Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (12): 300-310.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0171
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Received:
2023-03-01
Online:
2023-12-26
Published:
2024-01-11
Contact:
SONG Nan
E-mail:xingyulin666666@163.com;songnan@henau.edu.cn
LIN Xing-yu, SONG Nan. Comparative Mitochondrial Genome and Phylogenetic Analysis of Atteva charopis Turner, 1903[J]. Biotechnology Bulletin, 2023, 39(12): 300-310.
科 Family | 种名 Species | 基因组数据库编号 GenBank No. | 长度 Length/bp |
---|---|---|---|
潜叶蛾科 Lyonetiidae | Leucoptera malifoliella Lyonetia clerkella | JN790955 MF045483 | 15 646 15 259 |
Praydidae | Prays oleae | KM874804 | 16 499 |
斑巢蛾科 Attevidae | Atteva aurea Atteva charopis | ON480203 OQ130005 | 16 391 15 163 |
菜蛾科 Plutellidae | Acrolepiopsis assectella Plutella armoraciae | MW662615 MW662613 | 15 369 15 569 |
Plutella porrectella | MW662614 | 16 196 | |
Plutella australiana | MG787473 | 15 962 | |
Plutella xylostella | KM023645 | 16 014 | |
Scythropiidae | Scythropia crataegella | ON755208 | 15 350 |
外群 Outgroup | Caloptilia theivora Phyllocnistis citrella | MK541932 MN792920 | 15 297 15 416 |
Table 1 Species sample information used in the phylogenetic tree construction in this study
科 Family | 种名 Species | 基因组数据库编号 GenBank No. | 长度 Length/bp |
---|---|---|---|
潜叶蛾科 Lyonetiidae | Leucoptera malifoliella Lyonetia clerkella | JN790955 MF045483 | 15 646 15 259 |
Praydidae | Prays oleae | KM874804 | 16 499 |
斑巢蛾科 Attevidae | Atteva aurea Atteva charopis | ON480203 OQ130005 | 16 391 15 163 |
菜蛾科 Plutellidae | Acrolepiopsis assectella Plutella armoraciae | MW662615 MW662613 | 15 369 15 569 |
Plutella porrectella | MW662614 | 16 196 | |
Plutella australiana | MG787473 | 15 962 | |
Plutella xylostella | KM023645 | 16 014 | |
Scythropiidae | Scythropia crataegella | ON755208 | 15 350 |
外群 Outgroup | Caloptilia theivora Phyllocnistis citrella | MK541932 MN792920 | 15 297 15 416 |
基因 Gene | 基因长度 Gene length/bp | 起始位置 Start position/bp | 终止位置 Stop position/bp | 起始密码子 Start codon | 终止密码子 Stop codon | 编码链 Coding strand |
---|---|---|---|---|---|---|
trnI trnM | 64 69 | 399 464 | 462 532 | H H | ||
trnQ | 69 | 604 | 536 | L | ||
nad2 | 1 026 | 645 | 1 670 | ATT | TAA | H |
trnW | 66 | 1 669 | 1 734 | H | ||
trnC | 64 | 1 790 | 1 727 | L | ||
trnY | 66 | 1 855 | 1 790 | L | ||
cox1 | 1 536 | 1 859 | 3 394 | CGA | TAA | H |
trnL2 | 67 | 3 390 | 3 456 | H | ||
cox2 | 682 | 3 457 | 4 138 | ATG | T | H |
trnK | 71 | 4 139 | 4 209 | H | ||
trnD | 67 | 4 209 | 4 275 | H | ||
