海南澳洲管体星虫线粒体基因组特征及进化分析
黄培贤(1997—), 海南省琼海市人, 在读硕士研究生, 从事海洋生物学方面研究。email: |
Copy editor: 殷波
收稿日期: 2022-04-19
修回日期: 2022-07-22
网络出版日期: 2022-07-27
基金资助
海南省自然科学基金(319MS013)
Mitogenome characteristics and phylogenetic analysis of Siphonosoma australe in Hainan
Copy editor: YIN Bo
Received date: 2022-04-19
Revised date: 2022-07-22
Online published: 2022-07-27
Supported by
Hainan Provincial Natural Science Foundation of China(319MS013)
澳洲管体星虫是海南当地的特色海产资源, 隶属管体星虫属。该属在星虫动物门内的分类地位一直极具争议。文章通过高通量测序测定海南文昌地区澳洲管体星虫的线粒体基因组, 与GenBank中收集的星虫线粒体基因组进行比对分析, 解析其基因组序列特征, 并进一步探讨管体星虫属在星虫动物门内的进化地位。结果显示: 澳洲管体星虫线粒体基因组长度为16483bp, 包含38个基因(13个蛋白质编码基因、23个tRNAs和2个rRNAs)。线粒体基因组呈AT偏好, 其A+T的含量为65.87%。分析相对同义密码子使用度发现, 澳洲管体星虫线粒体蛋白质编码基因对结尾为A和U的密码子具有明显偏好性。澳洲管体星虫线粒体蛋白编码基因COX1、COX3、ND5的氨基酸数量与其他星虫比较, 差异较大。澳洲管体星虫与GenBank中收集的星虫线粒体基因组的主编码基因中, COX1、COX2和CYTB基因变异位点比例低, 而ND2、ND4L和ND6基因变异位点比例高, ATP8基因的变异位点的比例最高(83.33%)。采用邻接法(neighbor-joining, NJ)、最大似然法(maximum likelihood, ML)、贝叶斯法(Bayesian inference, BI), 利用线粒体基因组核酸序列构建进化树, 结果显示, 管体星虫属介于革囊星虫属和方格星虫属之间, 与革囊星虫属关系较近, 反而与方格星虫属的关系较远, 与传统的形态学分类不一致。形态学上, 管体星虫属混合了革囊星虫属和方格星虫属的形态特征, 而线粒体基因组构建的进化树更能体现管体星虫属真实且独特的进化地位。
黄培贤 , 姚雪梅 , 余巧驰 , 张佳玉 . 海南澳洲管体星虫线粒体基因组特征及进化分析[J]. 热带海洋学报, 2023 , 42(2) : 54 -63 . DOI: 10.11978/2022083
Siphonosoma australe is a local fishery resource in Hainan, which belongs to Siphonosoma. The taxonomic status of the genus in the phylum Sipuncula has been highly controversial. In this study, the mitogenome of S. australe in the Wenchang coast of Hainan was determined by high-throughput sequencing, and compared with the mitochondrial genomes collected from GenBank, characteristics of mitogenome sequence was analyzed, furthermore, the evolutionary position of the genus Siphonosoma in the phylum of Sipuncula was explored. The results show that the mitogenome of S. australe has 16483 base pairs and encodes a set of 38 genes (13 protein-coding, 23 transfer RNAs, and 2 ribosomal RNAs). The mitochondrial genome shows AT bias, and the content of nucleotides A+T is 65.87%. By the analysis of the relative synonymous codon usage (RSCU), the mitochondrial protein-coding genes of S. australe have obvious preference to the codons ending with A and U. The number of amino acids of mitochondrial protein coding genes (COX1, COX3 and ND5) of S. australe is quite different from that of other species. Compared with the mitochondrial genomes of sipunculans from GenBank, it was found that among the major coding genes of sipunculans, the proportions of variable sites in COX1, COX2 and CYTB genes are low, while the proportions of variable sites in ND2, ND4L and ND6 genes are high, and the highest proportion of variable sites in ATP8 gene is 83.33%. Based on the DNA sequences of sipunculan mitogenomes, the phylogenetic tree constructed using the methods of NJ (neighbor-joining), ML (maximum likelihood) and BI (Bayesian inference) showed that the genus Siphonosoma, as an independent clade, is between the genera of Phascolosoma and Sipunculus, even close to the genus of Phascolosoma instead far from the genus of Sipunculus. This result is inconsistent with the previously traditional classification based on morphological analyses. Taxonomically, Siphonosoma mixes the morphological characteristics of Phascolosoma and Sipunculus. The phylogenetic tree constructed with mitochondrial genome sequences could truly reflect the unique phylogenetic status of Siphonosoma. The mitogenome data of S. australe provides a theoretical basis for explaining the evolutionary relationship of the Siphonosoma in the phylum Sipuncula, and are beneficial to the protection and development of genetic resource of S. australe.
Key words: Siphonosoma australe; Hainan; mitogenome; phylogeny
表1 外源信息表Tab. 1 List of the outer groups |
属 | 物种 | 采样地 | GenBank 登录号 |
---|---|---|---|
方格星虫属Sipunculus | 光裸方格星虫(Sipunculus nudus) | Concarneau, France | FJ422961 |
Beibu Bay, China | MG873457 | ||
Gulei, China | KJ754934 | ||
Yantai, China | KP751904 | ||
革囊星虫属Phascolosoma | 可口革囊星虫(Phascolosoma esculenta) | Beibu Bay, China | MG873458 |
Wenzhou, China | EF583817 | ||
太平洋革囊星虫(Phascolosoma pacificum) | Chuuk, Micronesia | KU820989 | |
厥目革囊星虫(Phascolosoma scolops) | Beibu Bay, China | MT239480 | |
类革囊星虫(Phascolosoma similis) | Beibu Bay, China | MN813482 | |
管体星虫属Siphonosoma | 库岛管体星虫(Siphonosoma cumanense) | Beibu Bay, China | MN813483 |
表2 澳洲管体星虫线粒体基因组碱基组成Tab. 2 Composition of the mitochondrial genome in Siphonosoma australe |
基因序列 | T/% | C/% | A/% | G/% | (A+T)/% | (C+G)/% |
---|---|---|---|---|---|---|
全基因组 | 36.54 | 20.97 | 29.33 | 13.16 | 65.87 | 34.13 |
蛋白质编码基因 | 37.49 | 21.56 | 27.86 | 13.09 | 65.35 | 34.65 |
tRNA基因 | 31.04 | 18.02 | 32.79 | 18.15 | 63.83 | 36.17 |
rRNA基因 | 33.01 | 19.12 | 32.46 | 15.41 | 65.47 | 34.53 |
表3 澳洲管体星虫线粒体蛋白质编码基因的相对同义密码子使用度(RSCU)Tab. 3 RSCU of mtDNA protein-coding sequence in Siphonosoma australe |
氨基酸 | 密码子 | 次数 | RSCU | 氨基酸 | 密码子 | 次数 | RSCU |
---|---|---|---|---|---|---|---|
Phe | UUU | 236 | 1.45 | Tyr | UAU | 91 | 1.35 |
UUC | 90 | 0.55 | UAC | 44 | 0.65 | ||
Leu | UUA | 226 | 2.17 | His | CAU | 56 | 1.30 |
UUG | 20 | 0.19 | CAC | 30 | 0.70 | ||
CUU | 173 | 1.66 | Gln | CAA | 62 | 1.70 | |
CUC | 68 | 0.65 | CAG | 11 | 0.30 | ||
CUA | 127 | 1.22 | Asn | AAU | 71 | 1.31 | |
CUG | 10 | 0.10 | AAC | 37 | 0.69 | ||
Ile | AUU | 226 | 1.52 | Lys | AAA | 79 | 1.82 |
AUC | 71 | 0.48 | AAG | 8 | 0.18 | ||
Met | AUA | 161 | 1.71 | Asp | GAU | 34 | 1.05 |
AUG | 27 | 0.29 | GAC | 31 | 0.95 | ||
Val | GUU | 78 | 1.70 | Glu | GAA | 63 | 1.70 |
GUC | 25 | 0.55 | GAG | 11 | 0.30 | ||
GUA | 73 | 1.60 | Cys | UGU | 24 | 1.33 | |
GUG | 7 | 0.15 | UGC | 12 | 0.67 | ||
Ser | UCU | 117 | 2.77 | Trp | UGA | 87 | 1.81 |
UCC | 41 | 0.97 | UGG | 9 | 0.19 | ||
UCA | 84 | 1.99 | Arg | CGU | 22 | 1.22 | |
UCG | 7 | 0.17 | CGC | 11 | 0.61 | ||
AGU | 19 | 0.45 | CGA | 33 | 1.83 | ||
