Mitochondrial Genome and Phylogeny of Takifugu xanthopterus
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摘要:
目的 研究我国大洋河水域黄鳍东方鲀(Takifugu xanthopterus)的分子遗传学特性,为黄鳍东方鲀种质资源遗传多样性和系统发育分析提供基础数据。 方法 利用高通量测序技术,获得黄鳍东方鲀线粒体基因组全序列,分析线粒体基因组结构。 结果 黄鳍东方鲀线粒体基因组序列全长 16444 bp(GenBank 登录号:MT560586),由13 个蛋白质编码基因、22 个 tRNAs 基因、2 个 rRNAs 基因、1个控制区和1个轻链复制起始区组成。13个蛋白质编码基因中仅有cox1基因起始密码子为特殊的GTG,其余蛋白质编码基因均以ATG为起始密码子,cox2和nad4终止密码子以单独的T结尾。偏好密码子(RSCU>2)分别是Arg(CGA)和Ser(UCC)。22 个tRNAs基因除trnS1基因外,其余tRNAs二级结构均为典型的三叶草结构。以斑腰单孔鲀(Monotreta leiurus)为外类群,对16种东方鲀属线粒体基因组全序列进行进化关系分析。由贝叶斯法构建的系统发生树表明,黄鳍东方鲀与痣斑多纪鲀(T. chrysops)和豹纹多纪鲀(T. pardalis)的亲缘关系最近。结论 黄鳍东方鲀的线粒体基因组结构和基因排列顺序符合鱼类基因组典型结构和排列特征。 Abstract:Objective Mitochondrial genome of Yellowfin Puffer (Takifugu xanthopterus) was studied to analyze the genetic diversity and phylogeny of the fish. Method Mitochondrial genome of T. xanthopterus found in Dayang River was sequenced by high-throughput sequencing technology. Result The complete mitochondrial genome was 16444 bp (GenBank accession No. MT560586) consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, one control region, and one OL. The 13 protein-coding genes started with ATG codon except for cox1, which started with a special GTG codon. Cox2 and nad4 ended with codon T. The preference codon (RSCU>2) included Arg (CGA) and Ser (UCC). All 22 tRNA genes, except trnS1, had the typical cloverleaf-like secondary structure. Taking Monotreta leiurus as the outgroup, the complete mitochondrial genome sequences of 16 species of pufferfish were analyzed for evolutionary relationship. The phylogenetic tree constructed by Bayes software showed that T. xanthopterus was closely related to T. chrysops and T. pardalis.Conclusion The mitochondrial genome structure and gene order of T. xanthopterus as analyzed seemed to be typical of fish. -
Key words:
- Takifugu xanthopterus /
- mitochondrial genome /
- phylogenetic analysis
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表 1 黄鳍东方鲀线粒体基因组结构组成
Table 1. Composition of T. xanthopterus mitochondrial genome
名称
Name起始位点
Start site/bp终止位点
Stop site/bp编码链
Strand长度
Length/bp基因间隔
Intergenic length/bp起始/终止密码子
