Intra-genomic polymorphism in the internal transcribed spacer (ITS) regions of Cycas revoluta: evidence of incomplete concerted evolution

doi:10.3724/SP.J.1003.2009.09100

Abstract

Abstract:

In the present study, a high intra-genomic polymorphism was detected in the internal transcribed spacer (including ITS1, 5.8S and ITS2) regions of Cycas revoluta, suggestive of incomplete concerted evolution. Detailed comparisons of the ITS sequences from C. revoluta and those from other species further suggested that some divergent ITS paralogs from C. revoluta were likely pseudogenes. Some of these putative pseudogenes may have rather long evolutionary histories, because they have diverged substantially in sequences. We proposed that the incomplete concerted evolution in C. revoluta may have resulted from the high number and dispersed distribution of the nucleolus organizer regions (NORs) in the genome.

Key words: Cycas revoluta, nrDNA ITS, concerted evolution, pseudogenes, polymorphism

Longqian Xiao, Hua Zhu. Intra-genomic polymorphism in the internal transcribed spacer (ITS) regions of Cycas revoluta: evidence of incomplete concerted evolution[J]. Biodiv Sci, 2009, 17(5): 476-481.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2009.09100

https://www.biodiversity-science.net/EN/Y2009/V17/I5/476

Figures/Tables 3

References 36

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克隆编号 Clone No.	GenBank序列号 GenBank accession no.	长度(GC含量%) Length (bp) (GC content %)			5.8S基序5.8S motif	最小自由能5.8S Δ G (kcal/mol)
克隆编号 Clone No.	GenBank序列号 GenBank accession no.	ITS1	ITS2	5.8S	5.8S基序5.8S motif	最小自由能5.8S Δ G (kcal/mol)
D1	FJ907980	678(64.2)	246(65.0)	161(55.9)	V	-16.39
D2	FJ907972	677(64.2)	246(65.0)	161(55.9)	V	-16.39
D3	FJ908060	674(51.0)	243(46.1)	161(44.7)	V	-13.79
D4	FJ907973	677(63.8)	246(65.9)	161(55.9)	V	-16.39
D5	FJ907974	677(64.1)	246(65.0)	161(55.9)	V	-16.39
D6	FJ908059	676(49.4)	243(49.4)	161(43.5)	V	-8.54
D7	FJ908058	598(49.3)	243(46.1)	160(43.1)		-11.51
D8	FJ908051	672(51.0)	243(50.6)	161(37.9)		-10.95
D9	FJ907982	676(63.8)	246(65.0)	161(55.9)	V	-16.39
D11	FJ908056	679(50.5)	242(50.0)	161(42.9)		-9.42
D12	FJ907981	677(64.0)	246(65.0)	161(55.3)	V	-16.90
D13	FJ907983	674(62.7)	246(62.6)	161(54.7)	V	-19.39
D14	FJ908045	658(50.2)	243(50.6)	161(43.5)		-10.37
D15	FJ908067	671(48.7)	243(50.2)	161(44.7)	V	-13.21
C1	FJ907976	678(64.2)	246(65.0)	161(55.9)	V	-16.39
C2	FJ907979	678 (64.0)	246(65.0)	161(55.9)	V	-16.39
C3	FJ907978	679(64.1)	246(65.0)	161(55.3)	V	-16.59
C4	FJ907977	677 (64.1)	246(64.6)	161(55.9)	V	-16.39
C5	FJ907975	681(64.2)	230(65.6)	161(55.9)	V	-16.39

克隆编号 Clone No.	GenBank序列号 GenBank accession no.	长度(GC含量%) Length (bp) (GC content %)			5.8S基序5.8S motif	最小自由能5.8S Δ G (kcal/mol)
克隆编号 Clone No.	GenBank序列号 GenBank accession no.	ITS1	ITS2	5.8S	5.8S基序5.8S motif	最小自由能5.8S Δ G (kcal/mol)
D1	FJ907980	678(64.2)	246(65.0)	161(55.9)	V	-16.39
D2	FJ907972	677(64.2)	246(65.0)	161(55.9)	V	-16.39
D3	FJ908060	674(51.0)	243(46.1)	161(44.7)	V	-13.79
D4	FJ907973	677(63.8)	246(65.9)	161(55.9)	V	-16.39
D5	FJ907974	677(64.1)	246(65.0)	161(55.9)	V	-16.39
D6	FJ908059	676(49.4)	243(49.4)	161(43.5)	V	-8.54
D7	FJ908058	598(49.3)	243(46.1)	160(43.1)		-11.51
D8	FJ908051	672(51.0)	243(50.6)	161(37.9)		-10.95
D9	FJ907982	676(63.8)	246(65.0)	161(55.9)	V	-16.39
D11	FJ908056	679(50.5)	242(50.0)	161(42.9)		-9.42
D12	FJ907981	677(64.0)	246(65.0)	161(55.3)	V	-16.90
D13	FJ907983	674(62.7)	246(62.6)	161(54.7)	V	-19.39
D14	FJ908045	658(50.2)	243(50.6)	161(43.5)		-10.37
D15	FJ908067	671(48.7)	243(50.2)	161(44.7)	V	-13.21
C1	FJ907976	678(64.2)	246(65.0)	161(55.9)	V	-16.39
C2	FJ907979	678 (64.0)	246(65.0)	161(55.9)	V	-16.39
C3	FJ907978	679(64.1)	246(65.0)	161(55.3)	V	-16.59
C4	FJ907977	677 (64.1)	246(64.6)	161(55.9)	V	-16.39
C5	FJ907975	681(64.2)	230(65.6)	161(55.9)	V	-16.39

ITS区域 ITS region	序列类型 Sequence type	序列数目 Sequence number	多态位点数Polymorphic site no.	总突变数 Total mutation	核苷酸多态性 Nucleotide diversity (π)
ITS1	cDNA ITS	5	11	11	0.007
	功能 ITS Functional ITS	7	25	25	0.011
	假基因 Pseudogene	7	258	283	0.191
ITS2	cDNA ITS	5	2	2	0.003
	功能 ITS Functional ITS	7	11	11	0.013
	假基因 Pseudogene	7	120	142	0.222
5.8S	cDNA ITS	5	1	1	0.002
	功能 ITS Functional ITS	7	4	4	0.007
	假基因 Pseudogene	7	64	72	0.174
ITS	cDNA ITS	5	14	14	0.005
	功能 ITS Functional ITS	7	40	40	0.011
	假基因 Pseudogene	7	442	497	0.196

ITS区域 ITS region	序列类型 Sequence type	序列数目 Sequence number	多态位点数Polymorphic site no.	总突变数 Total mutation	核苷酸多态性 Nucleotide diversity (π)
ITS1	cDNA ITS	5	11	11	0.007
	功能 ITS Functional ITS	7	25	25	0.011
	假基因 Pseudogene	7	258	283	0.191
ITS2	cDNA ITS	5	2	2	0.003
	功能 ITS Functional ITS	7	11	11	0.013
	假基因 Pseudogene	7	120	142	0.222
5.8S	cDNA ITS	5	1	1	0.002
	功能 ITS Functional ITS	7	4	4	0.007
	假基因 Pseudogene	7	64	72	0.174
ITS	cDNA ITS	5	14	14	0.005
	功能 ITS Functional ITS	7	40	40	0.011
	假基因 Pseudogene	7	442	497	0.196