atp8 | 159 | 4 276 | 4 434 | ATT | TAA | H |
atp6 | 672 | 4 428 | 5 099 | ATG | TAA | H |
cox3 | 789 | 5 099 | 5 887 | ATG | TAA | H |
trnG | 67 | 5 890 | 5 956 | H | ||
nad3 | 354 | 5 957 | 6 310 | ATA | TAA | H |
trnA | 66 | 6 324 | 6 389 | H | ||
trnR | 62 | 6 391 | 6 452 | H | ||
trnN | 66 | 6 453 | 6 518 | H | ||
trnS1 | 60 | 6 518 | 6 577 | H | ||
trnE | 65 | 6 579 | 6 643 | H | ||
trnF | 67 | 6 708 | 6 642 | L | ||
nad5 | 1 734 | 8 440 | 6 708 | ATT | TA | L |
trnH | 64 | 8 504 | 8 441 | L | ||
nad4 | 1 342 | 9 846 | 8 505 | ATG | T | L |
nad4l | 285 | 10 131 | 9 847 | ATG | TAA | L |
trnT | 65 | 10 134 | 10 198 | H | ||
trnP | 65 | 10 263 | 10 199 | L | ||
nad6 | 502 | 10 265 | 10 766 | ATT | T | H |
cob | 1 152 | 10 799 | 11 950 | ATG | TAA | H |
trnS2 | 66 | 11 965 | 12 030 | H | ||
nad1 | 957 | 12 985 | 12 029 | ATG | TAA | L |
trnL1 | 68 | 13 054 | 12 987 | L | ||
rrnL | 1 330 | 14 359 | 13 030 | L | ||
trnV | 65 | 14 446 | 14 382 | L | ||
rrnS Control region | 697 426 | 15 143 15 136 | 14 447 398 | L Non-coding sequence |
Table 2 Annotation of A. charopis mitochondrial genome
基因 Gene | 基因长度 Gene length/bp | 起始位置 Start position/bp | 终止位置 Stop position/bp | 起始密码子 Start codon | 终止密码子 Stop codon | 编码链 Coding strand |
---|---|---|---|---|---|---|
trnI trnM | 64 69 | 399 464 | 462 532 | H H | ||
trnQ | 69 | 604 | 536 | L | ||
nad2 | 1 026 | 645 | 1 670 | ATT | TAA | H |
trnW | 66 | 1 669 | 1 734 | H | ||
trnC | 64 | 1 790 | 1 727 | L | ||
trnY | 66 | 1 855 | 1 790 | L | ||
cox1 | 1 536 | 1 859 | 3 394 | CGA | TAA | H |
trnL2 | 67 | 3 390 | 3 456 | H | ||
cox2 | 682 | 3 457 | 4 138 | ATG | T | H |
trnK | 71 | 4 139 | 4 209 | H | ||
trnD | 67 | 4 209 | 4 275 | H | ||
atp8 | 159 | 4 276 | 4 434 | ATT | TAA | H |
atp6 | 672 | 4 428 | 5 099 | ATG | TAA | H |
cox3 | 789 | 5 099 | 5 887 | ATG | TAA | H |
trnG | 67 | 5 890 | 5 956 | H | ||
nad3 | 354 | 5 957 | 6 310 | ATA | TAA | H |
trnA | 66 | 6 324 | 6 389 | H | ||
trnR | 62 | 6 391 | 6 452 | H | ||
trnN | 66 | 6 453 | 6 518 | H | ||
trnS1 | 60 | 6 518 | 6 577 | H | ||
trnE | 65 | 6 579 | 6 643 | H | ||
trnF | 67 | 6 708 | 6 642 | L | ||
nad5 | 1 734 | 8 440 | 6 708 | ATT | TA | L |
trnH | 64 | 8 504 | 8 441 | L | ||
nad4 | 1 342 | 9 846 | 8 505 | ATG | T | L |
nad4l | 285 | 10 131 | 9 847 | ATG | TAA | L |
trnT | 65 | 10 134 | 10 198 | H | ||
trnP | 65 | 10 263 | 10 199 | L | ||
nad6 | 502 | 10 265 | 10 766 | ATT | T | H |
cob | 1 152 | 10 799 | 11 950 | ATG | TAA | H |
trnS2 | 66 | 11 965 | 12 030 | H | ||
nad1 | 957 | 12 985 | 12 029 | ATG | TAA | L |
