长臂缨鲆核糖体RNA基因序列多态性特征分析

doi:10.11978/2018038

Abstract

Abstract:

To better understand the polymorphism characteristics of ribosomal RNA genes of Crossorhombus kobensis (Jordan & Starks, 1906) from Bothidae, Pleuronectiformes, a total of 128 clone sequences were obtained, including full-length sequences of 18S, ITS1, 5.8S, and ITS2 and partial fragments of 28S. After sequence alignments, clustering analyses and recombination detection, the results showed that only 5.8S (158 bp) had no length variation, while the other four gene fragments showed high length polymorphism and resulted in several distinct types: 18S (1856-1893 bp) with four types of Types A, B, C, and R; 28S (967-974) and ITS1 (407-505 bp) both had three types of Types A, B and R; ITS2 (423-447 bp) had two types of Types A and B. All five gene fragments showed GC-bias, and ITS2 (71.14%) > ITS1 (65.37%) > 28S (62.22%) > 5.8S (57.67%) > 18S (54.95%). The current characteristics criteria were not sufficient to provide strong evidence for the inference of functional gene or pseudogene of 18S, 28S and ITS sequences. Therefore, comparison with each of corresponding gene fragment of four affinis species from family Bothidae was conducted, Arnoglossus macrolophus, Crossorhombus azureus, Engyprosopon grandisquama, and Lophonectes gallus. The alignment showed that the indels and differential sites of Type A sequences of both 18S and 28S were the similar as those of the four species; and Type A of ITS1, as well as the four species, had no fragment deletion at the missing loci of Type B. Therefore, Type A sequences of 18S, 28S and ITS1 were speculated as functional genes, while the other types were putative pseudogenes. As for ITS2, the divergence loci of Type A and Type B compared to each of the four species had no consistency, and there was no evidence to infer the status of ITS2. In this study, 5.8S rDNA is the most conserved gene, suggesting a concerted evolution, while non-concerted evolution was confirmed in other four genes because of high intra-individual polymorphism.

Key words: ribosomal RNA gene, Crossorhombus kobensis, polymorphism, pseudogene, non-concerted evolution, recombination

Min YANG, Xiaoyu KONG, Wei SHI, Li GONG. Analysis of polymorphism characteristics of ribosomal RNA genes in Crossorhombus kobensis (Pleuronectiformes: Bothidae)[J].Journal of Tropical Oceanography, 2019, 38(1): 55-66.

Figures/Tables 6

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Tab. 2

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References 34

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基因	正/反向引物及序列(5'-3')		长臂缨鲆 C. kobensis	长冠羊舌鮃 A. macrolophus	青缨鲆 C. azureus	大鳞短额鲆 E. grandisquama	冠毛鲆 L. gallus
18S	Z-18S-10	5'-TCTGGTTGATTCTGCCAGTAG-3'	MH031723—MH031736	MH173821	MH173822	MH173823	MH173824
18S	F-18S-1874	5'-ATGATCCTTCCGCAGGTTCA-3'	MH031723—MH031736	MH173821	MH173822	MH173823	MH173824
ITS1-5.8S	Z-18S-1720	5ʹ-TCGCTACTACCGATTGGATGGTTTA-3’	MH036892—MH036912	MH179078	MH179079	MH179080	MH179081
ITS1-5.8S	F-5.8S-150	5'-AAGCGACCCTCAGACAGGCGTAG-3'	MH036892—MH036912	MH179078	MH179079	MH179080	MH179081
5.8S-ITS2	Z-5.8S-10	5'-CAACTCTTAGCGGTGGATCA-3'	MH036913—MH036924	MH179074	MH179075	MH179076	MH179077
5.8S-ITS2	F-28S-100	5'-GCTCTTCCCTCTTCACTCG-3'	MH036913—MH036924	MH179074	MH179075	MH179076	MH179077
ITSZ	Z-18S-1720	5ʹ-TCGCTACTACCGATTGGATGGTTTA-3’	MH036925—MH036936	—	—	—	—
ITSZ	F-28S-100	5'-GCTCTTCCCTCTTCACTCG-3'	MH036925—MH036936	—	—	—	—
28S*	Z-28S-900	5'-CCCACCCCGACCCGTCTTGAA-3'	MH031711—MH031722	MH173825	MH173826	MH173827	MH173828
28S*	F-28S-1800	5'-GACTGACCCATGTTCAACTGCTGT-3'	MH031711—MH031722	MH173825	MH173826	MH173827	MH173828

基因类型		克隆数	长度范围 /bp	保守位点	变异位点	简约位点	单碱基突变	单倍型	单倍型多样性	核苷酸多样度	平均核苷酸差异数	GC含量 /%	最小自由能 /(kcal·mol^-1)
18S	A	6	1856~1858	1829	28	0	28	6	1	0.00503	9.333	54.74~54.98	-715.1~-722.5
	B	2	1892~1893	1880	12	—	—	2	1	0.00634	12	55.18~55.20	-729.5~-730.4
	C	2	1877~1878	1868	9	—	—	2	1	0.00479	9	54.84~54.90	-715.8~-721.9
	R	4	1861~1865	1837	30	3	27	4	1	0.00836	15.5	54.83~55.16	-706.6~-722.7
	合计	14	1856~1893	1814	79	7	72	14	1	0.00734	13.462	54.74~55.20	-706.6~-730.4
ITS1	A	23	500~505	488	22	7	15	21	0.9921	0.00736	3.605	64.81~65.81	-223.6~-234.8
	B	6	407~408	403	5	0	5	4	0.8	0.0041	1.667	65.93~66.67	-190.2~-194.0
	R	4	430~463	417	13	0	13	4	1	0.01485	6	63.26~66.74	-193.9~-211.0
	合计	33	407~505	475	38	19	19	29	0.9905	0.01484	5.89	63.26~66.74	-190.2~-234.8
5.8S	合计	45	158	150	8	0	8	8	0.2899	0.00225	0.356	56.96~58.86	-58.2~-62.4
ITS2	A	9	439~447	438	8	1	7	8	0.9722	0.005	2.194	71.14~71.81	-208.8~-220.2
	B	15	423~429	418	12	6	6	11	0.9048	0.00648	2.743	71.56~71.96	-202.1~-216.8
	合计	24	423~447	430	20	8	12	19	0.9601	0.00797	3.862	71.14~71.96	-202.1~-220.2
28S	A	7	967~968	958	10	0	10	6	0.9524	0.00295	2.857	61.98~62.29	-398.3~-405.9
	B	4	973~974	972	2	0	2	3	0.8333	0.00103	1	62.22~62.38	-400.6~-403.9
	R	1	972	—	—	—	—	1	1	—	—	62.24	-403.5
	合计	12	967~974	962	12	1	11	10	0.9697	0.00246	2.379	61.98~62.38	-398.3~-405.9

Analysis of polymorphism characteristics of ribosomal RNA genes in Crossorhombus kobensis (Pleuronectiformes: Bothidae)

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