Sequence variation within the rRNA gene loci of 12 Drosophila species

被引:92
作者
Stage, Deborah E. [1 ]
Eickbush, Thomas H. [1 ]
机构
[1] Univ Rochester, Dept Biol, Rochester, NY 14627 USA
关键词
D O I
10.1101/gr.6376807
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
Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA ( rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads ( trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8-8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10-20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.
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页码:1888 / 1897
页数:10
相关论文
共 57 条
[1]   The genome sequence of Drosophila melanogaster [J].
Adams, MD ;
Celniker, SE ;
Holt, RA ;
Evans, CA ;
Gocayne, JD ;
Amanatides, PG ;
Scherer, SE ;
Li, PW ;
Hoskins, RA ;
Galle, RF ;
George, RA ;
Lewis, SE ;
Richards, S ;
Ashburner, M ;
Henderson, SN ;
Sutton, GG ;
Wortman, JR ;
Yandell, MD ;
Zhang, Q ;
Chen, LX ;
Brandon, RC ;
Rogers, YHC ;
Blazej, RG ;
Champe, M ;
Pfeiffer, BD ;
Wan, KH ;
Doyle, C ;
Baxter, EG ;
Helt, G ;
Nelson, CR ;
Miklos, GLG ;
Abril, JF ;
Agbayani, A ;
An, HJ ;
Andrews-Pfannkoch, C ;
Baldwin, D ;
Ballew, RM ;
Basu, A ;
Baxendale, J ;
Bayraktaroglu, L ;
Beasley, EM ;
Beeson, KY ;
Benos, PV ;
Berman, BP ;
Bhandari, D ;
Bolshakov, S ;
Borkova, D ;
Botchan, MR ;
Bouck, J ;
Brokstein, P .
SCIENCE, 2000, 287 (5461) :2185-2195
[2]   XENOPUS-BOREALIS AND XENOPUS-LAEVIS 28S RIBOSOMAL DNA AND THE COMPLETE 40S RIBOSOMAL PRECURSOR RNA CODING UNITS OF BOTH SPECIES [J].
AJUH, PM ;
HEENEY, PA ;
MADEN, BEH .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1991, 245 (1312) :65-71
[3]   Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus [J].
Averbeck, KT ;
Eickbush, TH .
GENETICS, 2005, 171 (04) :1837-1846
[4]   Tandem repeats finder: a program to analyze DNA sequences [J].
Benson, G .
NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580
[5]   Origin and evolution of paralogous rRNA gene clusters within the flatworm family Dugesiidae (Platyhelminthes, Tricladida) [J].
Carranza, S ;
Baguñà, J ;
Riutort, M .
JOURNAL OF MOLECULAR EVOLUTION, 1999, 49 (02) :250-259
[6]   The Jalview Java']Java alignment editor [J].
Clamp, M ;
Cuff, J ;
Searle, SM ;
Barton, GJ .
BIOINFORMATICS, 2004, 20 (03) :426-427
[7]   XENOPUS-LAEVIS-28S RIBOSOMAL-RNA - A SECONDARY STRUCTURE MODEL AND ITS EVOLUTIONARY AND FUNCTIONAL IMPLICATIONS [J].
CLARK, CG ;
TAGUE, BW ;
WARE, VC ;
GERBI, SA .
NUCLEIC ACIDS RESEARCH, 1984, 12 (15) :6197-6220
[8]   RATE OF TURNOVER OF STRUCTURAL VARIANTS IN THE RDNA GENE FAMILY OF DROSOPHILA-MELANOGASTER [J].
COEN, ES ;
THODAY, JM ;
DOVER, G .
NATURE, 1982, 295 (5850) :564-568
[9]   CONCERTED EVOLUTION, MOLECULAR DRIVE AND NATURAL-SELECTION [J].
DOVER, G .
CURRENT BIOLOGY, 1994, 4 (12) :1165-1165
[10]  
EICKBUSH DG, 1995, GENETICS, V139, P671