trnL1 | 68 | 13 054 | 12 987 | L | ||
rrnL | 1 330 | 14 359 | 13 030 | L | ||
trnV | 65 | 14 446 | 14 382 | L | ||
rrnS Control region | 697 426 | 15 143 15 136 | 14 447 398 | L Non-coding sequence |
特征 Feature | 长度 Size/bp | AT/% | AT偏倚 AT-skew | GC偏倚 GC-skew |
---|---|---|---|---|
PCGs-H | 6 870 | 78.30 | -0.145 | -0.113 |
PCGs-L | 4 314 | 81.70 | -0.171 | 0.316 |
rRNAs-L | 2 027 | 85.10 | 0.040 | 0.344 |
tRNAs-H | 921 | 80.90 | 0.031 | 0.023 |
tRNAs-L | 528 | 83.50 | 0.016 | 0.425 |
全基因组 Whole genome | 15 163 | 81.10 | -0.024 | -0.196 |
Table 3 Nucleotide composition and skewness of the A. charopis mitochondrial genome
特征 Feature | 长度 Size/bp | AT/% | AT偏倚 AT-skew | GC偏倚 GC-skew |
---|---|---|---|---|
PCGs-H | 6 870 | 78.30 | -0.145 | -0.113 |
PCGs-L | 4 314 | 81.70 | -0.171 | 0.316 |
rRNAs-L | 2 027 | 85.10 | 0.040 | 0.344 |
tRNAs-H | 921 | 80.90 | 0.031 | 0.023 |
tRNAs-L | 528 | 83.50 | 0.016 | 0.425 |
全基因组 Whole genome | 15 163 | 81.10 | -0.024 | -0.196 |
密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
UUU(F) | 444 | 1.57 | UCU(S) | 81 | 1.41 | UAU(Y) | 344 | 1.60 | UGU(C) | 46 | 1.35 | |||
UUC(F) | 123 | 0.43 | UCC(S) | 48 | 0.83 | UAC(Y) | 85 | 0.40 | UGC(C) | 22 | 0.65 | |||
UUA(L) | 366 | 3.24 | UCA(S) | 88 | 1.53 | UAA(*) | 377 | 1.69 | UGA(W) | 56 | 1.08 | |||
UUG(L) | 68 | 0.60 | UCG(S) | 21 | 0.36 | UAG(*) | 68 | 0.31 | UGG(W) | 48 | 0.92 | |||
CUU(L) | 87 | 0.77 | CCU(P) | 20 | 0.92 | CAU(H) | 62 | 1.68 | CGU(R) | 4 | 0.89 | |||
CUC(L) | 38 | 0.34 | CCC(P) | 39 | 1.79 | CAC(H) | 12 | 0.32 | CGC(R) | 2 | 0.44 | |||
CUA(L) | 93 | 0.82 | CCA(P) | 25 | 1.15 | CAA(Q) | 68 | 1.43 | CGA(R) | 9 | 2.00 | |||
CUG(L) | 25 | 0.22 | CCG(P) | 3 | 0.14 | CAG(Q) | 27 | 0.57 | CGG(R) | 3 | 0.67 | |||
AUU(I) | 342 | 1.62 | ACU(T) | 44 | 1.16 | AAU(N) | 391 | 1.56 | AGU(S) | 40 | 0.69 | |||
AUC(I) | 80 | 0.38 | ACC(T) | 50 | 1.32 | AAC(N) | 109 | 0.44 | AGC(S) | 55 | 0.95 | |||
AUA(M) | 250 | 1.66 | ACA(T) | 41 | 1.08 | AAA(K) | 356 | 1.67 | AGA(S) | 63 | 1.09 | |||
AUG(M) | 52 | 0.34 | ACG(T) | 17 | 0.45 | AAG(K) | 71 | 0.33 | AGG(S) | 65 | 1.13 | |||
GUU(V) | 21 | 1.53 | GCU(A) | 8 | 1.33 | GAU(D) | 51 | 1.65 | GGU(G) | 7 | 1.33 | |||
GUC(V) | 9 | 0.65 | GCC(A) | 3 | 0.50 | GAC(D) | 11 | 0.35 | GGC(G) | 4 | 0.76 | |||
GUA(V) | 22 | 1.60 | GCA(A) | 12 | 2.00 | GAA(E) | 47 | 1.47 | GGA(G) | 9 | 1.71 | |||
GUG(V) | 3 | 0.22 | GCG(A) | 1 | 0.17 | GAG(E) | 17 | 0.53 | GGG(G) | 1 | 0.19 |
Table 4 Relative synonymous codon usage of the mitochondrial genome of A. charopis
