Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

Comprehensive analysis of simple sequence repeats in pre-miRNAs

Simple sequence repeats (SSRs) are tandem repeat units of 1-6 bp that are identified in various complete sequences. However, the distribution, nature, and origination of SSRs in pre-miRNAs, which are characteristic stem-loop sequences and are finally processed into ∼22 nt functional miRNAs contributing to regulate several biological processes, are still not well studied. The availability of large numbers of pre-miRNAs makes it possible to analyze and compare the occurrences of SSRs, the relative count of SSRs, or the longest SSRs in pre-miRNAs. In this study, we analyzed SSRs in 8,619 pre-miRNAs from 87 species, including Arthropoda, Nematoda, Platyhelminthes, Urochordata, Vertebrata, Mycetozoa, Protistae, Viridiplantae, and Viruses. We find that SSRs widely exist in the pre-miRNAs analyzed. Our analysis shows that mononucleotide repeats are the most abundant repeats, followed by dinucleotide repeats, whereas tri-, tetra-, penta-, and hexanucleotide repeats rarely occurred in pre-miRNAs. The number of SSRs per pre-miRNA on average ranges from 4.1 for viruses to 13.5 for Mycetozoa. Our results confirm that the number of repeats correlates inversely to the length of repeats. Generally, in each taxonomic group, the occurrence and relative count of SSRs decrease with the increase of repeat unit. SSRs do not exhibit obvious preference for special location in pre-miRNAs. The repeats in pre-miRNAs are complementary to repeats in coding or noncoding regions of genomes, and no significant difference is observed between these two classes with respect to the occurrence of repeats. These data on SSRs may become a useful resource of pre-miRNAs, and their possible functions are discussed.

Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes

The survey of simple sequence repeats (SSRs) has been extensively made in eukaryotes and prokaryotes. However, its still rare in viruses. Thus, we undertook a survey of SSRs in Human Immunodeficiency Virus Type 1 (HIV-1) which is an excellent system to study evolution and roles of SSRs in viruses. Distribution of SSRs was examined in 81 completed HIV-1 genome sequences which come from 34 different countries or districts over 6 continents. In these surveyed sequences, although relative abundance and relative density exhibit very high similarity, some of these sequences show different preference for most common SSRs and longest SSRs. Our results suggest proportion of various repeat types might be related to genome stability.

Mononucleotide repeats are asymmetrically distributed in fungal genes

Background

Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that these motifs are skewed towards gene termini, specifically the 5' end of genes. For eukaryotes no such intragenic analysis has been performed, though this could indicate the pervasiveness of this distribution bias, thereby helping to expose the selective pressures causing it.

Results

In fungal gene repertoires we find a similar 5' bias of intragenic mononucleotide repeats, most notably for Candida spp., whereas e.g. Coccidioides spp. display no such bias. With increasing repeat length, ever larger discrepancies are observed in genome repertoire fractions containing such repeats, with up to an 80-fold difference in gene fractions at repeat lengths of 10 bp and longer. This species-specific difference in gene fractions containing large repeats could be attributed to variations in intragenic repeat tolerance. Furthermore, long transcripts experience an even more prominent bias towards the gene termini, with possibly a more adaptive role for repeat-containing short transcripts.

Conclusion

Mononucleotide repeats are intragenically biased in numerous fungal genomes, similar to earlier studies on prokaryotes, indicative of a similar selective pressure in gene organization.

Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes

Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication, and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs were evolutionarily labile, their functional associations appeared. To be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface-associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.

Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia)

Mining for microsatellites (also called simple sequence repeats [SSRs]) in public sequence databases of a common Indo-Pacific coral Acropora millepora identified 191 SSRs from 10 258 expressed sequence tag (EST) and 618 SSRs from 14 625 whole-genome shotgun (WGS) sequences. In contrast to other animals, trinucleotide repeats, rather than dinucleotide repeats, are dominant in the WGS-SSRs, and AAT is the most frequent trinucleotide motif in EST-SSRs. We successfully developed 40 polymorphic markers from EST-SSRs and WGS-SSRs. Both EST- and WGS-SSRs show high levels of polymorphism within corals from the same reef patch. Interestingly, markers WGS079 and WGS227 revealed SSR duplications in a few individuals, suggesting recent duplication events. Genotypic linkage disequilibrium was identified in 5 pairs of SSR markers, which will be invaluable for high-resolution studies of genetic admixture in natural populations of A. millepora. Transferability analysis showed that 25 of these markers can be successfully amplified in one of the most ubiquitous Indo-Pacific corals Acropora hyacinthus. The marker collection reported here is the largest ever developed for any reef-building coral. It holds great potential for addressing coral reef connectivity across the Indo-Pacific with an unprecedented precision, especially taking into account the cross-species transferability of a substantial number of markers.

Quantitative trait loci for the circadian clock in Neurospora crassa

Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 F(1) progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates < or =0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation.