ITS 假基因对栎属系统学研究的影响及其对分子系统学研究的启示*

摘要/Abstract

摘要：

核糖体rDNA ITS 是被子植物系统发育研究中应用最广泛的分子标记之一。以前人们认为同一物种
中的ITS 序列因致同进化而使不同拷贝高度一致, 在分子系统学研究中常以ITS1- 518S- ITS2 序列作为构建
系统进化树的基础。近年来, 在对一些被子植物的研究中发现这段序列在同一物种中具有多态性, 有些拷
贝中的518S 区不具编码功能, 人们把含有不具编码功能518S 区的ITS1-51 8S- ITS2 序列定义为ITS 假基因序
列, 它对同源基因致同进化的假设形成了新的挑战。在诸多应用ITS 序列重建系统进化关系的研究中, 栎
属系统学研究因ITS 假基因的发现而倍受关注。本文以栎属为例回顾了ITS 假基因的发现过程, 分析了其
对该属系统学研究的影响, 为分子生物学在植物系统进化研究中的应用提供一些新的参考。

关键词: ITS, 假基因, 栎属, 分子系统学

Abstract:

Sequences of ITS in nrDNA is one of the widely used markers in angiosperm systematics. Many early reports of
ITS reg ion ( ITS 1, 518S and ITS 2) variation in flowering plants indicated that nrDNA arrays within individuals are homogeneous.
However, recent studies have discovered that individuals often contain potentially non-functional nrDNA copies
( pseudogenes) . These findings suggest that complete concerted evolution should not be assumed when embarking on phylogenetic
studies using nrDNA sequences. ITS pseudogene has been detected in the genus of Quercus L. and misled the
phylogenetic reconstruction, which made this genus frequently focused in the related studies. The authors take this genus
as an example to discuss the influence of the pseudogene on the phylogenetic study, conclude that combining application of
molecular evolution and classic taxonomy knowledge in plant systematics study may lead to more convincible results.

Key words: ITS, Pseudogene, Quercus , Molecular phylogenetics

中图分类号:

Q 75
Q 949

马长乐1、2, 周浙昆1**. ITS 假基因对栎属系统学研究的影响及其对分子系统学研究的启示*[J]. Plant Diversity, 2006, 28(2): 127-132.

MA Chang-Le-, Zhou-Zhe-Kun-**. Effect of ITS Pseudogene on the Phylogenetic Study of Quercus ( Fagaceae) and Its Revelation on the Plant Molecular Phylogenetics[J]. Plant Diversity, 2006, 28(2): 127-132.

参考文献

陈焕镛, 黄成就, 1998. 5中国植物志6 ( 22 卷, 壳斗科)
[ M] .
北京: 科学出版社
邹喻苹, 葛颂, 王晓东, 2001. 系统与进化植物学中的分子标
记
[M] . 北京: 科学出版社
Alvarez I, Wendel JF, 2003. Ribosomal ITS sequences and plant phylogenetic
inference
[ J ] . Mol ecular Phyl ogenetics and Evolution ,
29: 417 ) 434
Axelord DI, 1983. Biogeography of oaks in the arcto-t ertiary province

[ J] . Ann Missouri Bot Gard , 70: 629) 657
Bailey CD, Carr TG, Harris SA, et al , 2003. Charact erization of angiosperm
nrDNA polymorphyism, paralogy, and pseudogenes
[ J ] .
Molecular Phylogenetics and Evoluti on, 29: 435 ) 455
Buckler ES, Ippolito A, Holtsford TP, 1996. The evolut ion of ribosomal
DNA: Divergent paralogous and phylogenetic implications
[ J] .
Genetics , 145: 821) 832
Elias TS, 1971. The genera of Fagaceae in the southeastern Unit ed
States
[ J] . J Arnold Arbor , 52: 159 ) 195
Flam F, 1994. Hints of a language in junk DNA
[ J] . Science , 266:
1320
Govaerts R, Frodin DG, 1998. Word checkl ist and bibl iography of Fagales

