Concerted evolution in the ribosomal RNA genes of an Epichloë endophyte hybrid: comparison between tandemly arranged rDNA and dispersed 5S rrn genes

We examined ribosomal RNA concerted evolution in an Epichlo? endophyte interspecific hybrid (Lp1) and its progenitors (Lp5 and E8). We show that the 5S rrn genes are organized as dispersed copies. Cloned 5S gene sequences revealed two subfamilies exhibiting 12% sequence divergence, with substitutions forming coevolving pairs that maintain secondary structure and presumably function. Observed sequence patterns are not fully consistent with either concerted or classical evolution. The 5S rrn genes are syntenic with the tandemly arranged rDNA genes, despite residing outside the rDNA arrays. We also examined rDNA concerted evolution. Lp1 has rDNA sequence from only one progenitor and contains multiple rDNA arrays. Using 5S rrn genes as chromosomal markers, we propose that interlocus homogenization has replaced all Lp5 rDNA sequence with E8 sequence in the hybrid. This interlocus homogenization appears to have been rapid and efficient and is the first demonstration of hybrid interlocus homogenization in the Fungi.     

Molecular Organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural Features and Evolution of Piscine 5S rRNA Genes and Nontranscribed Intergenic Spacers

The genomic and gene organisation of 5S rDNA clusters have been extensively characterized in bony fish and eukaryotes, providing general issues for understanding the molecular evolution of this multigene DNA family. By contrast, the 5S rDNA features have been rarely investigated in cartilaginous fish (only three species). Here, we provide evidence for a dual 5S rDNA gene system in the Rajidae by sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) in five Mediterranean species of rays (Rajidae), and in a large number of piscine taxa including lampreys and bony fish. As documented in several bony fish, two functional 5S rDNA types were found here also in the rajid genome: a short one (I) and a long one (II), distinguished by distinct 5S and NTS sequences. That the ancestral piscine genome had these two 5S rDNA loci might be argued from the occurrence of homologous dual gene systems that exist in several fish taxa and from 5S phylogenetic relationships. An extensive analysis of NTS-II sequences of Rajidae and Dasyatidae revealed the occurrence of large simple sequence repeat (SSR) regions that are formed by microsatellite arrays. The localization and organization of SSR within the NTS-II are conserved in Rajiformes since the Upper Cretaceous. The direct correlation between the SSRs extension and the NTS length indicated that they might play a role in the maintenance of the larger 5S rDNA clusters in rays. The phylogenetic analysis indicated that NTS-II is a valuable systematic tool limited to distantly related taxa of Rajiformes. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Rafael Zardoya]     

Molecular organization of 5S rDNA in bitterlings (Cyprinidae)

Molecular organization and nucleotide sequences of the 5S rRNA gene and NTS were investigated in freshwater fish, bitterlings (Acheilognathinae), including 10 species/subspecies of four genera, Acheilognathus, Pseudoperilampus, Rhodeus, and Tanakia, to understand the evolutionary trait of 5S rDNA arrays. Southern hybridization analysis revealed a general trend with tandem repeats of 5S rDNA in all the examined bitterlings. Sequence analysis demonstrated a conserved 120 bp sequence of the 5S rRNA gene and a short NTS of 56–67 bp with two distinct portions, a conserved (5′-flanking portion; at positions −1 to −38) and a variable part (3′-flanking portion), in 6 of 10 species/subspecies examined. The conserved NTS region was most likely an external promoter so far observed in various vertebrates, whereas the variable NTS region could be divided into two types due to its nucleotide polymorphisms. Molecular phylogeny using the 5S rRNA gene and NTS sequences suggested the occurrence of 5S rDNA duplication before speciation and a concerted evolution for the gene and conserved NTS regions, but a birth-and-death process to maintain the variable NTS region. Thus, the 5S rDNA in the examined bitterlings might have evolved under a mixed process of evolution.     

Disparate molecular evolution of two types of repetitive DNAs in the genome of the grasshopper Eyprepocnemis plorans

Wide arrays of repetitive DNA sequences form an important part of eukaryotic genomes. These repeats appear to evolve as coherent families, where repeats within a family are more similar to each other than to other orthologous representatives in related species. The continuous homogenization of repeats, through selective and non-selective processes, is termed concerted evolution. Ascertaining the level of variation between repeats is crucial to determining which evolutionary model best explains the homogenization observed for these sequences. Here, for the grasshopper Eyprepocnemis plorans, we present the analysis of intragenomic diversity for two repetitive DNA sequences (a satellite DNA (satDNA) and the 45S rDNA) resulting from the independent microdissection of several chromosomes. Our results show different homogenization patterns for these two kinds of paralogous DNA sequences, with a high between-chromosome structure for rDNA but no structure at all for the satDNA. This difference is puzzling, considering the adjacent localization of the two repetitive DNAs on paracentromeric regions in most chromosomes. The disparate homogenization patterns detected for these two repetitive DNA sequences suggest that several processes participate in the concerted evolution in E. plorans, and that these mechanisms might not work as genome-wide processes but rather as sequence-specific ones.     

