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Simple Summary: Metagenomic binning is a part of the metagenomic analysis process that can classify the genomes in complex microbial communities into possible source species. It is dedicated to restoring more complete genomes and is conducive to studying microbial community structure and function. Obtaining more effective feature representations of genome sequences to improve binning is still a major challenge. This study proposes a new metagenomic binning method called CedtBin, which uses an improved BERT model to obtain the embedded representation of contigs and splices it with the decomposed tetranucleotide frequencies into a new feature representation. Then, the Annoy-DBSCAN clustering algorithm is proposed, which can adaptively determine the parameters of the DBSCAN clustering algorithm for binning. The results show that CedtBin can achieve good binning effects on both simulated and real datasets, and can reconstruct more genomes. Metagenomic binning is a crucial step in metagenomic research. It can aggregate the genome sequences belonging to the same microbial species into independent bins. Most existing methods ignore the semantic information of contigs and lack effective processing of tetranucleotide frequency, resulting in insufficient and complex feature information extracted for binning and poor binning results. To address the above problems, we propose CedtBin, a metagenomic binning method based on contig embedding and decomposed tetranucleotide frequency. First, the improved BERT model is used to learn the contigs to obtain their embedding representation. Secondly, the tetranucleotide frequencies are decomposed using a non-negative matrix factorization (NMF) algorithm. After that, the two features are spliced and input into the clustering algorithm for binning. Considering the sensitivity of the DBSCAN clustering algorithm to input parameters, in order to solve the drawbacks of manual parameter input, we also propose an Annoy-DBSCAN algorithm that can adaptively determine the parameters of the DBSCAN algorithm. This algorithm uses Approximate Nearest Neighbors Oh Yeah (Annoy) and combines it with a grid search strategy to find the optimal parameters of the DBSCAN algorithm. On simulated and real datasets, CedtBin achieves better binning results than mainstream methods and can reconstruct more genomes, indicating that the proposed method is effective. [ABSTRACT FROM AUTHOR]

We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes. [ABSTRACT FROM AUTHOR]

We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50–60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes.

Abstract Background Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed. Results Here, we initially test a published approach called “genome-wide tetranucleotide frequency correlation coefficient” (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called “fragment tetranucleotide frequency correlation coefficient” (FRAGTE), which uses fragments rather than whole genomes for sieving. Our results show that FRAGTE achieves ~ 100% sensitivity and high specificity on simulated genomes, real genomes and metagenome-assembled genomes, demonstrating that FRAGTE is completeness-independent. Additionally, FRAGTE sieved a reduced number of total genomes for subsequent alignment and calculation to greatly improve computational efficiency for the process after sieving. Aside from this computational improvement, FRAGTE also reduces the computational cost for the sieving process. Consequently, FRAGTE extremely improves run efficiency for both the processes of sieving and after sieving (subsequent alignment and calculation) to together accelerate genome-wide species delineation. Conclusions FRAGTE is a completeness-independent algorithm for sieving. Due to its high sensitivity, high specificity, highly reduced number of sieved genomes and highly improved runtime, FRAGTE will be helpful for whole-genome approaches to facilitate taxonomic studies in prokaryotes.

Abstract Background While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution. Results Following a comparative genomics study of all human protein-coding genes annotated in the GeneCards database, here we provide a genome-scale portrait of human-specific short- and medium-size (≥ 3-repeats) tri- and tetranucleotide STRs and STR motifs in the critical core promoter region between − 120 and + 1 to the TSS and evidence of skewing of this compartment in reference to the STRs that are not human-specific (Levene’s test p

Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r = 0.310, p = 0.550), and were positively correlated with the total length of SSRs (Pearson, r = 0.992, p = 0.00). A total of 224,289 tetranucleotide orthologous microsatellites families and 367 single-copy orthologous SSRs loci were found in six primate species by homologous alignment. The inner mutation types of single-copy orthologous SSRs loci included the copy number variance, point mutation, and chromosomal translocation. The accumulated repeat times and average length of tetranucleotide orthologous microsatellites in Rhinopithecus roxellana , Papio anubis and Macaca mulatta were longer than Homo sapiens and Pan troglodytes , which showed the tetranucleotide orthologous SSRs loci had more repeat times and longer average length on the branches with earlier divergence time, one exception may be Microcebus murinus as a primitive monkey with a smallest morphology in Malagasy. Our conclusion indicated that single-copy tetranucleotide orthologous SSRs sequences accumulated individual mutation more slowly through time in H. sapiens and P. troglodytes than in R. roxellanae , P. anubis and M. mulatta . However, such divergence wouldn't arise uniformly in all branches of the primate tree. A comparison of genomic sequence assemblages would offer remarkable insights about comparisons and contrasts, and the evolutionary processes of the microsatellites involved in human and nonhuman primate species. [ABSTRACT FROM AUTHOR]

Background The genomic sequences of mycobacteriophages, phages infecting mycobacterial hosts, are diverse and mosaic. Mycobacteriophages often share little nucleotide similarity, but most of them have been grouped into lettered clusters and further into subclusters. Traditionally, mycobacteriophage genomes are analyzed based on sequence alignment or knowledge of gene content. However, these approaches are computationally expensive and can be ineffective for significantly diverged sequences. As an alternative to alignment-based genome analysis, we evaluated tetranucleotide usage in mycobacteriophage genomes. These methods make it easier to characterize features of the mycobacteriophage population at many scales. Description We computed tetranucleotide usage deviation (TUD), the ratio of observed counts of 4-mers in a genome to the expected count under a null model. TUD values are comparable between members of a phage subcluster and distinct between subclusters. With few exceptions, neighbor joining phylogenetic trees and hierarchical clustering dendrograms constructed using TUD values place phages in a monophyletic clade with members of the same subcluster. Regions in a genome with exceptional TUD values can point to interesting features of genomic architecture. Finally, we found that subcluster B3 mycobacteriophages contain significantly overrepresented 4-mers and 6-mers that are atypical of phage genomes. Conclusions Statistics based on tetranucleotide usage support established clustering of mycobacteriophages and can uncover interesting relationships within and between sequenced phage genomes. These methods are efficient to compute and do not require sequence alignment or knowledge of gene content. The code to download mycobacteriophage genome sequences and reproduce our analysis is freely available at https://github.com/bsiranosian/tango_final.

Background The genomic sequences of mycobacteriophages, phages infecting mycobacterial hosts, are diverse and mosaic. Mycobacteriophages often share little nucleotide similarity, but most of them have been grouped into lettered clusters and further into subclusters. Traditionally, mycobacteriophage genomes are analyzed based on sequence alignment or knowledge of gene content. However, these approaches are computationally expensive and can be ineffective for significantly diverged sequences. As an alternative to alignment-based genome analysis, we evaluated tetranucleotide usage in mycobacteriophage genomes. These methods make it easier to characterize features of the mycobacteriophage population at many scales. Description We computed tetranucleotide usage deviation (TUD), the ratio of observed counts of 4-mers in a genome to the expected count under a null model. TUD values are comparable between members of a phage subcluster and distinct between subclusters. With few exceptions, neighbor joining phylogenetic trees and hierarchical clustering dendrograms constructed using TUD values place phages in a monophyletic clade with members of the same subcluster. Regions in a genome with exceptional TUD values can point to interesting features of genomic architecture. Finally, we found that subcluster B3 mycobacteriophages contain significantly overrepresented 4-mers and 6-mers that are atypical of phage genomes. Conclusions Statistics based on tetranucleotide usage support established clustering of mycobacteriophages and can uncover interesting relationships within and between sequenced phage genomes. These methods are efficient to compute and do not require sequence alignment or knowledge of gene content. The code to download mycobacteriophage genome sequences and reproduce our analysis is freely available at https://github.com/bsiranosian/tango_final.

