Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci

Comparison of ddRAD derived genome-wide SSR markers in outbred and inbred Swiss albino mice

Genetic monitoring of inbred laboratory animal populations, developed at any laboratory, is one of the key elements of quality control and their colony management. The present study aimed to mine microsatellite (or SSR) markers from double digest restriction-site associated DNA (ddRAD) sequencing data of outbred foundation stock and F9 inbred generation of Swiss albino mice. Genomic DNA (12 F0 outbred and 12 F9 inbred) was isolated from tail tissue samples of F0 outbred and F9 inbred Swiss albino mice and processed for genotyping by sequencing using ddRAD platform. Double digestion of DNA was done using EcoR1 and Mse1 enzymes, and ddRAD data was subsequently analysed to identify and characterize microsatellite markers at genome-wide level. The analysis involved three key steps: pre-processing of reads, single sequence repeat (SSR) mining, and primer designing using different software i.e., PEAR, stacks and QDD. A total of 508 and 353 SSR motifs were identified in the outbred and inbred groups, respectively. Additionally, 828 and 551 primer sets were designed for the outbred and inbred groups, respectively. Furthermore, SSR loci specific to the outbred and inbred groups were also identified. Among these, eight SSR motifs (three each specific to the outbred and inbred groups, and two common) were validated using PCR amplification and gel electrophoresis. The designed primer sets successfully amplified respective SSR loci and produced reproducible bands on gel electrophoresis. The validated microsatellites were mapped to specific chromosomal locations using NCBI BLASTN with Mus musculus as the reference genome. In conclusion, the present study reports mining of SSR loci in outbred and inbred mice population. SSR loci were found to be more abundant and diverse in outbred population as compared to the inbred population. The unique SSRs identified for outbred and inbred groups will be helpful in checking the strain purity, marker assisted selection, and breeding programs without need for repeating the ddRAD sequencing in other laboratory animal population.

Genome-Wide Microsatellite Characterization and Molecular Marker Development of Himalayan Griffon (Gyps himalayensis)

The Himalayan griffon (Gyps himalayensis), an obligate scavenging bird in the Qinghai-Tibet Plateau, provides significant ecological services but is currently listed as near threatened. Despite their importance for conservation, genome-wide screening for microsatellites (or SSRs) in G. himalayensis and the development of corresponding molecular markers have been lacking. This study presents the first in-depth characterization of genome-wide microsatellites in G. himalayensis and the successful development of polymorphic SSR markers. A total of 240,741 microsatellite loci were detected in the G. himalayensis genome, with an average density of 202.2 SSRs per Mb, accounting for 0.44% of the genome. Mononucleotide repeats (53.2%) were the most prevalent among the different microsatellite motif types. Additionally, 100 primer pairs were initially identified, with 17 found to be polymorphic markers. These loci hold significant potential for revealing genotypic diversity in G. himalayensis, thereby laying a foundation for the conservation of this species.

Repeat expansion disorders

An increasing number of repeat expansion disorders have been found to cause both rare and common neurological disease. This is exemplified in recent discoveries of novel repeat expansions underlying a significant proportion of several late-onset neurodegenerative disorders, such as CANVAS (cerebellar ataxia, neuropathy and vestibular areflexia syndrome) and spinocerebellar ataxia type 27B. Most of the 60 described repeat expansion disorders to date are associated with neurological disease, providing substantial challenges for diagnosis, but also opportunities for management in a clinical neurology setting. Commonalities in clinical presentation, overarching diagnostic features and similarities in the approach to genetic testing justify considering these disorders collectively based on their unifying causative mechanism. In this review, we discuss the characteristics and diagnostic challenges of repeat expansion disorders for the neurologist and provide examples to highlight their clinical heterogeneity. With the ready availability of clinical-grade whole-genome sequencing for molecular diagnosis, we discuss the current approaches to testing for repeat expansion disorders and application in clinical practice.

Misconception of Schizophyllum commune strain 20R-7-F01 origin from subseafloor sediments over 20 million years old

Hole C0020A during Ocean Drilling Expedition 337 is the deepest hole in scientific ocean drilling (depth of 2466 m below the seafloor). The presence of microbial and fungal communities serves as firm evidence for life within sediments. The isolated from the core and cultivable in the laboratory strain S. commune 20R-7-F01, which has existed in a deep subseafloor environment for over 20 million years, is being considered a high-quality genome model for studying its evolution and environmental adaptation mechanism. We questioned the origin of the strain from the sediments using high mutagenic simple sequence repeats of DNA. The full genome analysis of mono-, di-, tri-, and tetra-motifs of DNA revealed no regularities in the quantitative distribution of motifs in different S. commune genomes. At of common trinucleotide motifs loci, strain 20R-7-F01 has the highest percentage of similarity (48.8%) among East Asian strains, which indicates an intensive genetic exchange. According to a multidimensional scaling of 1938 common simple sequence repeats of DNA loci, no signs were found that would indicate the spatial and temporal isolation of the 20R-7-F01 strain. The extreme insufficient of water, and oxygen, high temperature and pressure at the level of 2 km below the ocean floor, and the tetrapolar mating system make it impossible growth of mycelium with different nuclear status and formation of basidiocarps. The general obtained data confirm the terrestrial origin of S. commune strain 20R-7-F01 and the territory of the Far East of the Russian Federation (approximately Khabarovsk, Primorsky Krai) is the probable place of origin.

