蕨类植物rpoC1内含子缺失及其分子进化速率

doi:10.11983/CBB19105

摘要/Abstract

摘要： rpoC1基因编码RNA聚合酶β°亚基蛋白, 在转录过程中与DNA模板结合, 与β亚基形成的β-β°亚基复合体构成RNA合成的催化中心。以rpoC1基因为研究对象, 在贝叶斯因子大于20的条件下, 用HyPhy软件位点模型检测到3个正选择位点和541个负选择位点; 用PAML软件位点模型检测到10个正选择位点, 其中3个位点的后验概率超过99%。此外, 基于最大似然法构建64种蕨类植物的系统发育树, 结合HyPhy软件分析rpoC1基因的转换率、颠换率、转换率/颠换率、同义替换率、非同义替换率以及同义替换率/非同义替换率, 探讨rpoC1基因内含子丢失与分子进化速率的关系。结果表明, rpoC1基因内含子缺失对转换率、颠换率以及非同义替换率有一定影响。

关键词: rpoC1, 内含子, 正选择位点, 选择压力

Abstract: The rpoC1 gene encodes the RNA polymerase β' subunit protein, which binds to the DNA template during transcription, and the β-β' subunit complex formed with the β subunit constitutes a catalytic center for RNA synthesis. In this study, the rpoC1 gene mutations in ferns were surveyed. With Bayes factor greater than 20, HyPhy site model detected 3 positive selection sites and 541 negative selection sites; the PAML site model detected 10 positive selection sites, three of which had posterior probabilities greater than 99%. In addition, a phylogenetic tree of 64 ferns was constructed based on the maximum likelihood method. We calculated the transition rate, transversion rate, transition rate/transversion rate, synonymous substitution rate, nonsynonymous substitution rate, and synonymous substitution rate/nonsynonymous substitution rate by HyPhy to analyze the relationship between intron loss of rpoC1 gene and molecular evolution rates. The results indicate that intron loss of the rpoC1 gene might play a role in its transition rate, transversion rate and nonsynonymous substitution rate in ferns.

Key words: rpoC1, intron, positive selection site, selection pressure

彭阳, 苏应娟, 王艇. 蕨类植物rpoC1内含子缺失及其分子进化速率. 植物学报, 2020, 55(3): 287-298.

Yang Peng, Yingjuan Su, Ting Wang. Intron Loss and Molecular Evolution Rate of rpoC1 in Ferns. Chinese Bulletin of Botany, 2020, 55(3): 287-298.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB19105

