Structure and Genome Sequence of Papilio polytes Mitochondria
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摘要:
目的 对玉带凤蝶Papilio polytes的成虫形态特征和幼虫各龄期的特征进行描述，分析玉带凤蝶Papilio polytes完整的线粒体基因组结构特征，丰富蝶类基因组学数据。 方法 根据翅面斑纹描述形态特征，利用高通量第二代测序技术，构建玉带凤蝶线粒体基因组全序列，分析线粒体基因组结构。 结果 玉带凤蝶指名亚种和西藏亚种蝶翅面斑纹有较大区别。玉带凤蝶线粒体基因组序列全长15 267 bp（GenBank登录号为MZ188895），包括13个蛋白质编码基因、22个tRNAs基因、2个rRNAs基因和一段控制区。全序列的A+T的平均含量为80.6%，表现明显的A+T偏斜，有11处表现基因间隔，12处表现基因重叠。37个基因中除cox1基因是以TTG为起始密码子，其余蛋白质编码基因均以ATN起始，cox2基因以不完整终止密码子T结尾，核苷酸组成表现明显的AT偏斜，UUA的相对密码子使用频率最高。除trnS1基因，其余21个tRNAs的二级结构均为典型的三叶草结构，二级结构中有U-U或U-G碱基错配现象，其中有9个tRNAs没有出现碱基错配现象。控制区有最高的A+T平均含量，为94.5%。 结论 玉带凤蝶指名亚种和西藏亚种外部形态的区别主要是由于地位分布位置的不同。玉带凤蝶线粒体基因组结构和基因排列顺序与鳞翅目昆虫线粒体基因组结构和排列一致。 Abstract:Objective Adults and larvae of Papilio Polytes were studied with the complete mitochondrial genome sequenced for the butterfly genomics library collection. Method According to the morphological characteristics of wing markings, sequences of the mitochondrial genomes of P. Polytes were determined using the second-generation Illumina Hiseq 4 000 high-throughput sequencing technology. Result The wing markings of P. polytes polytes was found significantly different from those of P. polytes tibetanus’s. The length of complete mitochondrial genome was 15 267 bp (GenBank accession no. MZ188895) consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. The average contents of A+T was 80.6% of the entire sequence representing a significant A+T deflection that had 11 gene intervals and 12 gene overlaps. Except Cox1, all protein coding genes started with ATN, whereas Cox2 ended with codon T. The nucleotide composition showed a significant AT skew. The relative synonymous codon usage (RSCU) of UUA was the highest one. Other than trnS1, the transfer RNAs had the typical clover-leaf-like structure with U-U or U-G base mismatched in the secondary structure and 9 transfer RNAs without mismatch. The A+T average content was the highest in control region at 94.5%. Conclusion Morphologically, P. polytes polytes and P. polytes tibetanus mainly differed in location and distribution of the elements. The structures and sequences of the genomes of P. Polytes mitochondria as determined were in line with those of Lepidoptera insects. -
Key words:
- Papilio polytes /
- characteristics /
- mitochondrial genome /
- sequencing
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图 1 玉带凤蝶指明亚种
注：a，雌背面；b，雌腹面；c，雄背面；d，雄腹面；e，生态图。
Figure 1. P. polytes polytes
Note: a, female back; b, female abdomen; c, male back; d, male abdomen; e, Ecological photo.
图 2 玉带凤蝶西藏亚种
注：a，雌背面；b，雌腹面；c，雄背面；d，雄腹面。
Figure 2. P. polytes tibetanus
Note: a, female back; b, female abdomen; c, male back; d, male abdomen.
图 3 玉带凤蝶各幼虫时期的形态
注：a，3龄；b，4龄；c，5龄。
Figure 3. P. polytes polytes and P. polytes tibetanus at larvae stage
Note: a, 3 age; b, 4 age; c, 5 age.
图 4 玉带凤蝶线粒体基因组结构
注：箭头表示转录方向。
Figure 4. Structure of P. polytes mitochondrial genome
Note: Arrow means the transcription direction.
图 5 玉带凤蝶22个tRNAs的二级结构
注：+表示G-U和U-U配对。
Figure 5. Secondary structure of 22 tRNAs genes of P. polytes
Note:+ means G-U and U-U pairing.
表 1 玉带凤蝶线粒体基因组核苷酸组成
Table 1. Nucleotide composition of P. polytes mitochondrial genome
区域 Regions T/% C/% A/% G/% A+T/% AT偏好性 AT skew GC偏好性 GC skew 全序列 Complete sequence 41.1 11.8 39.5 7.5 80.6 −0.019 −0.223 转运 RNAs tRNAs 39.3 7.9 42.4 10.5 81.6 0.038 0.144 核糖体 RNAs rRNAs 40.5 4.9 43.9 10.7 84.4 0.040 0.376 控制区 Control region 45.8 4.2 48.7 1.3 94.5 0.030 −0.524 atp6 46.5 12.3 33.3 7.9 79.8 −0.165 −0.215 atp8 45.5 5.5 47.3 1.8 92.7 0.020 −0.500 cytb 42.9 14.9 32.3 10.0 75.1 −0.141 −0.199 cox1 41.0 15.0 30.8 13.2 71.7 −0.143 −0.065 cox2 42.6 12.5 35.1 9.8 77.8 −0.097 −0.122 cox3 42.1 14.0 31.8 12.2 73.8 −0.139 −0.069 nad1 46.6 8.1 30.2 15.1 76.8 −0.214 0.302 nad2 48.7 10.2 34.5 6.6 83.2 −0.171 −0.211 nad3 46.2 12.3 35.1 6.4 81.3 −0.137 −0.313 nad4 47.1 6.7 34.5 11.8 81.5 −0.155 0.276 nad4l 51.0 4.6 31.8 12.6 82.8 −0.231 0.467 nad5 47.5 6.0 34.6 11.9 82.0 −0.157 0.327 nad6 51.6 7.0 35.5 5.8 87.1 −0.184 −0.094 注：AT偏斜 =（A−T）/（A+T）, GC 偏斜 = （G-C）/（G+C）。
Note: AT skew =（A−T）/（A+T）, GC skew = （G−C）/（G+C）.