Start/stop codonstrnF(gaa) 1 68 H 68 0 12S rRNA 69 1015 H 947 0 trnV(tac) 1016 1088 H 73 38 16S rRNA 1127 2756 H 1630 0 trnL2(taa) 2757 2829 H 73 0 nad1 2830 3804 H 975 2 ATG/TAA trnI(gat) 3807 3876 H 70 −1 trnQ(ttg) 3876 3946 L 71 −1 trnM(cat) 3946 4014 H 69 0 nad2 4015 5061 H 1047 −1 ATG/TAA trnW(tca) 5061 5131 H 71 1 trnA(tgc) 5133 5201 L 69 2 trnN(gtt) 5204 5277 L 74 3 OL 5281 5312 H 32 −1 trnC(gca) 5312 5375 L 64 −1 trnY(gta) 5375 5444 L 70 1 cox1 5446 7005 H 1560 −9 GTG/AGG trnS2(tga) 6997 7067 L 71 3 trnD(gtc) 7071 7142 H 72 6 cox2 7149 7839 H 691 0 ATG/T(AA) trnK(ttt) 7840 7912 H 73 1 atp8 7914 8081 H 168 −10 ATG/TAA atp6 8072 8755 H 684 −1 ATG/TAA cox3 8755 9540 H 786 −1 ATG/TAA trnG(tcc) 9540 9610 H 71 0 nad3 9611 9961 H 351 −2 ATG/TAG trnR(tcg) 9960 10028 H 69 1 nad4l 10030 10326 H 297 −7 ATG/TAA nad4 10320 11700 H 1381 0 ATG/T(AA) trnH(gtg) 11701 11769 H 69 0 trnS1(gct) 11770 11837 H 68 5 trnL1(tag) 11843 11915 H 73 0 nad5 11916 13754 H 1839 −5 ATG/TAA nad6 13750 14271 L 522 0 ATG/AGG trnE(ttc) 14272 14340 L 69 4 cob 14345 15481 H 1137 3 ATG/TAA trnT(tgt) 15485 15556 H 72 −1 trnP(tgg) 15556 15625 L 70 0 D-loop 15626 16444 H 423 0 表 2 黄鳍东方鲀偏好密码子RSCU值
Table 2. RSCUs for preference codons in T. xanthopterus
密码子
Codon数量
Number相对密码子
使用频率
RSCU密码子
Codon数量
Number相对密码子
使用频率
RSCU密码子
Codon数量
Number相对密码子
使用频率
RSCU密码子
Codon数量
Number相对密码子
使用频率
RSCUUUU(F) 67 0.73 UCU(S) 89 1.42 UAU(Y) 54 0.82 UGU(C) 9 0.53 UUC(F) 116 1.27 UCC(S) 140 2.23 UAC(Y) 77 1.18 UGC(C) 25 1.47 UUA(L) 123 1.29 UCA(S) 72 1.15 UAA(*) 67 1.00 UGA(*) 67 1.00 UUG(L) 62 0.65 UCG(S) 38 0.60 UAG(*) 67 1.00 UGG(W) 31 1.00 CUU(L) 88 0.92 CCU(P) 92 1.15 CAU(H) 44 0.78 CGU(R) 7 0.66 CUC(L) 110 1.16 CCC(P) 109 1.36 CAC(H) 69 1.22 CGC(R) 8 0.75 CUA(L) 140 1.47 CCA(P) 81 1.01 CAA(Q) 94 1.26 CGA(R) 29 2.72 CUG(L) 48 0.50 CCG(P) 38 0.48 CAG(Q) 55 0.74 CGG(R) 8 0.75 AUU(I) 91 1.02 ACU(T) 75 0.90 AAU(N) 47 0.67 AGU(S) 9 0.14 AUC(I) 103 1.15 ACC(T) 124 1.49 AAC(N) 93 1.33 AGC(S) 29 0.46 AUA(I) 74 0.83 ACA(T) 106 1.27 AAA(K) 77 1.33 AGA(R) 7 0.66 AUG(M) 53 1.00 ACG(T) 29 0.35 AAG(K) 39 0.67 AGG(R) 5 0.47 GUU(V) 36 0.95 GCU(A) 61 0.98 GAU(D) 39 0.99 GGU(G) 22 0.63 GUC(V) 48 1.26 GCC(A) 109 1.76 GAC(D) 40 1.01 GGC(G) 49 1.41 GUA(V) 49 1.29 GCA(A) 67 1.08 GAA(E) 61 1.13 GGA(G) 49 1.41 GUG(V) 19 0.50 GCG(A) 11 0.18 GAG(E) 47 0.87 GGG(G) 19 0.55 表 3 黄鳍东方鲀线粒体基因组核苷酸组成
Table 3. Nucleotide composition of T. xanthopterus mitochondrial genome
项目
ItemT含量
T content/%C含量
C content/%A含量
A content/%G含量
G content/%AT含量
AT content/%GC 偏好性
GC-skewAT 偏好性
AT-skewtRNA 24.4 25.18 31.96 18.46 56.36 − 0.1539 0.1341 rRNA 21.11 24.78 34.46 19.66 55.56 − 0.1152 0.2402 蛋白质编码基因 PCGs 26.58 31.47 28.13 13.82 54.71 − 0.3897 0.0283 控制区 Control region 32.23 18.93 36.39 12.45 68.62 − 0.2065 0.0606 -
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