We describe ten microsatellite loci isolated for the oldest lineage of extant salamandrids, the spectacled salamanders ( Salamandrina), a genus of terrestrial salamanders endemic to the Apennine peninsula (Italy). Primers were tested in 24 individuals per species, the northern species ( Salamandrina perspicillata) and the southern species ( Salamandrina terdigitata). All loci were polymorphic in S. perspicillata with number of alleles ranging from three to eleven and observed heterozygosity ranging from 0.25 to 0.83. In S. terdigitata eight loci were polymorphic, the number of alleles ranged from two to nine, and observed heterozygosity from 0.04 to 0.92. [ABSTRACT FROM AUTHOR]

This study reports the first set of microsatellite markers for the weasel (Mustela nivalis). We chose to isolate loci with tetranucleotide repeat motifs because they can be scored less ambiguously than the more commonly used dinucleotide loci. All 11 loci showed considerable variation within a population sample of 28 individuals from Portugal, with number of alleles ranging from four to nine per locus and observed and expected heterozygosities ranging from 0.21 to 0.86 and from 0.40 to 0.84, respectively. No linkage disequilibrium was detected between pairs of loci, and only one locus (Mn 1.30) deviated from Hardy-Weinberg equilibrium expectations in the analyzed population sample. Among the 11 loci, Mn 1.30 was the only one for which all known males were homozygous. Analysis of an additional population sample of 23 individuals (14 males and 9 females) from Denmark revealed that all males, but only four females, were homozygous for Mn 1.30, supporting the idea that the locus is X-linked. These novel polymorphic microsatellite markers should be useful in studies of population genetics and molecular ecology of the weasel. [ABSTRACT FROM AUTHOR]

Nucleosomes are the basic structural units of eukaryotic chromatin and play a key role in the regulation of gene expression. Nucleosome formation depends on several factors, including properties of the sequence itself, but also physical constraints and epigenetic factors such as chromatin-remodelling enzymes. In this view, a sequence-dependent approach is able to capture a general tendency of a region to bind a histone octamer. A reference data set of positioned nucleosomes of Saccharomyces cerevisiae was used to study the role of DNA helical rise in histone–DNA interaction. Genomic sequences were transformed into arrays of helical rise values by a tetranucleotide code and then turned into profiles of mean helical rise values. These profiles resemble maps of nucleosome occupancy, suggesting that intrinsic histone–DNA interactions are linked to helical rise. The obtained results show that preferential nucleosome occupancy occurs where the mean helical rise reaches its largest values. Mean helical rise profiles obtained by using maps of positioned nucleosomes of the Drosophila melanogaster and Plasmodium falciparum genomes, as well as Homo sapiens chromosome 20 confirm that nucleosomes are mainly located where the mean helical rise reaches its largest values. [ABSTRACT FROM PUBLISHER]

The eastern indigo snake ( Drymarchon couperi) is the longest snake in North America. Population declines due to extensive loss of habitat led to federal listing as a threatened species in 1978. Knowledge deficiencies regarding the biology of the eastern indigo snake, including population connectivity and gene flow, are impediments to the development of effective conservation and restoration strategies. We describe primers and polymerase chain reaction (PCR) conditions to amplify 22 tetranucleotide and pentanucleotide nuclear microsatellite loci isolated from the eastern indigo snake. We tested primers using 28 shed skins representing 24 individuals from Fort Stewart, Georgia. Primers yielded an average of 4.6 alleles per locus (range 3-7) and an average observed heterozygosity of 0.63 (range 0.46-0.79). These loci should prove useful for individual identification as well as population level analyses of this federally threatened species. [ABSTRACT FROM AUTHOR]

We describe the isolation of ten microsatellite loci from the Rwenzori Double-collared Sunbird using an enrichment protocol. All loci were variable with the number of alleles ranging from 5 to 13, and observed heterozygosity ranging from 0.500 to 0.929. Nine of these loci were screened on a panel of seven additional Sunbird species from three genera. All nine were successfully amplified and remained highly variable. Given 10–15% sequence divergence among these species in the mtDNA ND2 gene, our results suggest that these markers will work broadly across most members of the species rich bird family Nectariniidae. [ABSTRACT FROM AUTHOR]

