Mitochondrial Genomes of Four Millipedes (Diplopoda: Spirostreptida and Spirobolida) Unveil Phylogenetic Novelty and Gene Rearrangement Patterns
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Next-Generation Sequencing and Assembling
2.3. Annotation and Sequence Analysis
2.4. Phylogenetic Analysis
3. Results and Discussion
3.1. Mitochondrial Genome Organization
3.2. Protein-Coding Genes and Codon Usage
3.3. tRNAs, rRNAs, and D-Loops
3.4. Phylogenetic Analyses
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Class | Order | Family | Species | Length(bp) | Accession |
---|---|---|---|---|---|
Diplopoda | Callipodida | Callipodidae | Abacion magnum Loomis, 1943 | 15,160 | JX437062.1 |
Playtdesmida | Andrognathidae | Brachycybe lecontii Wood, 1864 | 15,115 | JX437064.1 | |
polydesmida | Xystodesmidae | Appalachioria falcifera Keeton, 1959 | 15,282 | JX437063.1 | |
Xystodesmus sp. YD-2016 Cook, 1895 | 15,791 | KU721886.1 | |||
Paradoxosomatidae | Asiomorpha coarctata DeSaussure, 1860 | 15,644 | KU721885.1 | ||
Nedyopu patrioticus Attems, 1898 | 15,814 | OR755973.1 | |||
Polydesmidae | Epanerchodus koreanus Verhoeff, 1937 | 15,581 | MT898420.1 | ||
Nedyopus patrioticus unicolor Carl, 1902 | 15,798 | OR777861.1 | |||
Spirobolida | Trigoniulidae | Trigoniulus corallinus Gervais, 1847 | 14,906 | PQ459337 | |
Pachybolidae | Litostrophus scaber Verhoeff, 1938 | 15,081 | OR139892.1 | ||
Spirobolellidae | Paraspirobolus lucifugus Gervais, 1836 | 14,929 | PQ625794 | ||
Spirobolidae | Narceus annularus Rafinesque, 1820 | 14,868 | AY055727.1 | ||
Spirobolus bungii Keeton, 1960 | 14,879 | MT767838.1 | |||
Spirobolus grahami Keeton, 1960 | 14,875 | OR038162.1 | |||
Spirobolus walkeri Pocock, 1895 | 14,879 | OR078377.1 | |||
Julida | Nemasomatidae | Antrokoreana gracilipes Verhoeff, 1938 | 14,747 | DQ344025.1 | |
Julidae | Anaulaciulus koreanus Verhoeff, 1937 | 14,916 | KX096886.1 | ||
Spirostreptida | Cambalopsidae | Bilingulus sinicus Zhang & Li, 1981 | 15,879 | PQ568882 | |
Odontopygidae | Prionopetalum kraepelini Attems, 1896 | 15,114 | MT394524.1 | ||
Chaleponcus netus Enghoff, 2014 | 15,093 | MT394513.1 | |||
Harpagophoridae | Agaricogonopus acrotrifoliolatus Zhang, 1997 | 15,016 | PQ602473 | ||
Spirostreptidae | Pseudotibiozus cerasopus Attems, 1914 | 15,121 | MT394506.1 | ||
Archispirostreptus gigas Peters, 1985 | 15,177 | MT394525.1 | |||
Macrolenostreptus oreste Hoffman & Howell, 1996 | 15,367 | MT394512.1 | |||
