Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies
Abstract
:1. Introduction
2. Results and Discussion
2.1. Genome Organization and Base Composition
2.2. Protein-Coding Genes and Codon Usage
2.3. Transfer RNAs
2.4. Ribosomal RNAs
2.5. The Control Region
2.6. Phylogenetic Relationship
3. Materials and Methods
3.1. Specimens and DNA Extraction
3.2. Genome Sequencing, Assembly, and Annotation
3.3. Phylogenetic Analysis
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
mtDNA | Mitochondrial DNA |
PCG | Protein-Coding Gene |
tRNA | Transfer RNA |
rRNA | Ribosomal RNA |
CR | Control Region |
SL | Stem-Loop |
CSB | Conserved Sequence Block |
ML | Maximum Likelihood |
BI | Bayesian Inferences |
Appendix A
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Taxonomic Order | Family | Species | Number (bp) | Accession Number |
---|---|---|---|---|
Plecoptera | Perlidae | Acroneuria hainana | 15,804 | NC_026104 |
Togoperla sp. | 15,723 | KM409708 | ||
Kamimuria wangi | 16,179 | NC_024033 | ||
Kamimuria chungnanshana | 15,943 | NC_028076 | ||
Dinocras cephalotes | 15,666 | NC_022843 | ||
Pteronarcyidae | Pteronarcys princeps | 16,004 | NC_006133 | |
Pteronarcella badia | 15,585 | NC_029248 | ||
Capniidae | Apteroperla tikumana | 15,564 | NC_027698 | |
Capnia zijinshana | 16,310 | KX094942 | ||
Mesocapnia arizonensis | 14,921 | KP642637 * | ||
Mesocapnia daxingana | 15,524 | KY568983 * | ||
Peltoperlidae | Cryptoperla stilifera | 15,633 | KC952026 * | |
Soliperla sp. | 15,877 | MF716958 | ||
Styloperlidae | Styloperla sp. | 15,416 | KR088971 * | |
Styloperla spinicercia | 16,129 | KX845569 | ||
Chloroperlidae | Sweltsa longistyla | 16,151 | KM216826 | |
Suwallia teleckojensis | 16,146 | MF198253 | ||
Taeniopterygidae | Taeniopteryx ugola | 15,353 | MG589786 | |
Doddsia occidentalis | 16,020 | MG589787 | ||
Gripopterygidae | Zelandoperla fenestrata | 16,385 | KY522907 | |
Perlodidae | Perlodes sp. | 16,039 | MF197377 | |
Isoperla bilineata | 15,048 | MF716959 | ||
Ephemeroptera | Heptageniidae | Parafronurus youi | 15,481 | EU349015 |
Isonychiidae | Isonychia ignota | 15,105 | HM143892 |
Gene | Direction | Location | Size | Anticodon | Anticodon Positions | Start/Stop Codons | Intergenic Nucleotides |
---|---|---|---|---|---|---|---|
tRNAIle | Forward | 1–67 | 67 | GAT | 30–32 | ||
tRNAGln | Reverse | 65–133 | 69 | TTG | 101–103 | −3 | |
tRNAMet | Forward | 135–203 | 69 | CAT | 165–167 | 1 | |
ND2 | Forward | 204–1238 | 1035 | ATG/TAA | 0 | ||
