Effect of ITS Pseudogene on the Phylogenetic Study of Quercus ( Fagaceae) and Its Revelation on the Plant Molecular Phylogenetics

Abstract

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

CLC Number:

Q 75
Q 949

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.

References

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

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