Tropostreptus severus Enghoff, 2017 | 15,209 | MT394517.1 | |||
Tropostreptus austerus Attems, 1950 | 15,261 | MT394523.1 | |||
Tropostreptus hamatus Demange, 1977 | 15,156 | MT394508.1 | |||
Tropostreptus kipunji Enghoff, 2017 | 15,170 | MT394503.1 | |||
Tropostreptus droides Enghoff, 2017 | 15,172 | MT394522.1 | |||
Tropostreptus sigmatospinus Enghoff, 2017 | 15,176 | MT394504.1 | |||
Tropostreptus microcephalus Enghoff, 2017 | 15,169 | MT394516.1 | |||
Chilooda | Lithobiomorpha | Henicopidae | Cermatobius longicornis Takakuwa, 1939 | 16,833 | KC155628.1 |
Methods | Subset Partitions | Best Model |
---|---|---|
Cytb+ATP6+COII+COIII | TIM2+F+I+G4 | |
ML | ATP8 | GTR+F+I+G4 |
COI | ||
ND2+ND3+ND6 | ||
12S rRNA+16S rRNA | ||
ND1+ND4L+ND4+ND5 | GTR+F+I+I+R5 | |
BI | ATP8 | GTR+F+I+G4 |
COI | ||
Cytb+ATP6+CO+COII | ||
ND1+ND4L+ND4+ND5 | ||
ND2+ND3+ND6 | ||
Cytb+ATP6+COII+COIII | ||
12S rRNA+16S rRNA |
Gene | Location | Intergenic Nucleotides | Size (bp) | |
---|---|---|---|---|
From | To | |||
12S rRNA(+) | 1/1/1/1 | 768/758/784/764 | 0/0/0/0 | 768/758/784/764 |
tRNA-Val(+) | 769/760/789/766 | 829/821/849/820 | 0/1/4/1 | 61/62/61/55 |
16S rRNA(+) | 826/810/850/816 | 2081/2045/2138/2080 | −4/−12/0/−5 | 1256/1236/1289/1265 |
tRNA-Leu1(+) | 2059/2058/2139/2107 | 2120/2118/2202/2170 | −23/12/0/26 | 62/61/64/64 |
tRNA-Leu2(+) | 2122/2120/2204/2171 | 2183/2184/2269/2234 | 1/1/1/0 | 62/65/66/64 |
ND1(+) | 2184/2185/2270/2235 | 3102/3109/3193/3150 | 0/0/0/0 | 919/925/924/916 |
tRNA-Pro(+) | 3103/3110/3198/3151 | 3163/3171/3264/3213 | 0/0/4/0 | 61/62/67/63 |
ND4L(+) | 3169/3173/3256/3223 | 3441/3445/3546/3495 | 5/1/0/9 | 273/273/282/273 |
ND4(+) | 3447/3469/3540/3489 | 4764/4788/4839/4820 | 5/23/−7/−7 | 1318/1320/1300/1332 |
tRNA-His(+) | 4765/4848/4844/4820 | 4829/4909/4909/4884 | 0/59/4/−1 | 65/62/66/65 |
ND5(+) | 4830/4910/4910/4885 | 6534/6629/6608/6588 | 0/0/0/0 | 1705/1720/1699/1704 |
tRNA-Phe(+) | 6535/6630/6609/6589 | 6592/6687/6671/6649 | 0/0/0/0 | 58/58/63/61 |
tRNA-Tyr(+) | 6539/6687/6670/6646 | 6657/6749/6735/6709 | 0/−1/−2/−4 | 65/63/66/64 |
tRNA-Gln(+) | 6658/7972/6736/6711 | 6724/8027/6802/6775 | 0/0/0/1 | 67/56/67/65 |
tRNA-Thr(−) | 7206/8028/6853/6825 | 7268/8090/6921/6887 | 0/0/50/49 | 63/63/69/63 |
tRNA-Ser1(−) | 7269/8091/6928/6905 | 7334/8157/6996/6973 | 0/0/6/17 | 66/67/69/69 |
Cytb(−) | 7335/8156/6995/6972 | 8453/9268/8113/8090 | 0/−2/−2/−2 | 1119/1113/1119/1119 |