tRNATrp | Forward | 1237–1305 | 69 | TCA | 1267–1269 | −2 | |
tRNACys | Reverse | 1298–1364 | 67 | GCA | 1331–1333 | −8 | |
tRNATyr | Reverse | 1367–1433 | 67 | GTA | 1398–1400 | 2 | |
COI | Forward | 1426–2982 | 1557 | ATT/TAA | −8 | ||
tRNALeu(UUR) | Forward | 3002–3067 | 66 | TAA | 3031–3033 | 19 | |
COII | Forward | 3081–3768 | 688 | ATG/T- | 13 | ||
tRNALys | Forward | 3769–3839 | 71 | CTT | 3799–3801 | 0 | |
tRNAAsp | Forward | 3839–3907 | 69 | GTC | 3869–3871 | −1 | |
ATP8 | Forward | 3908–4066 | 159 | ATG/TAA | 0 | ||
ATP6 | Forward | 4060–4737 | 678 | ATG/TAA | −7 | ||
COIII | Forward | 4737–5525 | 789 | ATG/TAA | −1 | ||
tRNAGly | Forward | 5528–5593 | 66 | TCC | 5558–5560 | 2 | |
ND3 | Forward | 5594–5947 | 354 | ATC/TAG | 0 | ||
tRNAAla | Forward | 5946–6011 | 66 | TGC | 5975–5977 | −2 | |
tRNAArg | Forward | 6013–6077 | 65 | TCG | 6042–6044 | 1 | |
tRNAAsn | Forward | 6082–6147 | 66 | GTT | 6112–6114 | 4 | |
tRNASer(AGN) | Forward | 6148–6214 | 67 | GCT | 6173–6175 | 0 | |
tRNAGlu | Forward | 6215–6281 | 67 | TTC | 6246–6248 | 0 | |
tRNAPhe | Reverse | 6287–6351 | 65 | GAA | 6320–6322 | 5 | |
ND5 | Reverse | 6352–8086 | 1735 | GTG/T- | 0 | ||
tRNAHis | Reverse | 8087–8154 | 68 | GTG | 8121–8123 | 0 | |
ND4 | Reverse | 8159–9499 | 1341 | ATG/TAA | 4 | ||
ND4L | Reverse | 9493–9789 | 297 | ATG/TAA | −7 | ||
tRNAThr | Forward | 9792–9859 | 68 | TGT | 9822–9824 | 2 | |
tRNAPro | Reverse | 9861–9928 | 68 | TGG | 9896–9898 | 1 | |
ND6 | Forward | 9930–10,454 | 525 | ATC/TAA | 1 | ||
CytB | Forward | 10,454–11,590 | 1137 | ATG/TAA | −1 | ||
tRNASer(UCN) | Forward | 11,590–11,659 | 70 | TGA | 11,621–11,623 | −1 | |
ND1 | Reverse | 11,680–12,630 | 951 | TTG/TAG | 20 | ||
tRNALeu(CUN) | Reverse | 12,632–12,697 | 66 | TAG | 12,666–12,668 | 1 | |
lrRNA | Reverse | 12,698–14,026 | 1329 | 0 | |||
tRNAVal | Reverse | 14,027–14,097 | 71 | TAC | 14,062–14,064 | 0 | |
srRNA | Reverse | 14,098–14,897 | 800 | 0 | |||
CR | 14,898–16,146 | 1249 | 0 |
Feature | Proportion of Nucleotides | No. of Nucleotides | ||||||
---|---|---|---|---|---|---|---|---|
%T | %C | %A | %G | %A + T | AT Skew | GC Skew | ||
Whole genome | 30.2 | 21.7 | 36.5 | 11.6 | 66.7 | 0.09 | −0.303 | 16,146 |
PCGs | 37.6 | 18.9 | 26.5 | 17.0 | 64.1 | −0.17 | −0.052 | 11,244 |
First codon position | 40.6 | 20.7 | 21.9 | 16.9 | 62.4 | −0.30 | −0.102 | 3743 |
Second codon position | 37.5 | 18.1 | 28.5 | 15.9 | 66.0 | −0.14 | −0.063 | 3743 |
Third codon position | 34.8 | 17.8 | 29.1 | 18.2 | 64.0 | −0.09 | 0.011 | 3743 |