RNA gain-of-function mechanisms in short tandem repeat diseases

As adaptors, catalysts, guides, messengers, scaffolds, and structural components, RNAs perform an impressive array of cellular regulatory functions often by recruiting RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs). While this RNA-RBP interaction network allows precise RNP assembly and the subsequent structural dynamics required for normal functions, RNA motif mutations may trigger the formation of aberrant RNP structures that lead to cell dysfunction and disease. Here, we provide our perspective on one type of RNA motif mutation, RNA gain-of-function mutations associated with the abnormal expansion of short tandem repeats (STRs) that underlie multiple developmental and degenerative diseases. We first discuss our current understanding of normal polymorphic STR functions in RNA processing and localization followed by an assessment of the pathogenic roles of STR expansions in the neuromuscular disease myotonic dystrophy. We also highlight ongoing questions and controversies focused on STR-based insights into the regulation of nuclear RNA processing and export as well as the relevance of the RNA gain-of-function pathomechanism for other STR expansion disorders in both coding and noncoding genes.

Mosaicism in Short Tandem Repeat Disorders: A Clinical Perspective

Fragile X, Huntington disease, and myotonic dystrophy type 1 are prototypical examples of human disorders caused by short tandem repeat variation, repetitive nucleotide stretches that are highly mutable both in the germline and somatic tissue. As short tandem repeats are unstable, they can expand, contract, and acquire and lose epigenetic marks in somatic tissue. This means within an individual, the genotype and epigenetic state at these loci can vary considerably from cell to cell. This somatic mosaicism may play a key role in clinical pathogenesis, and yet, our understanding of mosaicism in driving clinical phenotypes in short tandem repeat disorders is only just emerging. This review focuses on these three relatively well-studied examples where, given the advent of new technologies and bioinformatic approaches, a critical role for mosaicism is coming into focus both with respect to cellular physiology and clinical phenotypes.

Copy Number Variations in Short Tandem Repeats Modulate Growth Traits in Penaeid Shrimp Through Neighboring Gene Regulation

Penaeid shrimp, with its genomes enriched in short tandem repeats (STRs), presents an ideal model for studying the distribution and biological functions of STRs. In this study, we systematically identified and compared STRs across multiple species, confirming a significantly higher prevalence of STRs (26-32%) in penaeid shrimp, which is markedly higher than that observed in other species, such as mammals (1.3-2.1%) and plants (0.21-0.73%). Further analysis utilizing a cohort of 326 Pacific white shrimp revealed a total of 672,507 high-quality STRs evenly distributed across the genome, with a notably lower frequency of SNPs within these STR regions. Focusing on growth traits as a case study, we conducted a genome-wide association study (GWAS) and correlation analyses to identify the regulatory relationship of STRs on complex traits. We discovered 84 STRs that showed a significant association with body weight. Interestingly, eleven of these STRs, with 81% being composed of an A/T base, showed a significant linear correlation with body weight, revealing the key role of A/T-related STRs in shrimp weight regulation. For instance, a significant association and a negative correlation were found between the copy number of the STR [(A)n] at NW_020872788.1:580574 and body weight. The cytokinesis protein 7-like (LOC113800912) gene, which contains this STR in its splice region, exhibits differential expression associated with body weight variation. These findings introduce a model for STR copy number regulation in non-human species, illuminating the influence of STRs on growth traits. It offers a valuable framework for investigating complex traits and the biological functions of STRs in agricultural animals.

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Identification of New Cultivar and Different Provenances of Dendrocalamus brandisii (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome

Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for distinguishing them. Although the new cultivar 'Manxie No.1' has significant differences in the branch characteristics and the color of shoot sheaths compared to the D. brandisii, it still lacks precise genetic information at the molecular level. This study identified 231,789 microsatellite markers based on the whole genome of D. brandisii and analyzed their type composition and distribution on chromosomes in detail. Then, using TP-M13-SSR fluorescence-labeling technology, 34 pairs of polymorphic primers were screened to identify the new cultivar 'Manxie No.1' and 11 different geographical provenances of D. brandisii. We also constructed DNA fingerprinting profiles for them. At the same time, we mapped six polymorphic SSRs to the gene of D. brandisii, among which SSR673 was mapped to DhB10G011540, which is related to plant immunity. The specific markers selected in this study can rapidly identify the provenances and the new cultivar of D. brandisii and help explore candidate genes related to some important traits.

TRGT-denovo: accurate detection of de novo tandem repeat mutations

Motivation

Identifying de novo tandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of the genome's TR regions for genotyping, simple de novo calling strategies often generate an excess of likely false positives, which can obscure true positive findings, particularly as the number of surveyed genomic regions increases.