AGC | 13 | 0.31 | CGG | 6 | 0.33 | ||
AGA | 51 | 1.21 | Pro | CCU | 71 | 1.41 | |
AGG | 6 | 0.14 | CCC | 29 | 0.57 | ||
Thr | ACU | 93 | 1.52 | CCA | 95 | 1.88 | |
ACC | 38 | 0.62 | CCG | 7 | 0.14 | ||
ACA | 102 | 1.67 | Gly | GGU | 44 | 0.91 | |
ACG | 12 | 0.20 | GGC | 28 | 0.58 | ||
Ala | GCU | 96 | 1.39 | GGA | 98 | 2.02 | |
GCC | 53 | 0.77 | GGG | 24 | 0.49 | ||
GCA | 115 | 1.67 | |||||
GCG | 12 | 0.17 |
表4 星虫动物3个属7个种的线粒体蛋白质编码基因的氨基酸数量Tab. 4 Amino acid quantity of protein-coding genes in sipunculan mitochondrial genomes of 7 species (3 genera) |
星虫名称 | ATP6 | ATP8 | CYTB | COX1 | COX2 | COX3 | ND1 | ND2 | ND3 | ND4 | ND4L | ND5 | ND6 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
可口革囊星虫 | 231 | 54 | 378 | 519 | 231 | 267 | 304 | 323 318 | 121 | 450 451 | 94 | 571 562 | 157 |
太平洋革囊星虫 | 231 | 49 | 378 | 518 | 227 | 263 | 308 | 319 | 118 | 450 | 94 | 572 | 157 |
类革囊星虫 | 231 | 53 | 378 | 519 | 230 | 267 | 303 | 327 | 121 | 450 | 94 | 571 | 157 |
厥目革囊星虫 | 231 | 54 | 378 | 519 | 229 | 291 | 304 | 320 | 121 | 451 | 94 | 572 | 157 |
光裸方格星虫 | 229 234 | 52 53 | 379 | 516 519 | 231 230 | 259 | 314 312 | 328 327 329 | 119 117 | 452 454 | 93 | 565 571 | 157 |
库岛管体星虫 | 231 | 54 | 379 | 513 | 231 | 275 | 303 | 318 | 114 | 448 | 94 | 569 | 155 |
澳洲管体星虫 | 231 | 56 | 377 | 510 | 232 | 293 | 303 | 327 | 116 | 452 | 94 | 559 | 155 |
注: 同一栏目中不同的数字表示同一物种的不同线粒体蛋白质编码基因的氨基酸数量差异 |
表5 星虫动物3个属7个种的线粒体基因组的主编码基因变异位点分析Tab. 5 Genetic variation analysis of major encoding genes in sipunculan mitochondrial genomes of 7 species (3 genera) |
基因名称 | 总位点数 | 保守位点数 | 变异位点数 | 变异位点比例/% |
---|---|---|---|---|
ATP6 | 669 | 226 | 443 | 66.22 |
ATP8 | 144 | 24 | 120 | 83.33 |
CYTB | 1131 | 550 | 581 | 51.37 |
COX1 | 1531 | 824 | 707 | 46.18 |
COX2 | 680 | 328 | 352 | 51.76 |
COX3 | 780 | 342 | 438 | 56.15 |
ND1 | 906 | 368 | 538 | 59.38 |
ND2 | 944 | 215 | 729 | 77.22 |
ND3 | 344 | 126 | 218 | 63.37 |
ND4 | 1329 | 402 | 927 | 69.75 |
ND4L | 282 | 77 | 205 | 72.70 |
ND5 | 1657 | 523 | 1134 | 68.44 |
ND6 | 466 | 118 | 348 | 74.68 |
12S rRNA | 753 | 295 | 458 | 60.82 |
16S rRNA | 980 | 423 | 557 | 56.84 |
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