We report the isolation and characterization of 11 polymorphic tetranucleotide microsatellite loci in the common genet (Genetta genetta) from genomic libraries enriched for (AAAG)n and (AGAT)n repeat sequences. We chose to develop tetranucleotide repeats because they can be scored less ambiguously. In a sample of 25 individuals, we observed between four and thirteen alleles per locus and their observed and expected heterozygosities ranged from 0.60 to 0.84 and from 0.68 to 0.92, respectively. All genotypic frequencies conformed to Hardy-Weinberg equilibrium expectations and there were no instances of linkage disequilibrium detected between pairs of loci. These loci will be of use in studies of population genetics, historical demography, and molecular ecology of the common genet. [ABSTRACT FROM AUTHOR]

We isolated nine new microsatellites for the deep-sea fish Coryphaenoides rupestris. These loci are highly polymorphic, with allele number ranging from 14 to 42 and heterozygosity ranging from 0.647 to 0.965. Four of these loci also amplified in C. brevibarbis. [ABSTRACT FROM AUTHOR]

Abstract: Hybridisation-capture was used to create 12 unique alpaca DNA libraries each enriched for a different tetranucleotide microsatellite motif. Two hundred and forty-nine microsatellites were found, of which 26 were polymorphic (motifs GGAT, GTTT and GCAC). Nine markers were fully characterised on 45 samples. Allele numbers ranged from 6 (locus P135) to 12 (loci P149 and PCTD17). There was no evidence of linkage disequilibrium at any locus (p =0.064–1). Deviation from Hardy–Weinberg equilibrium was observed in three loci after Bonferroni correction (PCTD17, P135 and P193). Null alleles were detected at loci P147, P193 and P194. Polymorphic information content ranged from 0.48 to 0.82. When combined, the markers had an exclusion probability of 97.7%. Two polymerase chain reaction multiplex sets comprising six and three markers each were optimized. These multiplex sets will be useful for parentage determination, and individually the markers will add to the pool of markers available for mapping of desirous or deleterious traits in alpacas. [Copyright &y& Elsevier]

We report the isolation of 11 polymorphic tetranucleotide microsatellite loci in the Egyptian mongoose ( Herpestes ichneumon). In a sample of 27 individuals, we observed between 4 and 7 alleles per locus and their observed and expected heterozygosities ranged from 0.37 to 0.85 and from 0.44 to 0.79, respectively. All genotypic frequencies conformed to Hardy–Weinberg equilibrium expectations and there were no instances of linkage disequilibrium detected between pairs of loci. [ABSTRACT FROM AUTHOR]

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as 'data deficiency' in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species' conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10-13 loci have successful cross-amplifications. [ABSTRACT FROM AUTHOR]

The pied flycatcher ( Ficedula hypoleuca) is a small migratory passerine bird commonly distributed across Europe which has been the focus of considerable ecological and evolutionary research. Here, we present details of 70 microsatellite markers for the species adding to the six which are currently available. Sixty-six markers were also polymorphic in the closely related collared flycatcher ( Ficedula albicollis), while 54 were polymorphic in another related passerine, the bluethroat ( Luscinia svecica), and 12 were polymorphic in the more distantly related Siberian jay ( Perisoreus infaustus). [ABSTRACT FROM AUTHOR]

A total of 45 microsatellite loci from yellow perch, Perca flavescens, were isolated and characterized. Among the 45 microsatellite loci, 32 had more than two alleles. A wild population of P. flavescens ( n = 48) was used to examine the allele range of the microsatellite loci. Mendelian inheritance of alleles was confirmed by examining the amplified products in pair-mated families. The number of alleles for the 32 polymorphic loci varied from two to 16, and observed heterozygosity ranged between 0.024 (YP79) and 0.979 (YP60). Cross-species polymorphic amplification in four other Percidae species was successful for 22 loci. [ABSTRACT FROM AUTHOR]