Results

We developed TRGT-denovo, a computational method designed to accurately identify all types of de novo TR mutations-including expansions, contractions, and compositional changes-within family trios. TRGT-denovo directly interrogates read evidence, allowing for the detection of subtle variations often overlooked in variant call format (VCF) files. TRGT-denovo improves the precision and specificity of de novo mutation (DNM) identification, reducing the number of de novo candidates by an order of magnitude compared to genotype-based approaches. In our experiments involving eight rare disease trios previously studiedTRGT-denovo correctly reclassified all false positive DNM candidates as true negatives. Using an expanded repeat catalog, it identified new candidates, of which 95% (19/20) were experimentally validated, demonstrating its effectiveness in minimizing likely false positives while maintaining high sensitivity for true discoveries.

Availability and implementation

Built in Rust, TRGT-denovo is available as source code and a pre-compiled Linux binary along with a user guide at: https://github.com/PacificBiosciences/trgt-denovo.

Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs

Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.

Machado-Joseph disease in a Sudanese family links East Africa to Portuguese families and allows reestimation of ancestral age of the Machado lineage

Machado-Joseph disease (MJD/SCA3) is the most frequent dominant ataxia worldwide. It is caused by a (CAG)n expansion. MJD has two major ancestral backgrounds: the Machado lineage, found mainly in Portuguese families; and the Joseph lineage, present in all five continents, probably originating in Asia. MJD has been described in a few African and African-American families, but here we report the first diagnosed in Sudan to our knowledge. The proband presented with gait ataxia at age 24; followed by muscle cramps and spasticity, and dysarthria, by age 26; he was wheel-chair bound at 29 years of age. His brother had gait problems from age 20 years and, by age 21, lost the ability to run, showed dysarthria and muscle cramps. To assess the mutational origin of this family, we genotyped 30 SNPs and 7 STRs flanking the ATXN3_CAG repeat in three siblings and the non-transmitting father. We compared the MJD haplotype segregating in the family with our cohort of MJD families from diverse populations. Unlike all other known families of African origin, the Machado lineage was observed in Sudan, being shared with 86 Portuguese, 2 Spanish and 2 North-American families. The STR-based haplotype of Sudanese patients, however, was distinct, being four steps (2 STR mutations and 2 recombinations) away from the founder haplotype shared by 47 families, all of Portuguese extraction. Based on the phylogenetic network constructed with all MJD families of the Machado lineage, we estimated a common ancestry at 3211 ± 693 years ago.

The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents

The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.

Postglacial phylogeography, admixture, and evolution of red spruce (Picea rubens Sarg.) in Eastern North America

Climate change is a major evolutionary force that can affect the structure of forest ecosystems worldwide. Red spruce (Picea rubens Sarg.) has recently faced a considerable decline in the Southern Appalachians due to rapid environmental change, which includes historical land use, and atmospheric pollution. In the northern part of its range, red spruce is sympatric with closely related black spruce (Picea mariana (Mill.) B.S.P.), where introgressive hybridization commonly occurs. We investigated range-wide population genetic diversity and structure and inferred postglacial migration patterns and evolution of red spruce using nuclear microsatellites. Moderate genetic diversity and differentiation were observed in red spruce. Genetic distance, maximum likelihood and Bayesian analyses identified two distinct population clusters: southern glacial populations, and the evolutionarily younger northern populations. Approximate Bayesian computation suggests that patterns of admixture are the result of divergence of red spruce and black spruce from a common ancestor and then introgressive hybridization during post-glacial migration. Genetic diversity, effective population size (Ne) and genetic differentiation were higher in the northern than in the southern populations. Our results along with previously available fossil data suggest that Picea rubens and Picea mariana occupied separate southern refugia during the last glaciation. After initial expansion in the early Holocene, these two species faced a period of recession and formed a secondary coastal refugium, where introgressive hybridization occurred, and then both species migrated northward. As a result, various levels of black spruce alleles are present in the sympatric red spruce populations. Allopatric populations of P. rubens and P. mariana have many species-specific alleles and much fewer alleles from common ancestry. The pure southern red spruce populations may become critically endangered under projected climate change conditions as their ecological niche may disappear.

The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats

Microsatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs' specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) - the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.

Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera)

BACKGROUND

Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance and wide genome coverage. We characterised microsatellites in the genomes and genes of two bat species, Pteropus vampyrus and Miniopterus natalensis. This characterisation was used for gene ontology analysis and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment of coding sequences (CDS).

RESULTS

Compared to M. natalensis, the genome size of P. vampyrus is larger and contains more microsatellites, but the total diversity of both species is similar. Mononucleotide and dinucleotide repeats were the most diverse in the genome of the two species. In each bat species, the microsatellite bias was obvious. The microsatellites with the largest number of repeat motifs in P. vampyrus from mononucleotide to hexanucleotide were (A)_n, (AC)_n, (CAA)_n, (AAAC)_n, (AACAA)_n and (AAACAA)_n, with frequencies of 97.94%, 58.75%, 30.53%, 22.82%, 54.68% and 22.87%, respectively, while in M. natalensis were (A)_n, (AC)_n, (TAT)_n, (TTTA)_n, (AACAA)_n and (GAGAGG)_n, with of 92.00%, 34.08%, 40.36%, 21.83%, 25.42% and 12.79%, respectively. In both species, the diversity of microsatellites was highest in intergenic regions, followed by intronic, untranslated and exonic regions and lowest in coding regions. Location analysis indicated that microsatellites were mainly concentrated at both ends of the genes. Microsatellites in the CDS are thus subject to higher selective pressure. In the GO analysis, two unique GO terms were found only in P. vampyrus and M. natalensis, respectively. In KEGG enriched pathway, the biosynthesis of other secondary metabolites and metabolism of other amino acids in metabolism pathways were present only in M. natalensis. The combined biological process, cellular components and molecular function ontology are reflected in the GO analysis and six functional enrichments in KEGG annotation, suggesting advantageous mutations during species evolution.