ND6(−) | 8454/9268/8114/8044 | 8910/9734/8564/8544 | 0/−1/0/−47 | 457/467/451/501 |
tRNA-Glu(−) | 8914/9741/8565/8542 | 8977/9806/8629/8603 | 3/6/0/−3 | 64/66/65/62 |
tRNA-Ser2(−) | 8978/9807/8630/8603 | 9037/9867/8687/8663 | 0/0/0/−1 | 60/61/58/61 |
tRNA-Asn(−) | 9038/9867/8688/8664 | 9105/9929/8754/8728 | 0/−1/0/0 | 68/63/67/65 |
tRNA-Arg(−) | 9106/9928/8754/8728 | 9172/9988/8815/8790 | 0/−2/−1/−1 | 67/61/62/63 |
tRNA-Ala(−) | 9173/9987/8816/8794 | 9236/10,050/8883/8858 | 0/−2/0/3 | 64/64/68/65 |
ND3(−) | 9235/10,050/8882/8857 | 9579/10,393/9232/9210 | −2/−1/−2/−2 | 345/344/351/354 |
tRNA-Gly(−) | 9580/10,394/9233/9205 | 9646/10,457/9295/9270 | 0/0/0/−6 | 67/64/63/66 |
COIII(−) | 9646/10,456/9299/9271 | 10,431/11,241/10,076/10,048 | −1/−2/3/0 | 786/786/778/778 |
ATP6(−) | 10,432/11,228/10,076/10,049 | 11,107/11,911/10,752/10,724 | 0/−14/−1/0 | 676/684/677/676 |
ATP8(−) | 11,101/11,905/10,746/10,718 | 11,256/12,060/10,901/10,873 | −7/−7/−7/−7 | 156/156/156/156 |
tRNA-Asp(−) | 11,257/12,061/10,902/10,874 | 11,319/12,126/10,965/10,937 | 0/0/0/0 | 63/66/64/64 |
tRNA-Lys(−) | 11,320/12,126/10,966/10,937 | 11,387/12,190/11,031/11,003 | 0/−1/0/−1 | 68/65/66/67 |
COII(−) | 11,388/12,192/11,032/11,004 | 12,069/12,872/11,707/11,682 | 0/1/0/0 | 682/681/676/679 |
COI(−) | 12,073/12,873/11,711/11,683 | 13,605/14,411/13,243/13,213 | 3/0/3/0 | 1533/1539/1533/1531 |
tRNA-Cys(+) | 13,616/14,412/13,248/13,219 | 13,680/14,473/13,310/13,281 | 10/0/4/5 | 65/62/63/63 |
tRNA-Trp(−) | 13,617/14,474/13,303/13,274 | 13,681/14,536/13,364/13,336 | −64/0/−8/−8 | 65/63/62/63 |
ND2(−) | 13,680/14,535/13,365/13,335 | 14,687/15,536/14,361/14,327 | −2/−2/0/−2 | 1008/1002/997/993 |
tRNA-Met(−) | 14,688/15,537/14,362/14,328 | 14,755/15,601/14,425/14,393 | 0/0/0/0 | 68/65/64/66 |
tRNA-Ile(−) | 14,756/15,601/14,425/14,393 | 14,821/15,666/14,491/14,457 | 0/−1/−1/−1 | 66/66/67/65 |
D-loop | 6725/6750/14,426/14,458 | 7205/7971/14,929/14,906 | 0/0/0/0 | 481/1222/504/449 |
Species | Region | Size (bp) | A+T % | AT-Skew | GC-Skew |
---|---|---|---|---|---|
Agaricogonopus acrotrifoliolatus | Whole genome | 15,016 | 72.57 | −0.068 | 0.342 |
PCGs | 10,971 | 71.58 | −0.106 | −0.066 | |
tRNAs | 1408 | 75.81 | 0.049 | 0.079 | |
rRNAs | 2024 | 75.10 | −0.084 | 0.385 | |
D-loop | 481 | 67.57 | 0.003 | 0.295 | |
Bilingulus sinicus | Whole genome | 15,879 | 75.43 | 0.033 | 0.323 |
PCGs | 11,022 | 74.31 | 0.091 | 0.025 | |
tRNAs | 1385 | 77.24 | 0.021 | 0.129 | |
