 5947/5973 | 6010/6033 | 4/9 | UCG | — | — |
trnN | 68/67 | 6016/6037 | 6083/6103 | 5/3 | GUU | — | — |
trnS1AGN | 70/69 | 6083/6103 | 6152/6171 | −1/−1 | GCU | — | — |
trnE | 68/69 | 6155/6173 | 6222/6241 | 2/2 | UUC | — | — |
trnF | 66/66 | 6221/6240 | 6286/6305 | −2/−2 | GAA | — | — |
nad5 | 1707/1706 | 6286/6307 | 7992/8011 | −1/1 | — | ATT | TAA/T |
trnH | 64/64 | 7994/8013 | 8057/8076 | 1/1 | GUG | — | — |
nad4 | 1329/1329 | 8061/8080 | 9389/9408 | 3/3 | — | ATT/ATG | TAA |
nad4L | 288/288 | 9383/9402 | 9670/9689 | −7/−7 | — | ATG/ATT | TAA |
trnT | 67/65 | 9673/9692 | 9739/9756 | 2/2 | UGU | — | — |
trnP | 66/66 | 9740/9757 | 9805/9822 | 0/0 | UGG | — | — |
nad6 | 465/480 | 9816/9833 | 10,280/10,312 | 10/10 | — | ATG/ATA | TAA |
cytb | 1137/1147 | 10,288/10,317 | 11,424/11,456 | 7/4 | — | ATG | TAA |
trnS2UCN | 69/69 | 11,426/11,465 | 11,494/11,533 | 1/8 | UGA | — | — |
nad1 | 924/924 | 11,522/11,558 | 12,445/12,481 | 27/24 | — | TTG | TAG |
trnL1CUN | 65/65 | 12,446/12,482 | 12,510/12,546 | 0/0 | UAG | — | — |
16S rRNA | 1282/1272 | 12,510/12,546 | 13,791/13,817 | −1/−1 | — | — | — |
trnV | 68/68 | 13,792/13,818 | 13,859/13,885 | 0/0 | UAC | — | — |
12S rRNA | 796/795 | 13,860/13,886 | 14,655/14,680 | 0/0 | — | — | — |
Control region | 717/768 | 14,656/14,681 | 15,372/15,448 | 0 | — | — | — |
Gene | A/% | T/% | G/% | C/% | (A + T)/% | AT-Skew | GC-Skew |
---|---|---|---|---|---|---|---|
Whole genome | 41.8/41.8 | 31.7/31.7 | 11.0/11.0 | 15.5/15.5 | 73.5/73.5 | 0.138/0.138 | −0.167/−0.167 |
13PCGs | 33.1/32.6 | 40.4/40.3 | 13.1/13.3 | 13.5/13.8 | 73.5/72.9 | −0.100/−0.105 | −0.015/−0.017 |
22tRNAs | 38.4/37.6 | 37.1/37.2 | 13.4/13.9 | 11.1/11.3 | 75.5/74.8 | 0.017/0.005 | 0.094/0.106 |
2rRNAs | 33.1/33.4 | 44.1/43.6 | 14.1/14.7 | 8.6/8.2 | 77.2/77.1 | −0.142/−0.132 | 0.242/0.283 |
Control region | 35.8/34.0 | 34.7/35.2 | 12.3/12.3 | 17.2/18.5 | 70.5/69.2 | 0.016/−0.017 | −0.166/−0.203 |
nad1 | 24.5/24.7 | 50.0/50.2 | 16.8/16.6 | 8.8/8.5 | 74.5/74.9 | −0.343/−0.341 | 0.313/0.319 |
nad2 | 44.2/44.3 | 35.6/34.5 | 8.9/9.2 | 11.3/12.0 | 79.8/78.8 | 0.108/0.123 | −0.120/−0.129 |
nad3 | 38.4/39.6 | 35.8/34.2 | 10.8/11.2 | 15.1/15.0 | 74.2/73.8 | 0.034/0.074 | −0.165/−0.146 |
nad4 | 26.4/25.8 | 49.3/50.6 | 14.6/13.9 | 9.6/10.3 | 75.7/75.8 | −0.318/−0.335 | 0.137/0.149 |
nad4L | 26.0/24.7 | 51.4/49.7 | 12.8/14.2 | 9.7/11.5 | 77.4/74.3 | −0.327/−0.336 | 0.323/0.108 |
nad5 | 26.5/24.6 | 49.3/49.1 | 14.6/15.4 | 9.6/11.0 | 75.8/73.6 | −0.301/−0.333 | 0.205/0.169 |
nad6 | 39.8/39.4 | 38.9/40.8 | 8.2/7.9 | 13.1/11.9 | 78.7/80.2 | 0.011/−0.0188 | −0.232/−0.200 |
cox1 | 34.8/34.1 | 32.9/32.9 | 14.7/15.2 | 17.5/17.8 | 67.7/67.0 | 0.027/0.018 | −0.091/−0.018 |
cox2 | 39.8/39.8 | 29.6/30.2 | 13.0/13.3 | 17.7/16.8 | 69.4/70.0 | 0.146/0.137 | −0.154/−0.118 |
cox3 | 34.1/34.3 | 34.0/33.8 | 15.0/14.6 | 17.0/17.2 | 68.1/68.2 | 0.002/0.007 | −0.063/−0.084 |
cytb | 34.5/34.8 | 35.1/35.4 | 12.8/12.1 | 17.7/17.7 | 69.6/70.2 | −0.009/−0.009 | −0.162/−0.187 |
atp6 | 38.1/37.2 | 35.1/35.3 | 10.7/10.7 | 16.1/16.9 | 73.2/72.4 | 0.041/0.027 | −0.204/−0.226 |
atp8 | 40.3/42.8 | 32.1/37.1 | 9.4/8.2 | 18.2/11.9 | 72.4/79.9 | 0.113/0.071 | −0.318/−0.188 |
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Liu, D.; Zhang, H.; Fu, S.; Wang, Y.; Zhao, W.; Zhao, Q. The Complete Mitochondrial Genomes of Aelia sibirica and A. fieberi (Hemiptera, Pentatomidae), and Phylogenetic Implications. Diversity 2024, 16, 111. https://doi.org/10.3390/d16020111
Liu D, Zhang H, Fu S, Wang Y, Zhao W, Zhao Q. The Complete Mitochondrial Genomes of Aelia sibirica and A. fieberi (Hemiptera, Pentatomidae), and Phylogenetic Implications. Diversity. 2024; 16(2):111. https://doi.org/10.3390/d16020111
Chicago/Turabian StyleLiu, Dajun, Hufang Zhang, Shuhui Fu, Yating Wang, Wanqing Zhao, and Qing Zhao. 2024. "The Complete Mitochondrial Genomes of Aelia sibirica and A. fieberi (Hemiptera, Pentatomidae), and Phylogenetic Implications" Diversity 16, no. 2: 111. https://doi.org/10.3390/d16020111