CONCLUSIONS

Our study gives a comparative characterization of the genomes of microsatellites composition in the two bat species. And also allow further study on the effect of microsatellites on gene function as well as provide an insight into the molecular basis for species adaptation to new and changing environments.

The mutational dynamics of short tandem repeats in large, multigenerational families

BACKGROUND

Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. These pedigrees contain both sets of grandparents, the parents, and an average of 9 grandchildren per family.

RESULTS

We use HipSTR to identify de novo STR mutations in the 2nd generation of these pedigrees and require transmission to the third generation for validation. Analyzing approximately 1.6 million STR loci, we estimate the empirical de novo STR mutation rate to be 5.24 × 10^-5 mutations per locus per generation. Perfect repeats mutate about 2 × more often than imperfect repeats. De novo STRs are significantly enriched in Alu elements.

CONCLUSIONS

Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. Phasing these mutations to the parent of origin shows that parental transmission biases vary among families. We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants.

Genome-wide survey and genetic characteristics of Ophichthus evermanni based on Illumina sequencing platform

Ophichthidae fishes limit to continental shelf of all tropical and subtropical oceans and contain more than 350 species, representing the greatest specialization diversity in the order Anguiliformes. In the present study, we conducted a genome survey sequencing (GSS) analysis of Ophichthus evermanni by Illumina sequencing platform to briefly reveal its genomic characteristics and phylogenetic relationship. The first de novo assembled 1.97 Gb draft genome of O. evermanni was predicted based on K-mer analysis without obvious nucleotide bias. The heterozygosity ratio was 0.70%, and the sequence repeat ratio was calculated to be 43.30%. A total of 9016 putative coding genes were successfully predicted, in which 3587 unigenes were identified by gene ontology (GO) analysis and 4375 unigenes were classified into cluster of orthologous groups for enkaryotic complete genomes (KOG) functional categories. About 2,812,813 microsatellite motifs including mono-, di-, tri-, tetra-, penta- and hexanucleotide motifs were identified, with an occurrence frequency of 23.32%. The most abundant type was dinucleotide repeat motifs, accounting for 49.19% of the total repeat types. The mitochondrial genome, as a byproduct of GSS, was assembled to investigate the evolutionary relationships between O. evermanni and its relatives. Bayesian inference (BI) phylogenetic tree inferring from concatenated 12 protein-coding genes (PCGs) showed complicated relationships among Ophichthidae species, indicating a polyphyletic origin of the family. The results would achieve more thorough genetic information of snake eels and provide a theoretical basis and reference for further genome-wide analysis of O. evermanni.

CLCC1 c. 75C>A Mutation in Pakistani Derived Retinitis Pigmentosa Families Likely Originated With a Single Founder Mutation 2,000-5,000 Years Ago

Background: A CLCC1 c. 75C > A (p.D25E) mutation has been associated with autosomal recessive pigmentosa in patients in and from Pakistan. CLCC1 is ubiquitously expressed, and knockout models of this gene in zebrafish and mice are lethal in the embryonic period, suggesting that possible retinitis pigmentosa mutations in this gene might be limited to those leaving partial activity. In agreement with this hypothesis, the mutation is the only CLCC1 mutation associated with retinitis pigmentosa to date, and all identified patients with this mutation share a common SNP haplotype surrounding the mutation, suggesting a common founder.

Methods: SNPs were genotyped by a combination of WGS and Sanger sequencing. The original founder haplotype, and recombination pathways were delineated by examination to minimize recombination events. Mutation age was estimated by four methods including an explicit solution, an iterative approach, a Bayesian approach and an approach based solely on ancestral segment lengths using high density SNP data.

Results: All members of each of the nine families studied shared a single autozygous SNP haplotype for the CLCC1 region ranging from approximately 1–3.5 Mb in size. The haplotypes shared by the families could be derived from a single putative ancestral haplotype with at most two recombination events. Based on the haplotype and Gamma analysis, the estimated age of the founding mutation varied from 79 to 196 generations, or approximately 2,000–5,000 years, depending on the markers used in the estimate. The DMLE (Bayesian) estimates ranged from 2,160 generations assuming a population growth rate of 0–309 generations assuming a population growth rate of 2% with broad 95% confidence intervals.

