Levels Of Sequence Divergence Research Articles

The genus Oidiodendron: species delimitation and phylogenetic relationships based on nuclear ribosomal DNA analysis

Nuclear ribosomal DNA sequences (ITS region) of fifteen species in the hyphomycete genus Oidiodendron and ten species from the 4 genera in the Myxotrichaceae, Byssoascus, Gymnostellatospora, Myxotrichum, and Pseudogymnoascus, were analysed to: (i) reveal the levels of intra- versus interspecific sequence variation within the genus Oidiodendron, clarify species delimitation and examine the usefulness of some morphological characters used for identification; (ii) assess the possible conspecificity of documented ericoid mycorrhizal strains of Oidiodendron; and (iii) test the hypothesis based on morphological inference that the genus Oidiodendron belongs with the genus Myxotrichum in the Myxotrichaceae (Onygenales). Comparison of molecular and morphological data for multiple strains of O. griseum, O. tenuissimum and O. maius revealed that conidiophore length and the production of a diffusing pigment are not reliable key characters for the genus. Several historically important ericoid mycorrhizal strains, documented as O. griseum, were reidentified as O. maius. Parsimony analyses of 23 Oidiodendron strains showed that three highly supported monophyletic groups, each one consisting of a pair of species, are resolved within the genus. A low level of sequence divergence between the species in these pairs suggests conspecificity for each pair. Other interspecific relationships were not well-supported by bootstrap values. Parsimony analysis of a second dataset composed of mitotic and meiotic taxa showed that Oidiodendron, Myxotrichum and Byssoascus form a well-supported monophyletic group within the Myxotrichaceae, and that this group has diverged significantly from the two other genera in the family. Relationships in the monophyletic group were correlated with anamorph state produced; three Myxotrichum spp., and B. striatosporus, all with distinct or reported Oidiodendron states, nested with anamorphic species, while species of Myxotrichum with other anamorph states were excluded. In addition, sequence divergence measures between the meiotic and mitotic species clustered in two monophyletic clades were found to be comparable to the intraspecific levels for Oidiodendron spp. These results support the initial hypothesis that Oidiodendron is closely related phylogenetically to the genus Myxotrichum and suggest that the generic concept of Byssoascus needs reexamination.

The Genus Oidiodendron: Species Delimitation and Phylogenetic Relationships Based on Nuclear Ribosomal DNA Analysis

Nuclear ribosomal DNA sequences (ITS region) of fifteen species in the hyphomycete genus Oidiodendron and ten species from the 4 genera in the Myxotrichaceae, Byssoascus, Gymnostellatospora, Myxotrichum, and Pseudogymnoascus, were analysed to: (i) reveal the levels of intra- versus interspecific sequence variation within the genus Oidiodendron, clarify species delimitation and examine the usefulness of some morphological characters used for identification; (ii) assess the possible conspecificity of documented ericoid mycorrhizal strains of Oidiodendron; and (iii) test the hypothesis based on morphological inference that the genus Oidiodendron belongs with the genus Myxotrichum in the Myxotrichaceae (Onygenales). Comparison of molecular and morphological data for multiple strains of O. griseum, O. tenuissimum and O. maius revealed that conidiophore length and the production of a diffusing pigment are not reliable key characters for the genus. Several historically important ericoid mycorrhizal strains, documented as O. griseum, were reidentified as O. maius. Parsimony analyses of 23 Oidiodendron strains showed that three highly supported monophyletic groups, each one consisting of a pair of species, are resolved within the genus. A low level of sequence divergence between the species in these pairs suggests conspecificity for each pair. Other interspecific relationships were not well-supported by bootstrap values. Parsimony analysis of a second dataset composed of mitotic and meiotic taxa showed that Oidiodendron, Myxotrichum and Byssoascus form a well-supported monophyletic group within the Myxotrichaceae, and that this group has diverged significantly from the two other genera in the family. Relationships in the monophyletic group were correlated with anamorph state produced; three Myxotrichum spp., and B. striatosporus, all with distinct or reported Oidiodendron states, nested with anamorphic species, while species of Myxotrichum with other anamorph states were excluded. In addition, sequence divergence measures between the meiotic and mitotic species clustered in two monophyletic clades were found to be comparable to the intraspecific levels for Oidiodendron spp. These results support the initial hypothesis that Oidiodendron is closely related phylogenetically to the genus Myxotrichum and suggest that the generic concept of Byssoascus needs reexamination.

Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation

Most surveys of mitochondrial DNA (mtDNA) in marine fishes reveal low levels of sequence divergence between haplotypes relative to the differentiation observed between sister taxa. It is unclear whether this pattern is due to rapid lineage sorting accelerated by sweepstakes recruitment, historical bottlenecks in population size, founder events, or natural selection, any of which could retard the accumulation of deep mtDNA lineages. Recent advances in paleoclimate research prompt a reexamination of oceanographic processes as a fundamental influence on genetic diversity; evidence from ice cores and anaerobic marine sediments document strong regime shifts in the world’s oceans in concert with periodic climatic changes. These changes in sea surface temperatures, current pathways, upwelling intensities, and retention eddies are likely harbingers of severe fluctuations in population size or regional extinctions. Sardines (Sardina, Sardinops) and anchovies (Engraulis) are used to assess the consequences of such oceanographic processes on marine fish intrageneric gene genealogies. Representatives of these two groups occur in temperate boundary currents on a global scale, and these regional populations are known to fluctuate markedly. Biogeographic and genetic data indicate that Sardinops has persisted for at least 20 million years, yet the mtDNA genealogy for this group coalesces in less than half a million years and points to a recent founding of populations around the rim of the Indian–Pacific Ocean. Phylogeographic analysis of Old World anchovies reveals a Pleistocene dispersal from the Pacific to the Atlantic, almost certainly via southern Africa, followed by a very recent recolonization from Europe to southern Africa. These results demonstrate that regional populations of sardines and anchovies are subject to periodic extinctions and recolonizations. Such climate-associated dynamics may explain the low levels of nucleotide diversity and the shallow coalescence of mtDNA genealogies. If these findings apply generally to marine fishes, management strategies should incorporate the idea that even extremely abundant populations may be relatively fragile on ecological and evolutionary time scales.

Large-scale sequence comparisons reveal unusually high levels of variation in the HLA-DQB1 locus in the class II region of the human MHC

Comparison of genomic sequences flanking the HLA-DQB1 locus in the human MHC class II region reveals local sequence variation of up to 10%, which is the highest level of sequence variation found in the human genome so far. The variation is haplotype-specific and extends far beyond the transcriptional unit of the DQB1 gene, suggesting hitch-hiking along with functionally selected alleles as the most likely mechanism. All major insertions/deletions (indels) were found to be of retroviral origin and in the immediate upstream region of DQB1. Possible cis-acting effects of these indels on the transcriptional regulation of DQB1 are discussed.

Molecular Phylogenetics of the Genus Piranga: Implications for Biogeography and the Evolution of Morphology and Behavior

Species in the genus Piranga vary in degree of sexual dimorphism, plumage coloration, morphology, song, migratory patterns, and geographic distribution. To study these aspects of Piranga biology in an evolutionary context, I constructed a phylogeny for this genus using cytochrome-b sequence data. Parsimony and maximum-likelihood analyses of DNA data reveal three possible phylogenies for species in this genus. All three trees identify a clade containing P. rubriceps, P. leucoptera, and P. erythrocephala and a clade containing P. rubra, P. ludoviciana, P. olivacea, P. bidentata, and P. flava. The trees differ in the placement of P. roseogularis. Morphology, song, and plumage data did not agree with these phylogenies. Levels of sequence divergence and the phylogeny of haplotypes are consistent with the idea that P. flava as currently described contains more than one evolutionary unit. Mapping the evolution of seasonal migration onto the DNA trees indicates that migration evolved once within Piranga.

Derivation and functional characterization of a consensus DNA binding sequence for the tas transcriptional activator of simian foamy virus type 1.

Although DNA binding sites specific for the Bel-1 and Tas transcriptional activators, encoded, respectively, by the human and simian foamy viruses, have been mutationally defined, they show little evident sequence identity. As a result, the sequence determinants for DNA binding by both Bel-1 and Tas have remained unclear. Here, we report the use of a novel in vivo randomization and selection strategy to identify a Tas DNA binding site consensus. This approach takes advantage of the fact that Tas can effectively activate gene expression in yeast cells via a Tas DNA binding site derived from the simian foamy virus type 1 (SFV-1) internal promoter. The defined Tas DNA binding site consensus extends over approximately 25 bp and contains a critical core sequence of approximately 5 bp. Positions adjacent to this core sequence, while clearly also subject to selection, show a significantly higher level of sequence variation. Surprisingly, the wild-type SFV-1 internal promoter Tas DNA binding site fails to conform to the consensus at several positions. Further analysis demonstrated that the consensus sequence bound Tas more effectively than did the wild-type sequence in vitro and could mediate an enhanced Tas response in vivo when substituted into the SFV-1 internal promoter context. These findings explain the limited sequence identity observed for mutationally defined Tas or Bel-1 response elements and should facilitate the identification of Tas DNA target sites located elsewhere in the SFV-1 genome.

