木珊瑚科Cladopsammia gracilis和Rhizopsammia wettsteini 线粒体全基因组比较与系统进化分析*

doi:10.11978/2022267

Abstract

Abstract:

There is a taxonomic uncertainty on the species classification of Cladopsammia gracilis and Rhizopsammia wettsteini as well as the unresolved status of the closely related genera Cladopsammia and Rhizopsammia. In order to further analyze the phylogenetic relationship between C. gracilis and R. wettsteini, we examined the micromorphological and microstructural features and systematically compared the gene structure, genetic distance and codon preference of two mitochondrial genomes. The results show that there are three distinct characteristics: reptoid budding, costae and septa. The genome composition of the two species is very similar, containing 13 protein-coding genes, 2 rRNA genes and 2 tRNA genes. Unlike most scleractinians, there were no overlaps between genes. In addition, phylogenetic analysis based on CO1 genes show that C. gracilis and R. wettsteini are closely related but distantly related to other species of the genera Cladopsammia. The present study highlights the need for an integrative approach to conduct a deeper species delimitation of genera Cladopsammia and Rhizopsammia.

Key words: Dendrophylliidae, mitochondrial genomes, taxonomy, phylogenetic analysis

HUO Jiaxin, LI Yingxin, SONG Yan, ZHU Qing, ZHOU Weihua, YUAN Xiangcheng, HUANG Hui, LIU Sheng. Complete mitochondrial genome of Cladopsammia gracilis and Rhizopsammia wettsteini (Scleractinia, Dendrophylliidae) and its phylogenetic implications^*[J].Journal of Tropical Oceanography, 2024, 43(3): 22-30.

Figures/Tables 8

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References 27

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物种	CO1基因序列
柔枝鹿角珊瑚Acropora tenuis	LC029008
Balanophyllia europaea^#	HG965310
江口枝沙珊瑚Cladopsammia eguchii	HG965319; HG965317.1
纤细枝沙珊瑚Cladopsammia gracilis	HG965320.1
Cladopsammia sp.^#	HG96531.6
Cladopsammia mamuelensis^#	MW250924.1; MW250928.1
Dendrophyllia cornigera^#	HG965322.1
Eguchipsammia serpentina^#	HG965327
耳蜗异沙珊瑚Heteropsammia cochlea	HG965331
Rhizopsammia verrilli^#	HG965336.1; HG965334; HG965335.1
Rhizopsammia wettsteini^#	HG965338; HG965337; HG965339.1
华丽筒星珊瑚Tubastraea cf. aurea	HG965342.1
猩红筒星珊瑚Tubastraea coccinea	HG965344
小花筒星珊瑚 Tubastraea micranthus	HG965347
皱折陀螺珊瑚Turbinaria mesenterina	HG965360
Turbinaria patula^#	HG965361

基因序列	Rhizopsammia wettsteini					Cladopsammia gracilis
基因序列	T/%	C/%	A /%	G /%	C+G /%	T/%	C/%	A /%	G /%	C+G /%
全基因组	39.7	16.0	21.1	23.2	39.4	37.4	13.6	25.4	23.7	37.2
蛋白编码基因	37.7	14.3	24.5	23.6	37.9	38.8	15.9	21.3	24.0	40.0

氨基酸	密码子	次数		RSCU		氨基酸	密码子	次数		RSCU
氨基酸	密码子	R.wet^*	C.gra	R.wet	C.gra	氨基酸	密码子	R.wet	C.gra	R.wet	C.gra
Phe	UUU	454	451	1.68	1.63	Ser	UCU	125	116	1.54	1.47
Phe	UUC	85	101	0.32	0.37		UCC	57	44	0.7	0.56
Leu	UUA	295	335	2.12	2.29		UCA	63	61	0.77	0.78
	UUG	207	216	1.49	1.48		UCG	50	55	0.61	0.7
	CUU	162	165	1.16	1.13	Pro	CCU	52	62	1.25	1.22
	CUC	49	48	0.35	0.33		CCC	53	51	1.28	1.00
	CUA	69	65	0.5	0.44		CCA	31	43	0.75	0.85
	CUG	54	48	0.39	0.33		CCG	30	47	0.72	0.93
Ile	AUU	262	240	1.7	1.68	Thr	ACU	82	76	1.63	1.70
	AUC	56	64	0.36	0.45		ACC	41	29	0.82	0.65
	AUA	143	124	0.93	0.87		ACA	55	46	1.09	1.03
Met	AUG	121	131	1	1.00		ACG	23	28	0.46	0.63
Val	GUU	233	203	1.93	1.75	Ala	GCU	110	101	1.62	1.60
	GUC	58	77	0.48	0.67		GCC	60	53	0.88	0.84
	GUA	83	86	0.69	0.74		GCA	42	51	0.62	0.81
	GUG	110	97	0.91	0.84		GCG	60	48	0.88	0.76
Tyr	UAU	197	192	1.66	1.54	Cys	UGU	136	130	1.42	1.38
Tyr	UAC	41	57	0.34	0.46	Cys	UGC	56	59	0.58	0.62
Asp	GAU	93	88	1.45	1.30	Glu	GAA	111	118	1.06	1.11
Asp	GAC	35	47	0.55	0.70	Trp	UGG	160	168	1	1.00
His	CAU	68	54	1.49	1.35	Arg	CGU	30	23	0.58	0.42
His	CAC	23	26	0.51	0.65		CGC	20	14	0.38	0.26
Gln	CAA	85	65	1.4	1.30		CGA	44	41	0.85	0.75
Gln	CAG	36	35	0.6	0.70		CGG	35	59	0.67	1.09
Asn	AAU	165	150	1.47	1.47		AGA	119	95	2.29	1.75
Asn	AAC	59	54	0.53	0.53		AGG	64	94	1.23	1.73
Lys	AAA	179	186	1.18	1.23	Ser	AGU	148	149	1.82	1.89
Lys	AAG	124	116	0.82	0.77	Ser	AGC	45	47	0.55	0.60
TER	UAA	119	167	1.17	1.43	Gly	GGU	137	139	1.09	1.15
	UAG	93	87	0.91	0.75		GGC	85	69	0.67	0.57
	UGA	93	96	0.91	0.82		GGA	92	92	0.73	0.76

密码子偏好性主要参数	R. wettsteini	C. gracilis
T3s	0.477	0.459
C3s	0.160	0.164
A3s	0.323	0.327
G3s	0.277	0.289
CAI	0.148	0.143
CBI	-0.152	-0.151
Fop	0.310	0.307
ENc	49.90	51.07
CG₃	0.330	0.343
GC	0.381	0.384

Complete mitochondrial genome of Cladopsammia gracilis and Rhizopsammia wettsteini (Scleractinia, Dendrophylliidae) and its phylogenetic implications^*

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Complete mitochondrial genome of Cladopsammia gracilis and Rhizopsammia wettsteini (Scleractinia, Dendrophylliidae) and its phylogenetic implications*

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Complete mitochondrial genome of Cladopsammia gracilis and Rhizopsammia wettsteini (Scleractinia, Dendrophylliidae) and its phylogenetic implications^*