Conclusion: These results provide insight into the origin of the CLCC1 mutation in the Pakistan population. This mutation is estimated to have occurred 2000–5,000 years ago and has been transmitted to affected families of Pakistani origin in geographically dispersed locations around the world. This is the only mutation in CLCC1 identified to date, suggesting that the CLCC1 gene is under a high degree of constraint, probably imposed by functional requirements for this gene during embryonic development.

Design of microsatellite markers for Schizophyllum commune (Agaricales, Basidiomycota) based on analysis of its genome

Simple sequence repeats of DNA (SSRs) are the most popular source of genetic markers used in population genetics, phylogenetics, and genetic mapping. A large number of nucleotide repeats enriched in G and C were identified. 336 mononucleotide motifs with more than ten repeats were recorded. 2020 nucleotide repeats were identified, of which 97.4% are di- (68.2%) and trinucleotides (29.2%). The total number of unique SSR loci, to which primers pairs were developed, was 1920. PCR primer sequences for unique SSR loci of the S. commune genome are presented. Of the twenty-two SSR markers synthesized for the S. commune genome, amplicons formed 64% on freshly isolated DNA samples.

Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad

Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (P_ST-F_ST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. P_ST-F_ST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.

How natural selection shapes genetic differentiation in the MHC region: A case study with Native Americans

The Human Leukocyte Antigen (HLA) loci are extremely well documented targets of balancing selection, yet few studies have explored how selection affects population differentiation at these loci. In the present study we investigate genetic differentiation at HLA genes by comparing differentiation at microsatellites distributed genomewide to those in the MHC region. Our study uses a sample of 494 individuals from 30 human populations, 28 of which are Native Americans, all of whom were typed for genomewide and MHC region microsatellites. We find greater differentiation in the MHC than in the remainder of the genome (FST-MHC = 0.130 and FST-Genomic = 0.087), and use a permutation approach to show that this difference is statistically significant, and not accounted for by confounding factors. This finding lies in the opposite direction to the expectation that balancing selection reduces population differentiation. We interpret our findings as evidence that selection favors different sets of alleles in distinct localities, leading to increased differentiation. Thus, balancing selection at HLA genes simultaneously increases intra-population polymorphism and inter-population differentiation in Native Americans.

Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions

BACKGROUND

Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species.

RESULTS

Here, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1-6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems.

CONCLUSIONS

Our data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.

Identification and characterization of microsatellite markers for population genetic studies of Panstrongylus megistus (Burmeister, 1835) (Triatominae: Reduviidae)

Background

Panstrongylus megistus is the most important vector of Chagas disease in Brazil. Studies show that the principal factor hindering the control of triatomines is reinfestation of houses previously treated with insecticides. Studies at the microgeographic level are therefore necessary to better understand these events. However, an efficient molecular marker is not yet available for carrying out such analyses in this species. The aim of the present study was to identify and characterize microsatellite loci for future population genetic studies of P. megistus.

Methods

This study work consisted of five stages: (i) sequencing of genomic DNA; (ii) assembly and selection of contigs containing microsatellites; (iii) validation of amplification and evaluation of polymorphic loci; (iv) standardization of the polymorphic loci; and (v) verification of cross-amplification with other triatomine species.

Results

Sequencing of males and females generated 7,908,463 contigs with a total length of 2,043,422,613 bp. A total of 2,043,690 regions with microsatellites in 1,441,091 contigs were obtained, with mononucleotide repeats being the most abundant class. From a panel of 96 loci it was possible to visualize polymorphisms in 64.55% of the loci. Of the 20 loci genotyped, the number of alleles varied from two to nine with an average of 4.9. Cross-amplification with other species of triatomines was observed in 13 of the loci.

Conclusions

Due to the high number of alleles encountered, polymorphism and the capacity to amplify from geographically distant populations, the microsatellites described here show promise for utilization in population genetic studies of P. megistus.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04771-w.

Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids

Homopeptides (runs of one amino-acid type) are evolutionarily important since they are prone to expand/contract during DNA replication, recombination and repair. To gain insight into the genomic/proteomic traits driving their variation, we analyzed how homopeptides and homocodons (which are pure codon repeats) vary across 405 Dikarya, and probed their linkage to genome GC/AT bias and other factors. We find that amino-acid homopeptide frequencies vary diversely between clades, with the AT-rich Saccharomycotina trending distinctly. As organisms evolve, homocodon and homopeptide numbers are majorly coupled to GC/AT-bias, exhibiting a bi-furcated correlation with degree of AT- or GC-bias. Mid-GC/AT genomes tend to have markedly fewer simply because they are mid-GC/AT. Despite these trends, homopeptides tend to be GC-biased relative to other parts of coding sequences, even in AT-rich organisms, indicating they absorb AT bias less or are inherently more GC-rich. The most frequent and most variable homopeptide amino acids favour intrinsic disorder, and there are an opposing correlation and anti-correlation versus homopeptide levels for intrinsic disorder and structured-domain content respectively. Specific homopeptides show unique behaviours that we suggest are linked to inherent slippage probabilities during DNA replication and recombination, such as poly-glutamine, which is an evolutionarily very variable homopeptide with a codon repertoire unbiased for GC/AT, and poly-lysine whose homocodons are overwhelmingly made from the codon AAG.

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs). We report a family-based study of germline mutations among 9,599 human genomes from 33 multigenerational CEPH-Utah families and 2,384 families from the Simons Foundation Autism Research Initiative. We find that de novo structural mutations detected by alignment-based, short-read WGS occur at an overall rate of at least 0.160 events per genome in unaffected individuals, and we observe a significantly higher rate (0.206 per genome) in ASD-affected individuals. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and we predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction, we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations and that these mechanisms most likely have markedly different rates and selective pressures than those leading to point mutations.

Comparison of MultiLocus Sequence Typing (MLST) and Microsatellite Length Polymorphism (MLP) for Pneumocystis jirovecii genotyping

Pneumocystis jirovecii is an atypical fungus responsible for severe respiratory infections, often reported as local outbreaks in immunocompromised patients. Epidemiology of this infection, and transmission risk emphasises the need for developing genotyping techniques. Currently, two methods have emerged: Multilocus Sequence typing (MLST) and microsatellite length polymorphism (MLP). Here we compare an MLST strategy, including 2 nuclear loci and 2 mitochondrial loci, with an MLP strategy including 6 nuclear markers using 37 clinical PCR-positive respiratory samples from two French hospitals. Pneumocystis jirovecii MLST and MLP provided 30 and 35 different genotypes respectively. A higher number of mixed infections was detected using MLP (48.6% vs. 13.5% respectively; p = 0.002). Only one MLP marker (STR279) was statistically associated with the geographical origin of samples. Haplotype network inferred using the available genotypes yielded expanded network for MLP, characterized by more mutational steps as compared to MLST, suggesting that the MLP approach is more resolutive to separate genotypes. The correlation between genetic distances calculated based on MLST and MLP was modest with a R² value = 0.32 (p < 0.001). Finally, both genotyping methods fulfilled important criteria: (i) a discriminatory power from 97.5% to 99.5% and (ii) being quick and convenient genotyping tools. While MLP appeared highly resolutive regarding genotypes mixture within samples, using one genotyping method rather than the other may also depend on the context (i.e., MLST for investigation of suspected clonal outbreaks versus MLP for population structure study) as well as local facilities.

Use of Eucalyptus DNA profiling in a case of illegal logging

Eucalyptus is grown world-wide for paper pulp, solid wood, and other industries. Theft or illegal cutting of the trees causes hardship to owners of plantations and countries whose economies rely on the sale and export of eucalyptus products. Unfortunately, many of these crimes go unpunished due to lack of forensic evidence. Over 1200 short tandem repeat (STR) markers have been identified in the genomes of genus Eucalyptus and related species. However, their importance and utility in aiding forensic investigations of wood theft have not been explored. This study evaluated nine STRs for diversity and applied them to a case involving suspected wood theft. As expected, three dinucleotide STR markers showed greater variability but resulted in harder to interpret profiles. Four STR tetranucleotide markers evaluated in this study were found to contain additional repeat structures (dinucleotide or trinucleotide) that enhanced their variability but resulted in profiles with peaks at multiple stutter positions and heterozygote peak imbalance. The most promising STR markers were EGM37 and EMBRA 1374. Though less variable, they yielded robust and reproducible DNA profiles. All nine STR markers were applied to a case involving suspected wood theft. Samples were collected from seized wood and from remaining stumps in a plantation. No DNA match was found, thus eliminating the evidence samples as having originated from the forest. Dendrochronology analysis also resulted in an exclusion. This case study represents the first report using STR markers in any eucalyptus species to provide DNA evidence in a case of suspected wood theft.

Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r² = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of F_ST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.

Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset

Short Tandem Repeats (STRs) are a type of DNA polymorphism. This study considers discriminant analysis to determine the population of test individuals using an STR database containing the lengths of STRs observed at more than one locus. The discriminant method based on the Bayes factor is discussed and an improved method is proposed. The main issues are to develop a method that is relatively robust to sample size imbalance, identify a procedure to select loci, and treat the parameter in the prior distribution. A previous study achieved a classification accuracy of 0.748 for the g-mean (geometric mean of classification accuracies for two populations) and 0.867 for the AUC (area under the receiver operating characteristic curve). We improve the maximum values for the g-mean to 0.830 and the AUC to 0.935. Computer simulations indicate that the previous method is susceptible to sample size imbalance, whereas the proposed method is more robust while achieving almost identical classification accuracy. Furthermore, the results confirm that threshold adjustment is an effective countermeasure to sample size imbalance.