[ M] . Royal botanic garden, Kew
Hartmann S, Nason JD, Bhattacharya D, 2001. Ext ensive ribosomal
DNA genic variat ion in the columnar cactusLophocereus
[ J] . J Mol
Evol , 53: 124) 134
Hirotsune S, Yoshida N, ChenA, et al , 2003. An expressed pseudogene
regulat es the messenger-RNA stability of its homologous coding
gene
[ J] . Nature, 423: 91) 96
Huang CJ ( 黄成就) , Zhang YT ( 张永田) , 1999. Flora of China
( Engl ish version) Vol. ( 4 ) (Cycadaceae through Fagaceae)
[M] .
Science Press. Beijing & Missouri Botanical Garden Press. St .
Louis. pp, 314 ) 400
ISCID, 2004. Pseudogene
[ DBPOL] . ISCID Encyclopedia of Science
and Philosophy. Ret rieved December 16, 2004 f rom http:PP
www1 iscid1 orgPencyclopediaPPseudogeneKita Y, Ito M, 2000. Nuclear ribosomal ITS sequences and phylogeny
in East Asian Aconitum subgenus Aconitum ( Ranunculaceae) , with
special reference to extensive polymorphism in individual plants
[ J] .
Plant Syst Evol , 225: 1 ) 13
Lawrence, George HM, 1951. Taxonomy of Vascular Plants
[M] . The
MacMillan Company, New York
Lee JT, 2003. Complicity of gene and pseudogene
[ J] . Nature , 423:
26 ) 28
Makalowski W, 2000. Genomic scrap yard: genomes utilize all that
junk
[ J] . Gene , 259: 61 ) 67
Manos PS, Doyel JJ, Nixon KC, 1999. Phylogeny, biogeography,
and processes of molecular different iation in Quercus Subgenus Quercus
(Fagaceae)
[ J ] . Molecular Phylogenetics and Ev olution, 12
( 3) : 333 ) 349
Manos PS, Stanford AM, 2001. The historical biogeography of fagaceae:
tracking the tertiary history of t emperat e and subtropical forest s
of the northern hemisphere
[ J] . Int J Plant Sci , 162 ( 6 Suppl ) :
s77) s93
Manos PS, Zhou ZK, Cannon CH, 2001. Systematics of Fagaceae:
phylogenetic tests of reproductive trait evolut ion
[ J ] . Int J Plant
Sci , 162 (6) : 1361) 1379
Manos PS, Doyle JJ, Nixon KC, 1999. Phylogeny, biogeography and
processes of molecular different iation in Quercus subgenus Quercus
( Fagaceae)
[ J ] . Molecular Phylogenetics and Evolution , 12:
333 ) 349
Mayol M, Rossello JA, 2001. Why nuclear ribosomal DNA spacers
( ITS) t ell different stories in Quercus
[ J] . Molecular Phyl ogenetics
and Evolution , 19: 167 ) 176
Muir G, SchlÊ tterer C, 1999. Limitat ions to the phylogenet ic use of ITS
sequences in closely relat ed species and populations- a case study in
Quercus petraea ( Matt. ) Liebl. Chapt er 11 in: Which DNA Marker
for Which Purpose?
[ M] . Final Compendium of the Research
Project: Development , optimization and val idation of molecular
tools for assessment of biodiversity in forest trees in the European
Union DGXII Biotechnology FW IV Research Program Molecular
Tools for Biodiversity. Gillet, EM ( ed. ) . URL http:PP
webdoc1sub1 gwdg1dePebookPyP1999PwhichmarkerPindex1htm
Muir G, Fleming CC, SchlÊ tterer C, 2001. Tree divergent rDNA clusters
predate the species divergence in Quercus petraea ( Matt . )
Liebl. and Quercus robur L.
[ J] . Mol Biol Evol , 18: 112 ) 119
Nixon KC, 1993. Infrageneri c classifi cation of Quercus ( Fagaceae) and
typification of sectional names
[ J] . Ann Sci For Suppl 1 ( Paris ) ,
50: 25) 34
Pu CX ( 普春霞) , Zhou ZK ( 周浙昆) , Luo Y ( 罗燕) , 2002. A
cladisti c analysis of Quercus ( Fagaceae) in China based on l eaf ep-i
dermis and architecture
[ J] . Acta Bot Yunnan ( 云南植物研究) ,
24 ( 6) : 689 ) 698
Samuel R, Bachmair A, Jobst J, et al , 1998. ITS sequences from nuclear
rDNA suggest phylogenetic relationships between Euro-Medit erranean,
East Asiat ic and North American taxa of Quercus ( Fagaceae)