rRNAs | 1994 | 75.68 | −0.054 | 0.381 | |
D-loop | 1222 | 78.47 | 0.051 | 0.353 | |
Paraspirobolus lucifugus | Whole genome | 15,016 | 60.50 | −0.068 | 0.342 |
PCGs | 10,971 | 58.54 | −0.106 | −0.066 | |
tRNAs | 1415 | 64.68 | 0.049 | 0.07 | |
rRNAs | 2024 | 65.90 | −0.084 | 0.385 | |
D-loop | 504 | 68.65 | 0.069 | 0.265 | |
Trigoniulus corallinus | Whole genome | 14,906 | 72.05 | 0.007 | 0.317 |
PCGs | 11,007 | 71.21 | −0.141 | 0.013 | |
tRNAs | 1402 | 75.32 | 0.017 | 0.092 | |
rRNAs | 2029 | 75.11 | 0.045 | 0.386 | |
D-loop | 449 | 71.04 | 0.065 | 0.246 |
Gene | Codon | |
---|---|---|
Start | Stop | |
ND1 | ATG/ATT/ATT/ATA | TAA/T/TAA/T |
ND4L | ATG/ATG/GTG/ATG | TAA/TAA/TAG/TAA |
ND4 | ATA/ATG/ATG/ATG | T/T/T/TAA |
ND5 | TTA/GTG/GTG/ATT | T/T/T/TAG |
Cytb | ATG/ATG/ATG/ATG | TAA/TAG/TAA/TAA |
ND6 | ATA/ATT/ATC/ATA | T/TA/T/TAA |
ND3 | ATA/ATT/ATA/ATA | TAG/TA/TAG/TAG |
COIII | ATG/ATG/ATG/ATG | TAG/TAA/T/T |
ATP6 | ATG/ATG/ATG/ATG | T/TAA/TA/T |
ATP8 | ATT/ATT/ATA/ATT | TAA/TAA/TAA/TAA |
COII | ATG/ATG/ATG/ATG | T/TAG/T/T |
COI | ACG/ATT/ACG/CGA | TAA/TAA/TAA/TTT |
ND2 | ATT/ATT/ATC/ATT | TAA/TAA/TAA/TAA |
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Li, Y.; Zhang, G.; Xu, W.; Xu, T.; Li, L.; Gao, M.; Wang, J.; Liu, H. Mitochondrial Genomes of Four Millipedes (Diplopoda: Spirostreptida and Spirobolida) Unveil Phylogenetic Novelty and Gene Rearrangement Patterns. Curr. Issues Mol. Biol. 2025, 47, 476. https://doi.org/10.3390/cimb47060476
Li Y, Zhang G, Xu W, Xu T, Li L, Gao M, Wang J, Liu H. Mitochondrial Genomes of Four Millipedes (Diplopoda: Spirostreptida and Spirobolida) Unveil Phylogenetic Novelty and Gene Rearrangement Patterns. Current Issues in Molecular Biology. 2025; 47(6):476. https://doi.org/10.3390/cimb47060476
Chicago/Turabian StyleLi, Yingzhu, Gaoji Zhang, Wei Xu, Tangjun Xu, Lingna Li, Ming Gao, Jiachen Wang, and Hongyi Liu. 2025. "Mitochondrial Genomes of Four Millipedes (Diplopoda: Spirostreptida and Spirobolida) Unveil Phylogenetic Novelty and Gene Rearrangement Patterns" Current Issues in Molecular Biology 47, no. 6: 476. https://doi.org/10.3390/cimb47060476
APA StyleLi, Y., Zhang, G., Xu, W., Xu, T., Li, L., Gao, M., Wang, J., & Liu, H. (2025). Mitochondrial Genomes of Four Millipedes (Diplopoda: Spirostreptida and Spirobolida) Unveil Phylogenetic Novelty and Gene Rearrangement Patterns. Current Issues in Molecular Biology, 47(6), 476. https://doi.org/10.3390/cimb47060476