Distribution of the CAG Triplet Repeat in ATXN1, ATXN3, and CACNA1A Loci in Peruvian Population

Spinocerebellar ataxia subtypes 1, 3, and 6 (SCA1, MJD/SCA3, and SCA6) are among the most prevalent autosomal dominant cerebellar ataxias worldwide, but their relative frequencies in Peru are low. Frequency of large normal (LN) alleles at spinocerebellar ataxia-causative genes has been proposed to be associated with disease prevalence. To investigate the allelic distribution of the CAG repeat in ATXN1, ATXN3, and CACNA1A genes in a Peruvian mestizo population and examine their association with the relative frequency of SCA1, MJD/SCA3, and SCA6 across populations. We genotyped 213 healthy mestizo individuals from Northern Lima, Peru, for ATXN1, ATXN3, and CACNA1A using polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE). We compared the frequency of LN alleles and relative disease frequency between populations. We also tested 40 samples for CAT repeat interruptions within the CAG tract of ATXN1. We found no association between disease frequency and population frequency of LN alleles at ATXN1 and ATXN3. All 40 ATXN1 samples tested for CAT interruptions were positive. Frequency of LN alleles at CACNA1A correlates with SCA6 frequency across several populations, but this effect was largely driven by data from a single population. Low frequency of SCA1 and MJD/SCA3 in Peru is not explained by frequency of LN alleles at ATXN1 and ATXN3, respectively. The observed correlation between CACNA1A LN alleles and SCA6 frequency requires further assessment.

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.

Human-specific tandem repeat expansion and differential gene expression during primate evolution

Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework to model the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A, CACNA1C). We show that short interspersed nuclear element-VNTR-Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissue-specific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.

Development of a multiplex, PCR-based genotyping assay for African and Asian elephants for forensic purposes

Wildlife crimes and the threats they present to elephant populations raise the need to develop and implement DNA-based methodology as an aid for wildlife forensic investigations and conservation efforts. This study describes the development of a tetra-nucleotide repeat STR multiplex, genotyping assay that will identify Asian elephant (Elephas maximus) and African elephant (Loxodonta africana) DNA. The assay targets six tetra-nucleotide STRs and two sex-typing markers simultaneously in both genera of elephants, a first for elephant genotyping assays. The developed assay has potential application in wildlife investigations to associate a biological sample to a particular individual elephant and additionally in conservation science for population management.

Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species

Background

Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites.

Results

The results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci.

Conclusions

These observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5329-y) contains supplementary material, which is available to authorized users.

A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species

Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.

Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here, we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA-Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and nondifferentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC and AAC in DE transcripts, are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.

Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres

The genomes of human herpesvirus 6A (HHV-6A) and HHV-6B have the capacity to integrate into telomeres, the essential capping structures of chromosomes that play roles in cancer and ageing. About 1% of people worldwide are carriers of chromosomally integrated HHV-6 (ciHHV-6), which is inherited as a genetic trait. Understanding the consequences of integration for the evolution of the viral genome, for the telomere, and for the risk of disease associated with carrier status is hampered by a lack of knowledge about ciHHV-6 genomes. Here, we report an analysis of 28 ciHHV-6 genomes and show that they are significantly divergent from the few modern nonintegrated HHV-6 strains for which complete sequences are currently available. In addition, ciHHV-6B genomes in Europeans are more closely related to each other than to ciHHV-6B genomes from China and Pakistan, suggesting regional variation of the trait. Remarkably, at least one group of European ciHHV-6B carriers has inherited the same ciHHV-6B genome, integrated in the same telomere allele, from a common ancestor estimated to have existed 24,500 ± 10,600 years ago. Despite the antiquity of some, and possibly most, germ line HHV-6 integrations, the majority of ciHHV-6B (95%) and ciHHV-6A (72%) genomes contain a full set of intact viral genes and therefore appear to have the capacity for viral gene expression and full reactivation.

IMPORTANCE Inheritance of HHV-6A or HHV-6B integrated into a telomere occurs at a low frequency in most populations studied to date, but its characteristics are poorly understood. However, stratification of ciHHV-6 carriers in modern populations due to common ancestry is an important consideration for genome-wide association studies that aim to identify disease risks for these people. Here, we present full sequence analysis of 28 ciHHV-6 genomes and show that ciHHV-6B in many carriers with European ancestry most likely originated from ancient integration events in a small number of ancestors. We propose that ancient ancestral origins for ciHHV-6A and ciHHV-6B are also likely in other populations. Moreover, despite their antiquity, all of the ciHHV-6 genomes appear to retain the capacity to express viral genes, and most are predicted to be capable of full viral reactivation. These discoveries represent potentially important considerations in immunocompromised patients, in particular in organ transplantation and in stem cell therapy.

Population Structure of the Blue Swimmer Crab Portunus pelagicus in Coastal Areas of Malaysia Inferred from Microsatellites

Chuan Jian Chai, Yuzine Bin Esa, Muhammad Fadhil Syukri Ismail, and Mohd. Salleh Kamarudin (2017) Portunus pelagicus, distributed throughout the Indo-West Paci c region, is one of the large and edible species of blue swimmer crabs. Increasing demand for the frozen and canned crabmeat industry worldwide has now relied mainly on P. pelagicus which in turn generates splendid income for the fisherman communities. In the present study, the population genetic structure of P. pelagicus was examined using six pairs of microsatellite loci. A total of 87 crab samples were collected from five different coastal areas of Malaysia. Genomic DNA was extracted from each sample for polymerase chain reaction (PCR) amplification and fragment analysis. Four out of six microsatellite primers revealed polymorphic loci in P. pelagicus sampled. The number of alleles per locus in P. pelagicus ranged from 14 to 34. Microsatellites analyses indicated low levels of genetic differentiation among the P. pelagicus populations. The average observed heterozygosity (HO = 0.48) obtained was lower than the standard heterozygosity found in most marine populations (H _O = 0.79). The high F _IS values (mean F _IS = 0.4756) and low F _ST values (mean F _ST = 0.0413) also suggested the existence of inbreeding among different populations of P. pelagicus. In conclusion, this study was able to shed light on the population structure of P. pelagicus in coastal areas of Malaysia.