Human rDNA: evolutionary patterns within the genes and tandem arrays derived from multiple chromosomes

Human rDNA forms arrays on five chromosome pairs and is homogenized by concerted evolution through recombination and gene conversion (loci RNR1, RNR2, RNR3, RNR4, RNR5, OMIM: 180450). Homogenization is not perfect, however, so that it becomes possible to study its efficiency within genes, within arrays, and between arrays by measuring and comparing DNA sequence variation. Previous studies with randomly cloned genomic DNA fragments showed that different parts of the gene evolve at different rates but did not allow comparison of rDNA sequences derived from specific chromosomes. We have now cloned and sequenced rDNA fragments from specific acrocentric chromosomes to (1) study homogenization along the rDNA and (2) compare homogenization within chromosomes and between homologous and nonhomologous chromosomes. Our results show high homogeneity among regulatory and coding regions of rDNA on all chromosomes, a surprising homogeneity among adjacent distal non-rDNA sequences, and the existence of one to three very divergent intergenic spacer classes within each array.     

Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune

The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution.     

Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications

The evolution of 5S rRNA gene unit (5S gene unit) was studied among the ten species belonging to Vigna subgenus Ceratotropis by sequencing and analyzing the intra- and inter-specific sequence heterogeneity. The 5S unit from these species ranged from 214 to 342 bp in length as a result of several indels in the intergenic spacer (IGS) region. A large deletion (>100 bp) was found specifically in the IGS of V. radiata accessions. IGS showed high sequence variation with more than 50% polymorphic and 35.4% parsimony informative sites. However, the coding region (5S gene) was highly conserved, both in length and in sequence. Intra-genomic and intra-specific divergence was observed among some species, which indicated that the 5S unit is evolving at different rates among the Vigna species. Most Vigna species harbored one type of 5S unit indicating complete homogenization among them. Vigna glabrescens, a tetraploid species, also showed single type of 5S rDNA from only one of the diploid progenitor indicating loss or homogenization of the other type. However, V. nakashimae and V. riukiuensis harbored multiple, diverse, ‘intra-genomic 5S types’ indicating that 5S rDNA is not completely homogenized by concerted evolution and is still evolving. In general, the phylogeny based on IGS sequences was in agreement with many of the earlier reports except some surprising observations such as, V. glabrescens clustered with V. mungo in section Ceratotropis and unlike most of the species, wild and cultivated types of V. umbellata were present in different subclusters. Presence of divergent 5S sequences in V. nakashimae and V. riukiuensis caused errors in phylogeny reconstruction at species level and suggested a horizontal ‘gene transfer’ as a result of inter-species hybridization. The comparative analysis showed that 5S IGS sequences have better phylogenetic utility than chloroplast DNA sequences, such as atpB-rbcL and is comparable to ITS1 and ITS2 in this respect.     

Molecular and cytological characterization of 5S rDNA in Oryza species: genomic organization and phylogenetic implications.

We investigated the molecular characteristics and chromosomal organization of 5S rDNA in the genus Oryza, including diploid and tetraploid species. A phylogenetic tree of Oryza species was constructed based on the non-transcribed spacer sequences of 5S rDNA, and some novel relationships were discovered. Specifically, comparative sequence analysis of 5S rDNA in several wild rice species showed unique characteristics inconsistent with the model of concerted evolution: (1) multiple distinct 5S rDNA types were detected within a species, leading to intraspecific divergence of 5S rDNA; (2) multiple identical 5S rDNA types were shared among species, resulting in interspecies clustering of 5S rDNA types; and (3) intraspecific nucleotide diversity was detected within a 5S rDNA class. Our results obtained by fluorescence in situ hybridization revealed that each rice species studied contained only one 5S rDNA locus with two hybridization sites, which were located on either chromosome 7 or chromosome 11. These results suggest that different 5S rDNA classes within the rice genome were arranged together and that one pair of 5S rDNA loci from a diploid progenitor of the tetraploid species might have been lost during evolution. Taken together, our data show that 5S rDNA in rice species is more informative at the gene level than at the chromosome level.