https://www.chinbullbotany.com/CN/Y2020/V55/I3/287

图/表 8

参考文献 39

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Family name	Species	GenBank accession number	Length (bp)
Aspleniaceae	Asplenium pekinense	KY427331	152479
	As. prolongatum	KY427332	151115
	Hymenasplenium unilaterale	KY427350	151723
Athyriaceae	Athyrium anisopterum	NC_035738	151284
	At. opacum	KY427335	150979
	At. sheareri	KY427330	151068
	At. sinense	KY427333	151319
	Deparia lancea	KY427338	151011
	De. pycnosora	KY427339	151126
	De. viridifrons	KY427340	150939
	Diplazium bellum	KY427343	151601
	Di. dilatatum	KY427344	151114
	Di. dushanense	KY427345	150179
	Di. striatum	KY427346	150779
	Di. unilobum	KY427347	127840
Blechnaceae	Austroblechnum melanocaulon	KY427334	150202
	Woodwardia unigemmata	NC_028543	153717
Cibotiaceae	Cibotium barometz	MH105066	166027
Cyatheaceae	Alsophila podophylla	MG262389	166151
	Al. spinulosa	NC_012818	156661
Cystopteridaceae	Cystopteris chinensis	KY427337	151269
Family name	Species	GenBank accession number	Length (bp)
Dennstaedtiaceae	Pteridium aquilinum	NC_014348	152362
Diplaziopsidaceae	Diplaziopsis cavaleriana	KY427341	151934
	Dip. javanica	KY427342	151496
	Homalosorus pycnocarpos	KY427349	152159
Dryopteridaceae	Cyrtomium devexiscapulae	NC_028542	151684
	C. falcatum	NC_028705	151628
	C. fortunei	MG913607	151699
	Dryopteris decipiens	KY427348	150987
	Dr. fragrans	KX418656	151978
Equisetaceae	Equisetum arvense	NC_014699	133309
	E. hyemale	NC_020146	131760
Hymenophyllaceae	Callistopteris apiifolia	MH265125	144918
	Hymenophyllum holochilum	MH265124	142214
	Vandenboschia speciosa	NC_041000	146874
Hypodematiaceae	Hypodematium crenatum	KY427351	149794
Lygodiaceae	Lygodium japonicum	NC_022136	157260
	L. microphyllum	NC_039378	158891
Marattiaceae	Angiopteris angustifolia	NC_026300	153596
	An. evecta	NC_008829	153901
Marsileaceae	Marsilea crenata	NC_022137	151628
	Pilularia americana	KY863504	153076
Onocleaceae	Matteuccia struthiopteris	KY427353	151003
	Onoclea sensibilis	KY427354	148395
Ophioglossaceae	Botrychium ternatum	KM817789	139127
	Helminthostachys zeylanica	KM817788	145120
	Mankyua chejuensis	NC_017006	146221
Osmundaceae	Osmundastrum cinnamomeum	NC_024157	142812
Polypodiaceae	Lepisorus clathratus	NC_035739	156998
	Polypodium glycyrrhiza	KP136832	129223
Psilotaceae	Psilotum nudum	NC_003386	138829
Pteridaceae	Adiantum shastense	MG432483	150414
	Ceratopteris richardii	KM052729	148444
	Myriopteris lindheimeri	NC_014592	155770
Rhachidosoraceae	Rhachidosorus consimilis	KY427356	152642
Schizaeaceae	Schizaea elegans	KX258660	156603
	S. pectinata	KX258661	156392
Thelypteridaceae	Ampelopteris prolifera	KY427329	151772
	Christella appendiculata	NC_035842	151571
	Macrothelypteris torresiana	KY427352	151130
	Pseudophegopteris aurita	KY427355	149917
	Stegnogramma sagittifolia	KY427357	151132
Woodsiaceae	Woodsia macrochlaena	KY427358	150987
	W. polystichoides	KY427359	150685

Family name	Species	GenBank accession number	Length (bp)
Aspleniaceae	Asplenium pekinense	KY427331	152479
	As. prolongatum	KY427332	151115
	Hymenasplenium unilaterale	KY427350	151723
Athyriaceae	Athyrium anisopterum	NC_035738	151284
	At. opacum	KY427335	150979
	At. sheareri	KY427330	151068
	At. sinense	KY427333	151319
	Deparia lancea	KY427338	151011
	De. pycnosora	KY427339	151126
	De. viridifrons	KY427340	150939
	Diplazium bellum	KY427343	151601
	Di. dilatatum	KY427344	151114
	Di. dushanense	KY427345	150179
	Di. striatum	KY427346	150779
	Di. unilobum	KY427347	127840
Blechnaceae	Austroblechnum melanocaulon	KY427334	150202
	Woodwardia unigemmata	NC_028543	153717
Cibotiaceae	Cibotium barometz	MH105066	166027
Cyatheaceae	Alsophila podophylla	MG262389	166151
	Al. spinulosa	NC_012818	156661
Cystopteridaceae	Cystopteris chinensis	KY427337	151269
Family name	Species	GenBank accession number	Length (bp)
Dennstaedtiaceae	Pteridium aquilinum	NC_014348	152362
Diplaziopsidaceae	Diplaziopsis cavaleriana	KY427341	151934
	Dip. javanica	KY427342	151496
	Homalosorus pycnocarpos	KY427349	152159
Dryopteridaceae	Cyrtomium devexiscapulae	NC_028542	151684
	C. falcatum	NC_028705	151628
	C. fortunei	MG913607	151699
	Dryopteris decipiens	KY427348	150987
	Dr. fragrans	KX418656	151978
Equisetaceae	Equisetum arvense	NC_014699	133309
	E. hyemale	NC_020146	131760
Hymenophyllaceae	Callistopteris apiifolia	MH265125	144918
	Hymenophyllum holochilum	MH265124	142214
	Vandenboschia speciosa	NC_041000	146874
Hypodematiaceae	Hypodematium crenatum	KY427351	149794
Lygodiaceae	Lygodium japonicum	NC_022136	157260
	L. microphyllum	NC_039378	158891
Marattiaceae	Angiopteris angustifolia	NC_026300	153596
	An. evecta	NC_008829	153901
Marsileaceae	Marsilea crenata	NC_022137	151628
	Pilularia americana	KY863504	153076
Onocleaceae	Matteuccia struthiopteris	KY427353	151003
	Onoclea sensibilis	KY427354	148395
Ophioglossaceae	Botrychium ternatum	KM817789	139127
	Helminthostachys zeylanica	KM817788	145120
	Mankyua chejuensis	NC_017006	146221
Osmundaceae	Osmundastrum cinnamomeum	NC_024157	142812
Polypodiaceae	Lepisorus clathratus	NC_035739	156998
	Polypodium glycyrrhiza	KP136832	129223
Psilotaceae	Psilotum nudum	NC_003386	138829
Pteridaceae	Adiantum shastense	MG432483	150414
	Ceratopteris richardii	KM052729	148444
	Myriopteris lindheimeri	NC_014592	155770
Rhachidosoraceae	Rhachidosorus consimilis	KY427356	152642
Schizaeaceae	Schizaea elegans	KX258660	156603
	S. pectinata	KX258661	156392
Thelypteridaceae	Ampelopteris prolifera	KY427329	151772
	Christella appendiculata	NC_035842	151571
	Macrothelypteris torresiana	KY427352	151130
	Pseudophegopteris aurita	KY427355	149917
	Stegnogramma sagittifolia	KY427357	151132
Woodsiaceae	Woodsia macrochlaena	KY427358	150987
	W. polystichoides	KY427359	150685

