海南澳洲管体星虫线粒体基因组特征及进化分析

doi:10.11978/2022083

摘要/Abstract

摘要：

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。

关键词: 澳洲管体星虫, 海南, 线粒体基因组, 进化

Abstract:

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

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.

HUANG Peixian, YAO Xuemei, YU Qiaochi, ZHANG Jiayu. Mitogenome characteristics and phylogenetic analysis of Siphonosoma australe in Hainan[J]. Journal of Tropical Oceanography, 2023, 42(2): 54-63.

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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
	可口革囊星虫(Phascolosoma esculenta)	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

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

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
Phe	UUC	90	0.55	Tyr	UAC	44	0.65
Leu	UUA	226	2.17	His	CAU	56	1.30
	UUG	20	0.19	His	CAC	30	0.70
	CUU	173	1.66	Gln	CAA	62	1.70
	CUC	68	0.65	Gln	CAG	11	0.30
	CUA	127	1.22	Asn	AAU	71	1.31
	CUG	10	0.10	Asn	AAC	37	0.69
Ile	AUU	226	1.52	Lys	AAA	79	1.82
Ile	AUC	71	0.48	Lys	AAG	8	0.18
Met	AUA	161	1.71	Asp	GAU	34	1.05
Met	AUG	27	0.29	Asp	GAC	31	0.95
Val	GUU	78	1.70	Glu	GAA	63	1.70
	GUC	25	0.55	Glu	GAG	11	0.30
	GUA	73	1.60	Cys	UGU	24	1.33
	GUG	7	0.15	Cys	UGC	12	0.67
Ser	UCU	117	2.77	Trp	UGA	87	1.81
	UCC	41	0.97	Trp	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

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

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