[ J] . Plant Syst Evol , 211: 129) 139
Savolainen V, Chase MW, 2003. A decade of progress in plant molecular
phylogenetics
[ J] . Trends in Genetics, 19 ( 12) : 717 ) 724
Solt is E. Douglas, Solt is S. Pamela, 2000. Contribut ions of plant molecular
systematics t o studies of molecular evolution
[ J] . Plant Mol
ecular Biology, 42: 45) 47
TianX ( 田欣) , Li DZ ( 李德铢) , 2002. Applicat ion of DNA sequences
in plant phylogenet ic study
[ J ] . Acta Bot Yunnan ( 云南
植物研究) , 24 ( 2) : 170 ) 184
Willem J, Ferguson H, 2002. On the use of genetic divergence for
ident ifying species
[ J] . Biological Joural of the Linnean Society ,
75: 509 ) 516
Yang YW, Lai KN, Tai PY, et al , 1999. Molecular phylogenet ics
studies of Brassica, Rorippa, Arabidopsis, and allied genera
based on the int ernal transcribed spacer region of 18s-25s rDNA

[ J] . Molecular Phylogenetics and Evolution , 13: 455) 462
Zhang DX, Hewitt GM, 2003. Nuclear DNA analyses in genetic studies
of populations: pract ice, problems and prospects
[ J ] . Mol ecular
Ecology , 12: 563 ) 584
Zhou ZK ( 周浙昆) , 1992a. Drigin, phylogeny and dispersal of Quercus
from China
[ J ] . Acta Bot Yunnan ( 云南植物研究) , 14
( 3) : 227) 236
Zhou ZK ( 周浙昆) , 1992b. A taxonomical revision of fossil evergreen
Sclerophyllous oaks from China
[ J] . Acta Bot Sin ( 植物学报) ,
34 ( 12) : 954 ) 961
Zhou ZK ( 周浙昆) , 1993. The fossil history of Quercus
[ J] . Acta
Bot Yunnan ( 云南植物研究) , 15 ( 1) : 21 ) 33
Zhou ZK ( 周浙昆) , 1999. Fossils of the Fagaceae and their implicat
ion in systematics and biogeography
[ J] . Acta Phytotax Sin ( 植
物分类学报) , 37 (4) : 369 ) 385
Zoldos V, Papes D, Cerbah M, et al , 1999. Molecular-cyt ogenetic
studies of ribosomal genes and het erochromatin reveal conserved genome
organisat ion among 11 Quercus species
[ J] . Theoretical and
Applied Genetics, 99: 969 ) 977