Nine highly polymorphic microsatellite markers were developed for Gehyra variegata from an enriched library screened for tetranucleotide repeats. An average of 19.44 alleles per locus and an average observed heterozygosity of 0.86 were found in 81 samples from fragmented populations in the Western Australian wheatbelt. Different gecko species exhibit varying rates of extinction in fragmented landscapes and the genetic markers were developed to test whether these difference are due to different rates of dispersal. The loci were tested for their ability to cross amplify in 12 species of Australian Gekkonidae and Pygopodidae, in an attempt to identify species which might be amenable to population genetic analysis using these microsatellite markers. [ABSTRACT FROM AUTHOR]

This paper reports 20 new microsatellite loci that are highly polymorphic in rhesus macaques (Macaca mulatta). We screened known human microsatellite loci to identify markers that are polymorphic in rhesus macaques, and then selected specific loci that show substantial levels of heterozygosity and robust, reliable amplification. The 20 loci reported here were chosen to include one highly informative microsatellite from each rhesus monkey autosomal chromosome. Fourteen of the 20 polymorphisms are tetranucleotide repeats, and all can be analyzed using standard PCR and electrophoresis procedures. These new rhesus markers have an average of 15.5 alleles per locus and average heterozygosity of 0.83. This panel of DNA polymorphisms will be useful for a variety of different genetic analyses, including pedigree testing, paternity analysis, and population genetic studies. Many of these loci are also likely to be informative in other closely related Old World monkey species. Am. J. Primatol. 67:377–383, 2005. © 2005 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Abstract: Myotonic dystrophy (dystrophia myotonica, DM) is the most common form of muscular dystrophy in adults. The presence of two genetic forms of this complex multisystemic disease (DM1 and DM2) was unrecognized until the genetic cause of DM1 was identified in 1992. The fact that the DM1 mutation is an untranslated CTG expansion led to extended controversy about the molecular pathophysiology of this disease. When the DM2 mutation was identified in 2001 as being a similarly untranslated CCTG expansion, the molecular and clinical parallels between DM1 and DM2 substantiated the role of a novel mechanism in generating the unusual constellation of clinical features seen in these diseases: the repeat expansions expressed at the RNA level alter RNA processing, at least in part by interfering with alternative splicing of other genes. For example, in both DM1 and DM2, altered splicing of chloride channel and insulin receptor transcripts leads to myotonia and insulin resistance, respectively. Although other mechanisms may underlie the differences between DM1 and DM2, the pathogenic effects of the RNA mechanism are now clear, which will facilitate development of appropriate treatments. [Copyright &y& Elsevier]

Microsatellite instability is a phenotype observed in tumors cells that have defects in DNA mismatch repair (MMR). Most markers used for detecting microsatellite instability are mono- and dinucleotide repeats, but one tetranucleotide repeat (MYCL1) has been reported to be useful for this purpose. The MYCL1 repeat is actually a complex repeat, made up of approximately 14 GAAA tetranucleotides plus various other GA-rich repeats. In order to determine the nature of the instability of the this sequence, we have used a frameshift-reversion assay in MMR-proficient and -deficient human cells to compare the mutation rates and the types of mutation of MYCL1 to those of the related simple repeats (GAAA)17, (GA)17, and (CA)17. We found that the complex repeat was the most stable of the repeats examined in cells deficient in MMR; the tetranucleotide was less stable, while the dinucleotides were the least stable. In MMR-proficient cells, the relative rates were reversed; the MYCL1 repeat was the least stable, the tetranucleotide was more stable, and the dinucleotides were the most stable. These results suggest that MYCL1 and the pure tetranucleotide have relatively low rates of errors during replication, but that the errors in these repeats are corrected less efficiently than those in the smaller repeats. Because of their high rate of instability in MMR-proficient cells, MYCL1 and other tetranucleotide repeats appear to lack specificity for detection of tumors with defective MMR. [Copyright &y& Elsevier]

