Deep-level diagnostic value of the rDNA-ITS region

被引:156
作者
Hershkovitz, MA
Lewis, LA
机构
[1] SMITHSONIAN INST,LAB MOL SYSTEMAT,WASHINGTON,DC 20560
[2] UNIV NEW MEXICO,DEPT BIOL,ALBUQUERQUE,NM 87131
关键词
ITS; 5.8S; rDNA evolution; eukaryotes; maximum-likelihood; among-site rate variation;
D O I
10.1093/oxfordjournals.molbev.a025693
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees similar to but less well supported than those generated by a ca. 10-fold longer alignment from rDNA-18S sequences, as well as independent evidence. We attribute this result to our finding that, compared to 18S, the 5.8S has a higher proportion of sites subject to vary and greater among-site substitution rate homogeneity. We also determined that our phylogenetic results are not likely affected by intramolecular compensatory mutation to maintain RNA secondary structure nor by evident systematic biases in base composition. Despite historical homology, there appears to be no ITS2 primary sequence similarity shared between fungi, green algae, and angiosperms. ITS2 sequences within each of these groups, however, share sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that ITS region sequences can diagnose organismal origins and phylogenetic relationships at many phylogenetic levels and provide a useful paradigm for molecular evolutionary study.
引用
收藏
页码:1276 / 1295
页数:20
相关论文
共 55 条
[1]   EVOLUTION OF NUCLEAR RDNA ITS SEQUENCES IN THE CLADOPHORA ALBIDA/SERICEA CLADE (CHLOROPHYTA) [J].
BAKKER, FT ;
OLSEN, JL ;
STAM, WT .
JOURNAL OF MOLECULAR EVOLUTION, 1995, 40 (06) :640-651
[2]   THE ITS REGION OF NUCLEAR RIBOSOMAL DNA - A VALUABLE SOURCE OF EVIDENCE ON ANGIOSPERM PHYLOGENY [J].
BALDWIN, BG ;
SANDERSON, MJ ;
PORTER, JM ;
WOJCIECHOWSKI, MF ;
CAMPBELL, CS ;
DONOGHUE, MJ .
ANNALS OF THE MISSOURI BOTANICAL GARDEN, 1995, 82 (02) :247-277
[3]   THE PHYLOGENY OF PLASTIDS - A REVIEW BASED ON COMPARISONS OF SMALL-SUBUNIT RIBOSOMAL-RNA CODING REGIONS [J].
BHATTACHARYA, D ;
MEDLIN, L .
JOURNAL OF PHYCOLOGY, 1995, 31 (04) :489-498
[4]  
Bold, 1985, INTRO ALGAE
[5]   Evolutionary Relationships within the Fungi: Analyses of Nuclear Small Subunit rRNA Sequences [J].
Bruns, Thomas D. ;
Vilgalys, Rytas ;
Barns, Susan M. ;
Gonzalez, Dolores ;
Hibbett, David S. ;
Lane, David J. ;
Simon, Luc ;
Stickel, Shawn ;
Szaro, Timothy M. ;
Weisburg, William G. ;
Sogin, Mitchell L. .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 1992, 1 (03) :231-241
[6]   PHYLOGENETICS OF SEED PLANTS - AN ANALYSIS OF NUCLEOTIDE-SEQUENCES FROM THE PLASTID GENE RBCL [J].
CHASE, MW ;
SOLTIS, DE ;
OLMSTEAD, RG ;
MORGAN, D ;
LES, DH ;
MISHLER, BD ;
DUVALL, MR ;
PRICE, RA ;
HILLS, HG ;
QIU, YL ;
KRON, KA ;
RETTIG, JH ;
CONTI, E ;
PALMER, JD ;
MANHART, JR ;
SYTSMA, KJ ;
MICHAELS, HJ ;
KRESS, WJ ;
KAROL, KG ;
CLARK, WD ;
HEDREN, M ;
GAUT, BS ;
JANSEN, RK ;
KIM, KJ ;
WIMPEE, CF ;
SMITH, JF ;
FURNIER, GR ;
STRAUSS, SH ;
XIANG, QY ;
PLUNKETT, GM ;
SOLTIS, PS ;
SWENSEN, SM ;
WILLIAMS, SE ;
GADEK, PA ;
QUINN, CJ ;
EGUIARTE, LE ;
GOLENBERG, E ;
LEARN, GH ;
GRAHAM, SW ;
BARRETT, SCH ;
DAYANANDAN, S ;
ALBERT, VA .
ANNALS OF THE MISSOURI BOTANICAL GARDEN, 1993, 80 (03) :528-580
[7]  
COLEMAN AW, 1994, J MOL EVOL, V30, P808
[8]  
CRONQUIST A, 1981, INTEGRATED SYSTEM CL
[9]  
CROUCH RJ, 1986, DNA SYSTEMATICS, V1, P47
[10]   PHYLOGENETIC ANALYSIS OF TUFA SEQUENCES INDICATES A CYANOBACTERIAL ORIGIN OF ALL PLASTIDS [J].
DELWICHE, CF ;
KUHSEL, M ;
PALMER, JD .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 1995, 4 (02) :110-128