RNA biology of disease-associated microsatellite repeat expansions

Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.

Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

BACKGROUND

Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags) molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants.

METHODS

In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX.

RESULTS

A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO) classifications and Cluster of Orthologous Groups (COG), respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with stable, highly polymorphic loci were selected for polymorphism screening. There was a total of 65 alleles, with 2-6 alleles at each locus. Primarily due to the unique biological characteristics of plants, the HE (0-0.196), HO (0.082-0.14) and PIC (0-0.155) per locus were very low. The functional annotation distribution centered on ESTs containing di- and tri-nucleotide SSRs, and the ESTs containing primers BC2, BC4 and BC12 were annotated to vegetative dehydration/desiccation pathways.

DISCUSSION

This work is the first genetic study of B. clarkeana as a new plant resource of DT genes. A substantial number of transcriptome sequences were generated in this study. These sequences are valuable resources for gene annotation and discovery as well as molecular marker development. These sequences could also provide a valuable basis for future molecular studies of B. clarkeana.

Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented by Anatolia, Italy and Iberia. Understanding modern patterns of diversity depends on understanding these historical population dynamics. Traditionally, European fallow deer (Dama dama dama) are thought to have been restricted to refugia in Anatolia and possibly Sicily and the Balkans. However, the distribution of this species was also greatly influenced by human-mediated translocations. We focus on fallow deer to better understand the relative influence of these natural and anthropogenic processes. We compared modern fallow deer putative populations across a broad geographic range using microsatellite and mitochondrial DNA loci. The results revealed highly insular populations, depauperate of genetic variation and significantly differentiated from each other. This is consistent with the expectations of drift acting on populations founded by small numbers of individuals, and reflects known founder populations in the north. However, there was also evidence for differentiation among (but not within) physically isolated regions in the south, including Iberia. In those regions we find evidence for a stronger influence from natural processes than may be expected for a species with such strong, known anthropogenic influence.

varver: a database of microsatellite variation in vertebrates

Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and F_ST ). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.

Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing

Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis. The INDEL marker allelic states range in size from 2 to 6 base pairs, enabling small amplicon size. In addition, heterozygote balance may be increased by minimizing preferential amplification of the smaller allele, as is more common with STR markers. Multiplexing a large number of INDELs allows for generating panels with high discrimination power. The Nextera™ Rapid Capture Custom Enrichment Kit (Illumina, Inc., San Diego, CA) and massively parallel sequencing (MPS) on the Illumina MiSeq were used to sequence 68 well-characterized INDELs in four major US population groups. In addition, the STR Allele Identification Tool: Razor (STRait Razor) was used in a novel way to analyze INDEL sequences and detect adjacent single nucleotide polymorphisms (SNPs) and other polymorphisms. This application enabled the discovery of unique allelic variants, which increased the discrimination power and decreased the single-locus random match probabilities (RMPs) of 22 of these well-characterized INDELs which can be considered as microhaplotypes. These findings suggest that additional microhaplotypes containing human identification (HID) INDELs may exist elsewhere in the genome.

Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime

Microsatellites are DNA sequences consisting of repeated, short (1–6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.

Population genetic structure and temporal stability among Trypanosoma brucei rhodesiense isolates in Uganda

Background

The population structure and role of genetic exchange in African trypanosomes have been previously analyzed albeit with contradictory findings. To further investigate the role of genetic polymorphism on the population genetic structure of Trypanosoma b. rhodesiense, we hypothesized that parasite genotypes are clonal and stable over time.

Methods

We have undertaken a microsatellite marker analysis of T. b. rhodesiense isolates in a relatively new active HAT focus in Uganda (Kaberamaido-Dokolo-Amolatar) over a six-year period (2006–2012). We amplified six microsatellite markers by PCR directly from blood spotted FTA cards following whole genome amplification.

Results

The majority of loci demonstrated an excess of heterozygosity (Ho > He, F_IS < 0). We identified 26 unique genotypes among the 57 isolates, accounting for 45.6 % genotypic polymorphism. The presence of a high proportion of samples with repeated genotypes (54.4 %, 31/57), disagreement with Hardy-Weinberg equilibrium, and significant linkage disequilibrium between loci pairs, provide evidence that T. b. rhodesiense isolates from this focus are clonal. Our results show low values of F_ST’ (0–0.115) indicating negligible genetic differentiation across temporal isolates. Furthermore, predominant genotypes isolated in 2006 were still detectable in 2012.

Conclusions

Our findings confirm the notion that endemicity is maintained by stable genotypes rather than an influx of new genotypes. Our results have considerable importance in understanding and tracking the spread of sleeping sickness with significant implication to disease control.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1542-1) contains supplementary material, which is available to authorized users.