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表 2 玉带凤蝶线粒体基因组结构组成
Table 2. Composition of P. polytes mitochondrial genome structure
基因
Gene起始位置
Start position/bp终止位置
Stop position/bp基因长度
Gene length/bp基因间隔
Intergenic length/bp起始密码子
Start codon终止密码子
Stop codon反密码子
AnticodontrnM 1 68 68 0 ATG trnI 69 132 64 −3 ATC trnQ 130 197 68 53 CAA nad2 251 1 264 1 014 −2 ATT TAA trnW 1 263 1 327 65 −8 TGA trnC 1 320 1 384 65 1 TGC trnY 1 386 1 450 65 −1 TAC cox1 1 450 2 988 1 539 −5 TTG TAA trnL2 2 984 3 051 68 0 TTA cox2 3 052 3 733 682 0 ATG T trnK 3 734 3 803 70 0 AAG trnD 3 804 3 871 68 0 GAC atp8 3 872 4 039 168 −4 ATT TAA atp6 4 036 4 713 678 6 ATA TAA cox3 4 720 5 508 789 3 ATG TAA trnG 5 512 5 577 66 0 GGA nad3 5 578 5 931 354 −2 ATT TAG trnA 5 930 5 993 64 −1 GCA trnR 5 993 6 056 64 −1 CGA trnN 6 056 6 121 66 0 AAC trnS1 6 122 6 182 61 1 AGA trnE 6 184 6 249 66 −2 GAA trnF 6 248 6 311 64 0 TTC nad5 6 312 8 048 1 737 0 ATA TAA trnH 8 049 8 113 65 −1 CAC nad4 8 113 9 453 1 341 −1 ATG TAA nad4l 9 453 9 737 285 2 ATG TAA trnT 9 740 9 804 65 0 ACA trnP 9 805 9 868 64 2 CCA nad6 9 871 10 404 534 7 ATA TAA cytb 10 412 11 560 1 149 2 ATG TAA trnS2 11 563 11 628 66 16 TCA nad1 11 645 12 583 939 1 ATG TAG trnL1 12 585 12 653 69 0 CTA rrnL 12 654 13 980 1 327 0 trnV 13 981 14 043 63 0 GTA rrnS 14 044 14 823 780 0 控制区
Cortrol region14 824 15 267 444
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表 3 玉带凤蝶线粒体基因组相对密码子使用频率
Table 3. Relative synonymous codon usage of P. polytes mitochondrial genome
密码子
Codon数量
Count相对密
码子使
用频率
RSCU密码子
Codon数量
Count相对密
码子使
用频率
RSCU密码子
Codon数量
Count相对密
码子使
用频率
RSCU密码子
Codon数量
Count相对密
码子使
用频率
RSCUUUU(F) 23.9 1.81 UCU(S) 8.5 2.82 UAU(Y) 13.8 1.92 UGU(C) 2.2 1.75 UUC(F) 2.5 0.19 UCC(S) 1.2 0.38 UAC(Y) 0.5 0.08 UGC(C) 0.3 0.25 UUA(L) 33.8 4.93 UCA(S) 5.8 1.9 UAA(*) 0 0 UGA(W) 6.8 1.93 UUG(L) 1.1 0.16 UCG(S) 0.2 0.05 UAG(*) 0 0 UGG(W) 0.2 0.07 CUU(L) 3.8 0.56 CCU(P) 5.9 2.59 CAU(H) 4.8 1.85 CGU(R) 1.4 1.36 CUC(L) 0.2 0.03 CCC(P) 0.9 0.4 CAC(H) 0.4 0.15 CGC(R) 0.1 0.08 CUA(L) 2.1 0.3 CCA(P) 2.1 0.91 CAA(Q) 4.8 1.94 CGA(R) 2.5 2.42 CUG(L) 0.1 0.01 CCG(P) 0.2 0.1 CAG(Q) 0.2 0.06 CGG(R) 0.2 0.15 AUU(I) 31.7 1.9 ACU(T) 7.2 2.58 AAU(N) 18.2 1.88 AGU(S) 1.8 0.61 AUC(I) 1.7 0.1 ACC(T) 0.2 0.08 AAC(N) 1.2 0.12 AGC(S) 0 0 AUA(M) 20.1 1.88 ACA(T) 3.5 1.28 AAA(K) 6.2 1.74 AGA(S) 6.5 2.13 AUG(M) 1.2 0.12 ACG(T) 0.2 0.06 AAG(K) 0.9 0.26 AGG(S) 0.3 0.1 GUU(V) 6 2.24 GCU(A) 6.2 2.62 GAU(D) 3.9 1.65 GGU(G) 4.8 1.29 GUC(V) 0.1 0.03 GCC(A) 0.9 0.39 GAC(D) 0.8 0.35 GGC(G) 0.2 0.04 GUA(V) 4.5 1.7 GCA(A) 2 0.85 GAA(E) 5.4 1.84 GGA(G) 8.4 2.27 GUG(V) 0.1 0.03 GCG(A) 0.3 0.13 GAG(E) 0.5 0.16 GGG(G) 1.5 0.4 注：RSCU：相对密码子使用频率。 *：终止密码子Stop codon。
Note: RSCU: Relative synonymous codon usage. *: Stop codon.
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