Intraindividual and Interspecies Variation in the 5S rDNA of Coregonid Fish

This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate DNA sequence for comparisons of closely related taxa.

MOLECULAR AND MORPHOLOGICAL ANALYSIS OF ENTEROMORPHA INTESTINALIS AND E. COMPRESSA (CHLOROPHYTA) IN THE BRITISH ISLES

The very common green seaweeds Enteromorpha intestinalis (L.) Nees and E. compressa (L.) Nees are important fouling organisms and have commonly been used as indicators of eutrophication, but their taxonomic status is problematic. The genus presents extreme difficulties because there is wide intraspecific variation in morphology, but morphological differences between species are small and difficult to detect. In this study, molecular data were used in parallel with morphological characters to resolve the taxonomic problems. Phylogenetic analysis of sequences of the internal transcribed spacers ITS1 and ITS2 and the 5.8S gene distinguished two groups of samples, which were identified by morphological characters as E. compressa (branched) and E. intestinalis (normally unbranched). There was a low level of sequence divergence within each group of samples, but divergence between groups was as great as that between either of the two species and the outgroup E. prolifera. Clades representing E. compressa and E. intestinalis were also found in analyses of an independent molecular data set, chloroplast DNA restriction fragment length polymorphisms (RFLPs). Enteromorpha intestinalis and E. compressa represent two distinct, genetically divergent species. Reinterpretation of published studies shows that these species are reproductively isolated. However, E. compressa and E. intestinalis are sometimes very difficult to distinguish from each other and could be regarded as cryptic species. The presence or absence of branching was the most useful character distinguishing these two species, but there was an element of ambiguity because low salinity or salinity shock can induce branching in E. intestinalis. If environmental factors such as salinity are taken into account, branching can be used to identify the great majority of thalli correctly. This study therefore provides a basis for identifying the two most important marine fouling macroalgae and for their use in environmental monitoring and experimentation. Typification of these two Linnaean species showed that current usage of the names accords with the lectotype and protologue of both species. Samples that resembled E. usneoides did not form a clade in any of the trees, and constraining the data to support the monophyly of this group incurred a penalty. Enteromorpha usneoides appears to be an ecotype of E. compressa.

Mitochondrial ND1 gene sequences used to identify echinostome isolates from Australia and New Zealand

Echinostomes were collected in Australia and New Zealand as cercariae, metacercariae or adults. Using DNA sequences from the mitochondrial ND1 gene Echinostoma revolutum and Echinostoma paraensei were discovered in Australia. The presence of a further five, as yet unidentified, echinostome species was inferred in Northern Australia and a further isolate, closely allied to E. revolutum, occurs in New Zealand. ND1 sequences of species within the genus diverge from each other by 9.6–30.8%. Sequence divergence levels among strains within a single species are 0–3.6%. The phylogenetic tree produced from the Australasian isolates, in addition to species described previously, identifies the 37-collar-spine species as a well supported monophyletic group. The five unidentified Australian species cluster away from the 37-collar-spine group. These unidentified species appear to divide further into > 37-collar-spine and < 37-collar-spine clusters. Three strains of E. revolutum, collected as metacercariae from snails, were identified from two ponds located 6 km apart. Two of these strains may be cycling through a planorbid snail, Glyptophysa sp., as first intermediate host; however, this hypothesis could not be confirmed as specimens could not be obtained to match sequences between larvae and adults.

On the best evolutionary rate for phylogenetic analysis.