PCG-J | 32.9 | 24.5 | 28.9 | 13.7 | 61.8 | −0.07 | −0.281 | 6921 |
First codon position | 36.4 | 23.1 | 24.5 | 16.0 | 60.9 | −0.20 | −0.182 | 2307 |
Second codon position | 32.0 | 27.2 | 30.4 | 10.3 | 62.4 | −0.03 | −0.450 | 2307 |
Third codon position | 30.4 | 23.0 | 31.8 | 14.8 | 62.1 | 0.02 | −0.217 | 2307 |
PCG-N | 45.1 | 9.9 | 22.7 | 22.2 | 67.8 | −0.33 | 0.383 | 4323 |
First codon position | 41.9 | 9.5 | 25.0 | 23.6 | 66.9 | −0.25 | 0.427 | 1441 |
Second codon position | 47.1 | 16.9 | 17.8 | 18.3 | 64.9 | −0.45 | 0.040 | 1441 |
Third codon position | 46.4 | 3.4 | 25.4 | 24.8 | 71.8 | −0.29 | 0.759 | 1441 |
tRNA genes | 34.6 | 13.9 | 34.6 | 16.9 | 69.2 | 0.00 | 0.100 | 1487 |
tRNA-J | 33.8 | 15.1 | 36.2 | 14.9 | 70.0 | 0.03 | −0.007 | 946 |
tRNA-N | 36.0 | 11.6 | 31.8 | 20.5 | 67.8 | −0.06 | 0.276 | 541 |
rRNA genes | 39.9 | 9.4 | 31.6 | 19.1 | 71.5 | −0.12 | 0.338 | 2129 |
lrRNA | 40.3 | 8.3 | 32.9 | 18.5 | 73.2 | −0.10 | 0.382 | 1329 |
srRNA | 39.1 | 11.4 | 29.5 | 20.0 | 68.6 | −0.14 | 0.275 | 800 |
CR | 35.5 | 13.3 | 43.6 | 7.6 | 79.1 | 0.10 | −0.272 | 1249 |
Amino Acid | Codon | N | RSCU | N+ | RSCU | N− | RSCU |
---|---|---|---|---|---|---|---|
Phe (F) | UUU | 208 | 1.36 | 85 | 0.98 | 123 | 1.86 |
UUC | 98 | 0.64 | 89 | 1.02 | 9 | 0.14 | |
Leu (L) | UUA | 280 | 2.6 | 131 | 2.13 | 149 | 3.23 |
UUG | 108 | 1 | 12 | 0.2 | 96 | 2.08 | |
CUU | 67 | 0.62 | 53 | 0.86 | 14 | 0.3 | |
CUC | 67 | 0.62 | 66 | 1.07 | 1 | 0.02 | |
CUA | 112 | 1.04 | 97 | 1.58 | 15 | 0.32 | |
CUG | 12 | 0.11 | 10 | 0.16 | 2 | 0.04 | |
Ile (I) | AUU | 213 | 1.46 | 133 | 1.29 | 80 | 1.86 |
AUC | 79 | 0.54 | 73 | 0.71 | 6 | 0.14 | |
Met (M) | AUA | 141 | 1.45 | 100 | 1.72 | 41 | 1.04 |
AUG | 54 | 0.55 | 16 | 0.28 | 38 | 0.96 | |
Val (V) | GUU | 82 | 1.38 | 29 | 0.88 | 53 | 2.02 |
GUC | 44 | 0.74 | 37 | 1.12 | 7 | 0.27 | |
GUA | 70 | 1.18 | 55 | 1.67 | 15 | 0.57 | |
GUG | 41 | 0.69 | 11 | 0.33 | 30 | 1.14 | |
Ser (S) | UCU | 94 | 2.32 | 39 | 1.72 | 55 | 3.08 |
UCC | 30 | 0.74 | 29 | 1.28 | 1 | 0.06 | |
UCA | 63 | 1.56 | 48 | 2.12 | 15 | 0.84 | |
UCG | 15 | 0.37 | 7 | 0.31 | 8 | 0.45 | |
Pro (P) | CCU | 59 | 1.55 | 34 | 1.21 | 25 | 2.5 |
CCC | 48 | 1.26 | 45 | 1.61 | 3 | 0.3 | |
CCA | 36 | 0.95 | 29 | 1.04 | 7 | 0.7 | |
CCG | 9 | 0.24 | 4 | 0.14 | 5 | 0.5 | |
Thr (T) | ACU | 66 | 1.25 | 43 | 1.07 | 23 | 1.8 |
ACC | 59 | 1.11 | 58 | 1.44 | 1 | 0.08 | |
ACA | 73 | 1.38 | 56 | 1.39 | 17 | 1.33 | |
ACG | 14 | 0.26 | 4 | 0.1 | 10 | 0.78 | |
Ala (A) | GCU | 84 | 1.51 | 48 | 1.29 | 36 | 1.97 |