The unambiguous identification of Central Valley spring-run chinook salmon has become imperative since their proposed listing in 1998. The accuracy of methods used to assign individuals to their stock of origin is critical for understanding juvenile migration patterns and determining the success of protection measures. Existing microsatellites discriminate between the endangered winter-run and other chinook but are insufficient to characterize phylogenetically less distinct runs. Here, we isolated and developed highly variable tetranucleotide microsatellites for the specific goal of increasing discriminatory power among closely related populations, providing a new power towards the reliable differentiation of nonwinter runs [ABSTRACT FROM AUTHOR]

Twelve highly polymorphic microsatellite markers were isolated and characterized for the frog Yerana yei. Loci were isolated from a genomic library from Y. yei enriched for (ATAG) repetitive elements. We designed primers that reliably amplified twelve polymorphic loci and tested them on 32 individuals from two populations. The number of alleles per locus ranged from 3-20, the observed and expected heterozygosity ranged within 0.500-1.000 and 0.752-0.964 respectively, and the polymorphic information content (PIC) value ranged from 0.683-0.930. These microsatellite markers could be valuable in future research concerning the conservation genetics and molecular ecology of this species. [ABSTRACT FROM AUTHOR]

Eleven microsatellite markers were isolated from an enriched library developed specifically for the tuco-tuco Ctenomys torquatus, using tri and tetranucleotide probes. Ten of these were successfully amplified, and only one was monomorphic for the populations that have so far been analyzed. Analysis of two different populations yielded a mean of 2.6 (Cachoeira do Sul-CAC) and 4.3 (Butiá-BUT) alleles per locus, with a range from 1 to 6. The means for observed and expected heterozygosity were also lower in the CAC population (Ho = 0.37 and He = 0.39), but in BUT they were 0.63 and 0.61 respectively. These are the first microsatellite markers reported for a Brazilian species of tuco-tuco, and will be applied to investigate the genetic structure of their populations in the widely impacted Pampa Biome. [ABSTRACT FROM AUTHOR]

Fifteen microsatellite loci are described for the lizard Podarcis lilfordi from the Balearic Islands. Loci were isolated from partial genomic libraries that had been enriched for AAAG and ACAG repeat sequence. All loci were highly polymorphic (six to 19 alleles) in a sample of 26 individuals from the island of Dragonera. Observed and expected heterozygosities ranged from 0.46 to 0.92 and 0.78 to 0.95, respectively. These loci will be used to study the evolutionary history of different forms, the occurrence of cross-islet introductions, and the validity of subspecific designations in this species . [ABSTRACT FROM AUTHOR]

Eight polymorphic microsatellite markers were developed for the grasshopper Mioscirtus wagneri. Polymorphism at these loci was evaluated in 25 individuals from Central Spain. The number of alleles per locus ranged from 3 to 9 and their observed and expected heterozygosities ranged from 0.28 to 0.80 and 0.25 to 0.84, respectively. All genotypic frequencies conformed to Hardy–Weinberg equilibrium expectations, with no evidence of genotypic linkage disequilibrium between any pair of loci. These loci will be highly useful for the study of the population genetic structure and diversity of this grasshopper species forming highly fragmented populations of great conservation concern. [ABSTRACT FROM AUTHOR]

We describe primers and PCR conditions to amplify nine new tetranucleotide loci and one new dinucleotide locus isolated from the strawberry poison frog (Oophaga pumilio). In 21 individuals from Costa Rica, the number of alleles ranged from 4 to 16, observed heterozygosities from 40 to 100%, and polymorphic information content ranged from 0.60 to 0.90 per locus. Evidence for linkage disequilibrium was found only between two loci, but this pattern was not found in other populations tested. All primer pairs cross-amplified in Oophaga vicentei from Panama. [ABSTRACT FROM AUTHOR]