密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | 密码子 Codon | 数量(次) Count | RSCU | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
UUU(F) | 444 | 1.57 | UCU(S) | 81 | 1.41 | UAU(Y) | 344 | 1.60 | UGU(C) | 46 | 1.35 | |||
UUC(F) | 123 | 0.43 | UCC(S) | 48 | 0.83 | UAC(Y) | 85 | 0.40 | UGC(C) | 22 | 0.65 | |||
UUA(L) | 366 | 3.24 | UCA(S) | 88 | 1.53 | UAA(*) | 377 | 1.69 | UGA(W) | 56 | 1.08 | |||
UUG(L) | 68 | 0.60 | UCG(S) | 21 | 0.36 | UAG(*) | 68 | 0.31 | UGG(W) | 48 | 0.92 | |||
CUU(L) | 87 | 0.77 | CCU(P) | 20 | 0.92 | CAU(H) | 62 | 1.68 | CGU(R) | 4 | 0.89 | |||
CUC(L) | 38 | 0.34 | CCC(P) | 39 | 1.79 | CAC(H) | 12 | 0.32 | CGC(R) | 2 | 0.44 | |||
CUA(L) | 93 | 0.82 | CCA(P) | 25 | 1.15 | CAA(Q) | 68 | 1.43 | CGA(R) | 9 | 2.00 | |||
CUG(L) | 25 | 0.22 | CCG(P) | 3 | 0.14 | CAG(Q) | 27 | 0.57 | CGG(R) | 3 | 0.67 | |||
AUU(I) | 342 | 1.62 | ACU(T) | 44 | 1.16 | AAU(N) | 391 | 1.56 | AGU(S) | 40 | 0.69 | |||
AUC(I) | 80 | 0.38 | ACC(T) | 50 | 1.32 | AAC(N) | 109 | 0.44 | AGC(S) | 55 | 0.95 | |||
AUA(M) | 250 | 1.66 | ACA(T) | 41 | 1.08 | AAA(K) | 356 | 1.67 | AGA(S) | 63 | 1.09 | |||
AUG(M) | 52 | 0.34 | ACG(T) | 17 | 0.45 | AAG(K) | 71 | 0.33 | AGG(S) | 65 | 1.13 | |||
GUU(V) | 21 | 1.53 | GCU(A) | 8 | 1.33 | GAU(D) | 51 | 1.65 | GGU(G) | 7 | 1.33 | |||
GUC(V) | 9 | 0.65 | GCC(A) | 3 | 0.50 | GAC(D) | 11 | 0.35 | GGC(G) | 4 | 0.76 | |||
GUA(V) | 22 | 1.60 | GCA(A) | 12 | 2.00 | GAA(E) | 47 | 1.47 | GGA(G) | 9 | 1.71 | |||
GUG(V) | 3 | 0.22 | GCG(A) | 1 | 0.17 | GAG(E) | 17 | 0.53 | GGG(G) | 1 | 0.19 |
基因 Gene | 核苷酸多样性 Nucleotide diversity | 非同义进化率(Ka) Non-synonymous evolutionary rate | 同义进化率(Ks) Synonymous evolutionary rate | 非同义进化率与同义进化率的比值(Ka/Ks) Non-synonymous evolutionary rate/Synonymous evolutionary rate |
---|---|---|---|---|
atp6 | 0.179 | 0.117 | 0.391 | 0.299 |
atp8 | 0.205 | 0.187 | 0.292 | 0.640 |
cox1 | 0.129 | 0.050 | 0.375 | 0.133 |
cox2 | 0.127 | 0.065 | 0.349 | 0.186 |
cox3 | 0.160 | 0.087 | 0.413 | 0.210 |
cob | 0.159 | 0.085 | 0.410 | 0.207 |
nad1 | 0.174 | 0.131 | 0.316 | 0.414 |
nad2 | 0.204 | 0.160 | 0.370 | 0.432 |
nad3 | 0.192 | 0.134 | 0.407 | 0.329 |
nad4 | 0.167 | 0.137 | 0.276 | 0.496 |
nad4l | 0.160 | 0.128 | 0.277 | 0.462 |
nad5 | 0.168 | 0.135 | 0.286 | 0.472 |
nad6 | 0.247 | 0.203 | 0.406 | 0.500 |
Table 5 Nucleotide diversity and evolutionary rate analyses of 13 protein-coding genes of the mitochondrial genome of Yponomeutoidea
基因 Gene | 核苷酸多样性 Nucleotide diversity | 非同义进化率(Ka) Non-synonymous evolutionary rate | 同义进化率(Ks) Synonymous evolutionary rate | 非同义进化率与同义进化率的比值(Ka/Ks) Non-synonymous evolutionary rate/Synonymous evolutionary rate |