GCC | 76 | 1.37 | 72 | 1.93 | 4 | 0.22 | |
GCA | 37 | 0.67 | 27 | 0.72 | 10 | 0.55 | |
GCG | 25 | 0.45 | 2 | 0.05 | 23 | 1.26 | |
Tyr (Y) | UAU | 106 | 1.39 | 32 | 0.84 | 74 | 1.95 |
UAC | 46 | 0.61 | 44 | 1.16 | 2 | 0.05 | |
Stop (*) | UAA | 9 | 1.64 | 7 | 1.75 | 2 | 1.33 |
UAG | 2 | 0.36 | 1 | 0.25 | 1 | 0.67 | |
His (H) | CAU | 46 | 1.12 | 30 | 0.91 | 16 | 2 |
CAC | 36 | 0.88 | 36 | 1.09 | 0 | 0 | |
Gln (Q) | CAA | 70 | 1.71 | 57 | 1.97 | 13 | 1.08 |
CAG | 12 | 0.29 | 1 | 0.03 | 11 | 0.92 | |
Asn (N) | AAU | 110 | 1.44 | 63 | 1.19 | 47 | 2 |
AAC | 43 | 0.56 | 43 | 0.81 | 0 | 0 | |
Lys (K) | AAA | 35 | 1.03 | 29 | 1.66 | 6 | 0.36 |
AAG | 33 | 0.97 | 6 | 0.34 | 27 | 1.64 | |
Asp (D) | GAU | 51 | 1.4 | 31 | 1.19 | 20 | 1.9 |
GAC | 22 | 0.6 | 21 | 0.81 | 1 | 0.1 | |
Glu (E) | GAA | 55 | 1.34 | 43 | 1.87 | 12 | 0.67 |
GAG | 27 | 0.66 | 3 | 0.13 | 24 | 1.33 | |
Cys (C) | UGU | 38 | 1.69 | 7 | 1 | 31 | 2 |
UGC | 7 | 0.31 | 7 | 1 | 0 | 0 | |
Trp (W) | UGA | 82 | 1.56 | 63 | 1.85 | 19 | 1.03 |
UGG | 23 | 0.44 | 5 | 0.15 | 18 | 0.97 | |
Arg (R) | CGU | 13 | 0.81 | 4 | 0.41 | 9 | 1.44 |
CGC | 2 | 0.13 | 2 | 0.21 | 0 | 0 | |
CGA | 33 | 2.06 | 29 | 2.97 | 4 | 0.64 | |
CGG | 16 | 1 | 4 | 0.41 | 12 | 1.92 | |
Ser (S) | AGU | 49 | 1.21 | 22 | 0.97 | 27 | 1.51 |
AGC | 18 | 0.44 | 12 | 0.53 | 6 | 0.34 | |
AGA | 52 | 1.28 | 24 | 1.06 | 28 | 1.57 | |
AGG | 3 | 0.07 | 0 | 0 | 3 | 0.17 | |
Gly (G) | GGU | 56 | 0.91 | 21 | 0.6 | 35 | 1.32 |
GGC | 22 | 0.36 | 14 | 0.4 | 8 | 0.3 | |
GGA | 92 | 1.5 | 79 | 2.27 | 13 | 0.49 | |
GGG | 75 | 1.22 | 25 | 0.72 | 50 | 1.89 |
Gene | Best Model |
---|---|
ATP6 | GTR + I + G |
ATP8 | GTR + G |
COI | GTR + G |
COII | GTR + G |
COIII | GTR + I + G |
CytB | GTR + G |
ND1 | GTR + I + G |
ND2 | GTR + I + G |
ND3 | GTR + I + G |
ND4 | GTR + I + G |
ND4L | GTR + I + G |
ND5 | GTR + I + G |
ND6 | GTR + I + G |
srRNA | GTR + I + G |
lrRNA | GTR + G |
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Wang, Y.; Cao, J.-J.; Li, W.-H. Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies. Int. J. Mol. Sci. 2018, 19, 680. https://doi.org/10.3390/ijms19030680
Wang Y, Cao J-J, Li W-H. Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies. International Journal of Molecular Sciences. 2018; 19(3):680. https://doi.org/10.3390/ijms19030680
Chicago/Turabian StyleWang, Ying, Jin-Jun Cao, and Wei-Hai Li. 2018. "Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies" International Journal of Molecular Sciences 19, no. 3: 680. https://doi.org/10.3390/ijms19030680