[1]	Zhi-Chao Li, Chao-Qun Xu, Wei Zhao, Shuai Nie, Yu-Tao Bao, Hui Liu, Zhen Xing, Jian-Feng Mao, Xiao-Ru Wang. Ecophysiological transition mediated by hybridization in a hybrid pine species complex[J]. Plant Diversity, 2025, 47(04): 604-619.
[2]	Yu-Mei Yan, Ze-Xin Fan, Pei-Li Fu, Zhi-Yong Zhang. Drought tolerance traits explain differential stem growth rates of evergreen and deciduous trees in a tropical karst forest[J]. Plant Diversity, 2025, 47(03): 454-465.
[3]	Xue Wang, Xinrui Liu, Shuang Chen, Jiang Zhu, Yanqi Yuan, Rong Zhu, Kaixi Chen, Xue Yang, Xiaochun Wang, Weiyi Mo, Ruili Wang, Shuoxin Zhang. Elevational variation in anatomical traits of the first-order roots and their adaptation mechanisms[J]. Plant Diversity, 2025, 47(02): 291-299.
[4]	Wenjie Guo, Lu Gong, Yan Luo, Qian Guo. Does season regulate heterochronous leaf growth? Mechanisms of petiole-lamina trade-offs in broad-leaved woody plants of the Tianshan Mountains[J]. Plant Diversity, 2024, 46(06): 755-765.
[5]	Tana Wuyun, Lu Zhang, Tiina Tosens, Bin Liu, Kristiina Mark, José ángel Morales-Sánchez, Jesamine Jöneva Rikisahedew, Vivian Kuusk, ülo Niinemets. Extremely thin but very robust: Surprising cryptogam trait combinations at the end of the leaf economics spectrum[J]. Plant Diversity, 2024, 46(05): 621-629.
[6]	Jingya Zhang, Cui Xiao, Xiaoyu Duan, Xin Gao, Hao Zeng, Rong'an Dong, Gang Feng, Keping Ma. Species' geographical range, environmental range and traits lead to specimen collection preference of dominant plant species of grasslands in Northern China[J]. Plant Diversity, 2024, 46(03): 353-361.
[7]	Rong Ma, Qi Xu, Yongqian Gao, Deli Peng, Hang Sun, Bo Song. Patterns and drivers of plant sexual systems in the dry-hot valley region of southwestern China[J]. Plant Diversity, 2024, 46(02): 158-168.
[8]	Ju Li, Shu-Bin Zhang, Yang-Ping Li. Photosynthetic response dynamics in the invasive species Tithonia diversifolia and two co-occurring native shrub species under fluctuating light conditions[J]. Plant Diversity, 2024, 46(02): 265-273.
[9]	Ming-Yue Jin, Daniel J. Johnson, Guang-Ze Jin, Qing-Xi Guo, Zhi-Li Liu. Soil water content and nitrogen differentially correlate with multidimensional leaf traits of two temperate broadleaf species[J]. Plant Diversity, 2023, 45(06): 694-701.
[10]	Yan Ke, Feng-Ping Zhang, Yun-Bing Zhang, Wei Li, Qin Wang, Da Yang, Jiao-Lin Zhang, Kun-Fang Cao. Convergent relationships between flower economics and hydraulic traits across aquatic and terrestrial herbaceous plants[J]. Plant Diversity, 2023, 45(05): 601-610.
[11]	Amarpreet Kaur, Shalinder Kaur, Harminder Pal Singh, Daizy R. Batish. Is intraspecific trait differentiation in Parthenium hysterophorus a consequence of hereditary factors and/or phenotypic plasticity?[J]. Plant Diversity, 2023, 45(05): 611-620.
[12]	Korina Ocampo-Zuleta, Ángela Parrado-Rosselli. Functional diversity in an Andean subpáramo affected by wildfire in Colombia[J]. Plant Diversity, 2023, 45(04): 385-396.
[13]	Harshita Bhatia, Gaurav Srivastava, R. C. Mehrotra. Legumes from the Paleocene sediments of India and their ecological significance[J]. Plant Diversity, 2023, 45(02): 199-210.
[14]	Chao Liu, Huan-Huan Chen, Li-Zhou Tang, Phyo Kay Khine, Li-Hong Han, Yu Song, Yun-Hong Tan. Plastid genome evolution of a monophyletic group in the subtribe Lauriineae (Laureae, Lauraceae)[J]. Plant Diversity, 2022, 44(04): 377-388.
[15]	Guo-Qiang Zhang, Gui-Zhen Chen, Li-Jun Chen, Jun-Wen Zhai, Jie Huang, Xin-Yi Wu, Ming-He Li, Dong-Hui Peng, Wen-Hui Rao, Zhong-Jian Liu, Si-Ren Lan. Phylogenetic incongruence in Cymbidium orchids[J]. Plant Diversity, 2021, 43(06): 452-461.