---|---|---|---|---|
atp6 | 0.179 | 0.117 | 0.391 | 0.299 |
atp8 | 0.205 | 0.187 | 0.292 | 0.640 |
cox1 | 0.129 | 0.050 | 0.375 | 0.133 |
cox2 | 0.127 | 0.065 | 0.349 | 0.186 |
cox3 | 0.160 | 0.087 | 0.413 | 0.210 |
cob | 0.159 | 0.085 | 0.410 | 0.207 |
nad1 | 0.174 | 0.131 | 0.316 | 0.414 |
nad2 | 0.204 | 0.160 | 0.370 | 0.432 |
nad3 | 0.192 | 0.134 | 0.407 | 0.329 |
nad4 | 0.167 | 0.137 | 0.276 | 0.496 |
nad4l | 0.160 | 0.128 | 0.277 | 0.462 |
nad5 | 0.168 | 0.135 | 0.286 | 0.472 |
nad6 | 0.247 | 0.203 | 0.406 | 0.500 |
种名 Species | 韭菜蛾 A. assectella | 臭椿网蛾 A. aurea | A. charopis | 旋纹潜蛾 L. malifoliella | 桃潜叶蛾 L. clerkella | P. armoraciae | P. australiana | P. porrectella | 小菜蛾 P. xylostella | P. oleae | S. crataegella |
---|---|---|---|---|---|---|---|---|---|---|---|
韭菜蛾A. assectella | |||||||||||
臭椿网蛾A. aurea | 0.193 | ||||||||||
A. charopis | 0.190 | 0.122 | |||||||||
旋纹潜蛾L. malifoliella | 0.239 | 0.250 | 0.235 | ||||||||
桃潜叶蛾L. clerkella | 0.222 | 0.231 | 0.222 | 0.259 | |||||||
P. armoraciae | 0.173 | 0.202 | 0.194 | 0.239 | 0.216 | ||||||
P. australiana P. porrectella | 0.175 0.181 | 0.203 0.209 | 0.198 0.201 | 0.243 0.248 | 0.222 0.218 | 0.092 0.073 | 0.094 | ||||
小菜蛾P. xylostella | 0.167 | 0.194 | 0.188 | 0.235 | 0.217 | 0.083 | 0.055 | 0.089 | |||
P. oleae | 0.195 | 0.204 | 0.193 | 0.251 | 0.229 | 0.193 | 0.199 | 0.198 | 0.192 | ||
S. crataegella | 0.179 | 0.205 | 0.196 | 0.235 | 0.223 | 0.182 | 0.184 | 0.186 | 0.177 | 0.204 |
Table 6 Genetic distances of mitochondrial protein-coding gene sequences in Yponomeutoidea based on Kimura-2-Parameters
种名 Species | 韭菜蛾 A. assectella | 臭椿网蛾 A. aurea | A. charopis | 旋纹潜蛾 L. malifoliella | 桃潜叶蛾 L. clerkella | P. armoraciae | P. australiana | P. porrectella | 小菜蛾 P. xylostella | P. oleae | S. crataegella |
---|---|---|---|---|---|---|---|---|---|---|---|
韭菜蛾A. assectella | |||||||||||
臭椿网蛾A. aurea | 0.193 | ||||||||||
A. charopis | 0.190 | 0.122 | |||||||||
旋纹潜蛾L. malifoliella | 0.239 | 0.250 | 0.235 | ||||||||
桃潜叶蛾L. clerkella | 0.222 | 0.231 | 0.222 | 0.259 | |||||||
P. armoraciae | 0.173 | 0.202 | 0.194 | 0.239 | 0.216 | ||||||
P. australiana P. porrectella | 0.175 0.181 | 0.203 0.209 | 0.198 0.201 | 0.243 0.248 | 0.222 0.218 | 0.092 0.073 | 0.094 | ||||
小菜蛾P. xylostella | 0.167 | 0.194 | 0.188 | 0.235 | 0.217 | 0.083 | 0.055 | 0.089 | |||
P. oleae | 0.195 | 0.204 | 0.193 | 0.251 | 0.229 | 0.193 | 0.199 | 0.198 | 0.192 | ||
S. crataegella | 0.179 | 0.205 | 0.196 | 0.235 | 0.223 | 0.182 | 0.184 | 0.186 | 0.177 | 0.204 |
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