The effect of the evolutionary rate of a gene on the accuracy of phylogeny reconstruction was examined by computer stimulation. The evolutionary rate is measured by the tree length, that is, the expected total number of nucleotide substitutions per site on the phylogeny. DNA sequence data were simulated using both fixed trees with specified branch lengths and random trees with branch lengths generated from a model of cladogenesis. The parsimony and likelihood methods were used for phylogeny reconstruction, and the proportion of correctly recovered branch partitions by each method was estimated. Phylogenetic methods including parsimony appear quite tolerant of multiple substitutions at the same site. The optimum levels of sequence divergence were even higher than upper limits previously suggested for saturation of substitutions, indicating that the problem of saturation may have been exaggerated. Instead, the lack of information at low levels of divergence should be seriously considered in evaluation of a gene's phylogenetic utility, especially when the gene sequence is short. The performance of parsimony, relative to that of likelihood, does not necessarily decrease with the increase of the evolutionary rate.

Taxonomy of Cyanastroideae (Tecophilaeaceae): A Multidisciplinary Approach

Summary. Cyanastrum has previously been considered to include four species, all from the African continent. One of these, C. hostifolium from eastern Tanzania and northern Mozambique, is now transferred to a new genus, Kabuyea (K. hostifolia). This differs from Cyanastrum in several respects: vegetative morphology, perianth colour, anther dehiscence, pollen grain morphology, seed structure, chromosome number and karyotype. Karyotype analysis indicates that the individuals examined of the new genus are triploids. Analysis of rbcL DNA sequences for Cyanastraceae and Tecophilaeaceae places K. hostifolia as sister to C. cordifolium, but the level of sequence divergence between these two species is similar to that between genera in Tecophilaeaceae. The presence of a 'chalazosperm' in seeds of Cyanastrum was the primary reason for former recognition of the monogeneric family Cyanastraceae, but this structure is absent from seeds of Kabuyea. Relationships of Cyanastrum and Kabuyea with other Tecophilaeaceae are discussed.

MITOCHONDRIAL DNA SEQUENCE EVIDENCE SUPPORTING THE RECOGNITION OF TWO SUBSPECIES OR SPECIES OF THE FLORIDA SPINY LOBSTER PANULIRUS ARGUS

Samples of the spiny lobster Panulirus argus from populations in the western Atlantic and Caribbean were compared with spiny lobsters from Brazil for DNA sequence variation for 2 mitochondrial genes. Phylogenetic analyses of 16S sequence data reveal 2 distinct clades of P. argus, a clade consisting of Caribbean populations and a second clade of samples from Brazil. Mean sequence divergence estimates between Brazilian and western Atlantic/Caribbean populations were 8.32% for the mitochondrial large subunit ribosomal RNA (16S) and 19.82% for the cytochrome oxidase I subunit (COI). Levels of sequence divergence among sister species of Panulirus in the japonicus-group were similar to that observed between Brazilian and Caribbean/western Atlantic P. argus. In addition to large mitochondrial DNA sequence differences between western Atlantic/Caribbean and Brazilian P. argus, characteristic color patterns also distinguish Brazilian P. argus. Based on the results presented here, Brazilian P. argus is distinct from populations in the Caribbean and western Atlantic and may represent a complex of 2 species or subspecies. The degree of differentiation between the Caribbean and Brazilian clades indicates that formal recognition is warranted.

A multigene phylogeny of the Gelidiales including nuclear large-subunit rRNA sequence data

Partial sequences (1032 bp) of the nuclear-encoded large ribosomal RNA gene (LSU) were determined for 16 gelidialean species, and analyzed separately and in combination with plastid rbcL and nuclear SSU gene sequences. The number of informative characters and levels of sequence divergence among taxa are intermediate in LSU sequences as compared to that for rbcL and SSU. Analyses of the separate LSU, and a combined LSU, SSU, and rbcL data sets have identified early-diverging lineages within the Gelidiales including Gelidiella, Pterocladia, Pterocladiella, and a lineage including Gelidium and species classified in other genera. The relationships among most gelidialean taxa are well-resolved and well-supported by analyses of the combined data; however, the relationships of Ptilophora and Capreolia remain unclear. It is speculated that these two lineages have diverged from a common ancestor over an evolutionarily short period of time.

The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms.