Eleven microsatellite markers were developed for the Common ringtail possum, an arboreal marsupial abundant in fragmented forests of south-eastern Australia. Loci were highly polymorphic (4–32 alleles per locus) and heterozygosity ranged from 0.66 to 1. Two loci deviated significantly from Hardy–Weinberg equilibrium proportions, possibly because of low-frequency null alleles. These markers will be informative for examining patterns of gene flow, relatedness and mating systems within fragmented populations of the Common ringtail possum and have potential for use in other Pseudocheirids. [ABSTRACT FROM AUTHOR]

The article cites a study on the isolation and characterization of microsatellite loci in the longsnout catfish in China. The researchers isolated the microsatellite loci using an enrichment protocol. They extracted genomic DNA samples from muscle tissues using a standard proteinase K/phenol extraction protocol, which were pooled and digested with Sau3AI restriction enzyme. They designed forty primer sets through PRIMER 3 software and synthesized them. The researchers than screened the primers for polymorphism in 30 individuals from three locations. They concluded that the microsatellite loci will be useful for investigation of population structure, genetic diversity and phylogeography of longsnout catfish and other related species.

We describe eight new polymorphic tetranucleotide microsatellite loci isolated from the agile frog ( Rana dalmatina). In 25 individuals from the Nature Reserve Lüneburger Heide (Lower Saxony, Germany), the number of alleles per locus ranged from four to nine and average observed heterozygosities from 69.1% to 80.7%. No evidence for linkage disequilibrium was found and none of the loci showed significant deviation from Hardy–Weinberg expectations. These microsatellite DNA markers are suitable tools for addressing population genetics issues in this endangered species. [ABSTRACT FROM AUTHOR]

The finless porpoise, Neophocaena phocaenoides, is endemic to the coastal waters of the Indo-Pacific, ranging from the Persian Gulf to Japan. Nine tetranucleotide microsatellite loci were isolated from the finless porpoise (Neophocaena phocaenoides). Polymorphism of each locus was assessed in 39 unrelated individuals from the Yellow Sea and the South China Sea of the Chinese waters. The number of alleles per locus varied from 2 to 11. The ranges of observed and expected heterozygosity were 0.154-0.795 and 0.146-0.839, respectively. Cross-species amplification of these loci was tested in other cetacean species. These microsatellite markers described here will be suitable for population genetic studies of finless porpoises and other cetacean species. [ABSTRACT FROM AUTHOR]

Thirteen polymorphic microsatellite loci are described for the South American freshwater fish Percichthys trucha. Number of alleles per locus ranged from two to 21 and observed heterozygosities ranged from 0.304 to 0.915 in a sample of 47 individuals from four different sampling locations. [ABSTRACT FROM AUTHOR]

Thirteen polymorphic microsatellite loci were identified and developed for the coastal tailed frog, Ascaphus truei, from sites within the Olympic Peninsula of Washington, USA. These tetranucleotide repeat loci were highly variable, averaging 19 alleles per locus and expected heterozygosity of 0.91. In addition, these loci cross-amplify in the sister species, Ascaphus montanus. These markers will prove useful in identifying fine-scale genetic structure, as well as provide insight into the evolution and conservation of this group across fragmented landscapes. [ABSTRACT FROM AUTHOR]

We isolated 15 polymorphic microsatellite loci for the Baw Baw frog, Philoria frosti, from a genomic library enriched for (AAC)n and (AAAG)n repetitive elements. The number of alleles ranges from two to 14 per locus with the observed heterozygosity ranging from 0.04 to 0.96. [ABSTRACT FROM AUTHOR]

Eight microsatellite loci are described for the lizard Psammodromus algirus, a species widely used as a model in behavioural and ecological studies. All loci were highly polymorphic (six alleles or more per locus) in a sample of 24 individuals from a single site near Navacerrada (central Spain). Observed heterozygosity ranged from 0.29 to 0.96. These markers will be used to study mating strategies and determinants of reproductive success in this species. [ABSTRACT FROM AUTHOR]