	E_t	E_v	trsv/trst	trst	trsv	d_N	d_S	ω
Lygodium	0.014	0.004	0.118	0.579	0.007	0.022	0.147	0.144
Other ferns	0.022	0.005	0.096	0.088	0.010	0.045	0.201	0.256
P value	1.000	1.000	1.000	0.008	0.036	0.000	0.517	1.000
Mann-Whitney	0.834	0.778	0.362	0.834	0.778	0.502	0.923	0.316

	E_t	E_v	trsv/trst	trst	trsv	d_N	d_S	ω
Lygodium	0.014	0.004	0.118	0.579	0.007	0.022	0.147	0.144
Other ferns	0.022	0.005	0.096	0.088	0.010	0.045	0.201	0.256
P value	1.000	1.000	1.000	0.008	0.036	0.000	0.517	1.000
Mann-Whitney	0.834	0.778	0.362	0.834	0.778	0.502	0.923	0.316

	Model	Np	?	Parameter estimate	Positive selection sites
Branch model	M0	128	-33984.0181	ω=0.18862	Not allowed
	MA	129	-33971.0708	ω₁=0.19344, ω₂=0.07154	Not allowed
Site model	Model 1a (M1a)	129	-33025.1095	P₀=0.77581, ω₀=0.09604	Not allowed
				P₁=0.22419, ω₁=1.00000
	Model 2a (M2a)	131	-33003.8671	P₀=0.77323, ω₀=0.09782	687P, 697S
				P₁=0.20583, ω₁=1.00000	692S*, 700A
				P₂=0.02094, ω₂=2.53148
	Model 3 (M3)	132	-32770.6265	P₀=0.45915, ω₀=0.02383	None
				P₁=0.39593, ω₁=0.23422
				P₂=0.14492, ω₂=0.91531
	Model 7 (M7)	129	-32768.3591	P=0.36168, q=1.11178	Not allowed
	Model 8 (M8)	131	-32715.0671	P₀=0.95310, P=0.46388	578V, 579Y, 686S*
				q=2.02806, P₁=0.04690	687P*, 689T, 692S**
				ω=1.62513	693I, 696T, 697S*, 700A
	Model 8a (M8a)	130	-32735.2130	P₀=0.91188, P=0.48169	None
				q=2.38635, P₁=0.08812
				ω=1.00000
Branch-site model	Ma0	130	-33025.1095	P₀=0.77581, P₁=0.22419	Not allowed
				P_2a+P_2b=0.00000, ω₂=1.00000
	Ma1	131	-33025.1095	P₀=0.77581, P₁=0.22419	None
				P_2a+P_2b=0.00000, ω₂=1.00000