We have isolated and characterized conserved regions of the reverse transcriptase gene from non-LTR retrotransposons, also called long interspersed nuclear elements (LINEs), from Beta vulgaris, B. lomatogona and B. nana. The novel elements show strong homology to other non-LTR retrotransposons from plants, man and animals. LINEs are present in all species of the genus Beta tested, but there was variation in copy number. Analysis by Southern hybridization and fluorescent in situ hybridization revealed the clustered organization of these retroelements in beet species. PCR amplification using degenerate primers to conserved motifs of the predicted LINE protein sequence enabled the cloning of LINEs from both Monocotyledonae (Allium cepa, Oryza sativa and Secale cereale) and Dicotyledonae (Nicotiana tabacum and Antirrhinum majus) indicating that LINEs are a universal feature of plant genomes. A dendrogram of fifteen new and six previously isolated sequences showed the high level of sequence divergence while revealing families characteristic of some genera. The genomic organization of non-LTR retrotransposons was examined more detailed in A. majus and O. sativa.

Purification and characterization of viral dsRNA genome profiles by crosshybridization.

AbstractDouble-stranded (ds) RNA present as genetic elements are widely distributed in nature and include genomes of viruses that can infect both eukaryotic and prokaryotic cells. These include members of the family Reoviridae, Birnaviridae, Partitiviridae, Hypoviridae, Totiviridae, and Cytovzridae, yeast killer factors and virus-like particles occurring as dsRNA plasmids in fungi (1). In most cases, the genomes of these viruses are segmented and can be separated into different bands when analyzed by SDS-PAGE or agarose gel electrophoresis, making them ideal candidates for analysis by crosshybridization. The advantage of this method is that it allows a rapid comparison of the sequence homology in every segment of the whole viral genome, of several viruses at once. Although this would also be possible, and a more definitive result can be obtained by full sequence analysis, it inevitably takes much longer particularly in the case of viruses that contam 10–12 genome segments (Reoviridae). The data obtained using this method allows individual homologous genome segments to be specifically identified and compared (using probes made from either isolated dsRNA segments or separate cDNA clones) (Fig. 1). Similarly the levels of sequence variation in different genome segments of different virus isolates can be correlated with variations in serotype and geographical origin (2–6).KeywordsGenome SegmentDiglycidyl EtherIsoamyl AlcoholViral dsRNASaran WrapThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Population genetics and biogeography of vestimentiferan tube worms

Molecular markers were used to assess the geographical ranges and estimate rates of gene flow in several species of vestimentiferan tube worm from the eastern Pacific Ocean. Small specimens (<5 cm) of Tevnia jerichonana and Oasisia alvinae are difficult to distinguish morphologically; however, species-specific allozymes allowed unequivocal identification of specimens from sites along the East Pacific Rise (EPR). Both T. jerichonana and O. alvinae were found at 9°, 11° and 13°N latitude; only O. alvinae occurred at 21°N; and neither occurred along the Galapagos Rift. Estimated rates of gene flow were sufficient (i.e. Nm>1.0) to counteract significant genetic drift in each species, and dispersal appeared to occur in a predominantly stepping-stone fashion. In addition, DNA sequence information from a 637 bp region of the mitochondrial COI gene was used to examine genetic diversity and geographical continuity in new Ridgeia piscesae specimens from the northeastern Pacific. The range of this species is now known to include sites ranging between 41°N on the Gorda Ridge and 49°N on the Southern Explorer Ridge. Sequence divergence throughout this range did not exceed 0.8%, which is consistent with intraspecific levels of sequence variation in other vent and seep species. Finally, the global distribution of vestimentiferan tube worms is reviewed.

Criteria for Sampling in Allium Based on Chloroplast DNA PCR-RFLP'S

Variation of approximately 20 kb of non-coding regions of the chloroplast genome of 29 species of Allium and 7 species of related genera have been cladistically analyzed. Both restriction site mutations and length mutations have been included in these analyses. The cladograms obtained with both types of mutation are highly similar topologically and display similar levels of homoplasy. No indication of significant between-data-set incongruence was found. The results of Wagner, Dollo and weighted parsimony indicate that recognition of the monotypic Nectaroscordum siculuim renders Allium paraphyletic. The two large subgenera Rhizirideum and Bromatorrhiza are probably not monophyletic. Two strongly supported clades, both of which comprise species of different subgenera, are not characterized by morphological synapomorphies when analyzed a posteriori. Furthermore, the position of Allium tuberosum (subg. Rhizirideum) and A. fimbriatuim (subg. Amerallium) changes considerably with different types of analysis, which suggests that inclusion of these and affiliated taxa may strongly influence the relationships found among chloroplast types in the genus. The highly artificial nature of the subgenera (subg. Bromatorrhiza is also indicated to be para- or polyphyletic) is not unexpected given the taxonomic complexity of Alli/hm. As a consequence, however, many more taxa have to be included in an analysis of the phylogenetic relationships of chloroplast DNA's in the genus. The trnK, trnC - trnD, psbA - trnS, and rbcL - ORF106 regions are most suited for further use because these regions are easily amplified and exhibit a considerable level of sequence variation with a restricted degree of length variation.