Eight tetranucleotide microsatellite loci were isolated from the haplochromine cichlid fish, Pseudocrenilabrus multicolor victoriae, an important model species for studies in respiratory ecology, conservation, and evolution. We surveyed variation at these loci in 23 individuals from western Uganda, finding four to 19 alleles per locus and an average expected heterozygosity of 0.8575. These microsatellite loci will be used to examine gene flow and population structure in Ugandan P. m. victoriae. [ABSTRACT FROM AUTHOR]

We isolated 10 polymorphic microsatellite loci for the giant Australian cuttlefish, Sepia apama, from a genomic library enriched for (AAC) n and (AAAG) n repetitive elements. In the nine loci that reliably amplified, the number of alleles ranged from four to 12 per locus with observed heterozygosity ranging from 0.343 to 0.926. These and a previously developed set of six loci will be useful for analysis of genetic structure of populations and determining input to a massive seasonal breeding aggregation in northern Spencer Gulf, Australia. [ABSTRACT FROM AUTHOR]

Eight polymorphic microsatellite loci are described for the Iberian rock lizard species, Iberolacerta cyreni. Loci were isolated from a partial genomic library that had been enriched for AAAG repeat sequence. Number of alleles per locus ranged from two to 13 in a sample of 24 individuals from the Sierra de Guadarrama (central Spain). Observed heterozygosity ranged from 0.13 to 0.96. At least three loci were amplified and polymorphic in four other Iberian rock lizard species: Iberolacerta monticola, Iberolacerta bonnali, Iberolacerta aranica and Iberolacerta aurelioi. These markers will be used to study mating strategies and reproductive success in I. cyreni. [ABSTRACT FROM AUTHOR]

We have isolated 16 polymorphic microsatellite markers for the green-eyed tree frog, Litoria genimaculata, from genomic libraries enriched for (AAGG) n and (AAAG) n repetitive elements. The number of alleles ranges from four to 14 per locus with the observed heterozygosity ranging from 0.36 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and speciation. [ABSTRACT FROM AUTHOR]

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG) n, (AACC) n and (AAGG) n repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation. [ABSTRACT FROM AUTHOR]

Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedura reticulata. The species is endemic to the southwest of Western Australia, known to be a habitat specialist, and exposed to severe habitat fragmentation in the Western Australian wheatbelt. These highly polymorphic markers (two to 25 alleles) will facilitate the population genetic analyses of this species. In particular, they will enable estimates of gene flow between remnant populations — a critical element in assessing extinction dynamics in fragmented populations. [ABSTRACT FROM AUTHOR]

We have isolated 10 polymorphic microsatellite markers for the black-bellied seedcracker ( Pyrenestes ostrinus) from genomic libraries enriched either for (AAGG)n or (ATCT)n repetitive elements and characterized them in 39 individuals. The number of alleles ranged from two to 27 per locus with the observed heterozygosity ranging from 0.38 to 0.94. These markers will be useful for analysis of questions concerning parentage and population genetic structure. [ABSTRACT FROM AUTHOR]

We have isolated 13 polymorphic microsatellite markers for the pygmy kingfisher, Ceyx picta, from genomic libraries enriched for either (AAGG) n or (AACC) n repetitive elements. The number of alleles range from three to 15 per locus with an observed heterozygosity ranging from 0.46 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation. [ABSTRACT FROM AUTHOR]

We isolated 13 polymorphic microsatellite markers from the satin bowerbird, Ptilonorhynchus violaceus from a genomic library enriched in (AAGG)n repetitive elements and characterized them in 20 individuals. The number of alleles ranged from two to 18 per locus with the observed heterozygosity ranging from 0.15 to 1.00. These markers will be useful for analysing questions concerning parentage, population genetic structure and models of speciation. [ABSTRACT FROM AUTHOR]

Ten tetranucleotide microsatellite loci are characterized for guppy, Poecilia reticulata, an important model species in the study of adaptation and mating systems. Loci were isolated following a microsatellite enrichment procedure using probe-labelled magnetic beads. These microsatellites were designed for use in examining gene flow, reproductive isolation, and parentage within natural guppy populations. [ABSTRACT FROM AUTHOR]