Allelic variation at a hypervariable compound microsatellite locus in the ascomycete Ascochyta rabiei

The genome of the fungal chickpea pathogen Ascochyta rabiei was screened for polymorphisms by microsatellite-primed PCR. While ethidium-bromide staining of electrophoretically separated amplification products showed only limited polymorphism among 24 Tunisian A. rabiei isolates, Southern hybridization of purified PCR fragments to restriction digests of fungal DNA revealed polymorphic DNA fingerprints. One particular probe that gave rise to a hypervariable single-locus hybridization signal was cloned from the Syrian isolate AA6 and sequenced. It contained a large compound microsatellite harbouring the penta- and decameric repeat units (CATTT)n, (CATTA)n, (CATATC-ATTT)n and (TATTT)n. We call this locus ArMS1 (Ascochyta rabiei microsatellite 1). Unique flanking sequences were used to design primer pairs for locus-specific microsatellite amplification and direct sequencing of additional ArMS1 alleles from Tunisian and Pakistani isolates. A high level of sequence variation was observed, suggesting that multiple mutational mechanisms have contribute to polymorphism. Hybridization and PCR analyses were performed on the parents and 62 monoascosporic F1 progeny derived from a cross between two different mating types of the fungus. Progeny alleles could be traced back to the parents, with one notable exception, where a longer than expected fragment was observed. Direct sequencing of this new length allele revealed an alteration in the copy number of the TATTT repeat [(TATTT)53 to (TATTT)65], while the remainder of the sequence was unchanged.

Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast.

Sequence divergence acts as a potent barrier to homologous recombination; much of this barrier derives from an antirecombination activity exerted by mismatch repair proteins. An inverted repeat assay system with recombination substrates ranging in identity from 74% to 100% has been used to define the relationship between sequence divergence and the rate of mitotic crossing-over in yeast. To elucidate the role of the mismatch repair machinery in regulating recombination between mismatched substrates, we performed experiments in both wild-type and mismatch repair defective strains. We find that a single mismatch is sufficient to inhibit recombination between otherwise identical sequences, and that this inhibition is dependent on the mismatch repair system. Additional mismatches have a cumulative negative effect on the recombination rate. With sequence divergence of up to approximately 10%, the inhibitory effect of mismatches results mainly from antirecombination activity of the mismatch repair system. With greater levels of divergence, recombination is inefficient even in the absence of mismatch repair activity. In both wild-type and mismatch repair defective strains, an approximate log-linear relationship is observed between the recombination rate and the level of sequence divergence.

Striking sequence similarity in inter- and intra-specific comparisons of class I SLG alleles from Brassica oleracea and Brassica campestris: implications for the evolution and recognition mechanism.

Self-incompatibility in Brassica is controlled by a single multi-allelic locus (S locus), which contains at least two highly polymorphic genes expressed in the stigma: an S glycoprotein gene (SLG) and an S receptor kinase gene (SRK). The putative ligand-binding domain of SRK exhibits high homology to the secretory protein SLG, and it is believed that SLG and SRK form an active receptor kinase complex with a self-pollen ligand, which leads to the rejection of self-pollen. Here, we report 31 novel SLG sequences of Brassica oleracea and Brassica campestris. Sequence comparisons of a large number of SLG alleles and SLG-related genes revealed the following points. (i) The striking sequence similarity observed in an inter-specific comparison (95.6% identity between SLG14 of B. oleracea and SLG25 of B. campestris in deduced amino acid sequence) suggests that SLG diversification predates speciation. (ii) A perfect match of the sequences in hypervariable regions, which are thought to determine S specificity in an intra-specific comparison (SLG8 and SLG46 of B. campestris) and the observation that the hypervariable regions of SLG and SRK of the same S haplotype were not necessarily highly similar suggests that SLG and SRK bind different sites of the pollen ligand and that they together determine S specificity. (iii) Comparison of the hypervariable regions of SLG alleles suggests that intragenic recombination, together with point mutations, has contributed to the generation of the high level of sequence variation in SLG alleles. Models for the evolution of SLG/SRK are presented.