Microsatellites: consensus and controversy

What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools

Microsatellites, also known as SSR or STR, are essential molecular markers in genomic research, playing crucial roles in genetic mapping, population genetics, and evolutionary studies. Their applications range from plant breeding to forensics, highlighting their diverse utility across disciplines. Despite their widespread use, traditional methods for SSR analysis are often laborious and time-consuming, requiring significant resources and expertise. To address these challenges, a variety of computational tools for SSR analysis have been developed, offering faster and more efficient alternatives to traditional methods. However, selecting the most appropriate tool can be daunting due to rapid technological advancements and the sheer number of options available. This study presents a comprehensive review and analysis of 74 SSR tools, aiming to provide researchers with a valuable resource for SSR analysis tool selection. The methodology employed includes thorough literature reviews, detailed tool comparisons, and in-depth analyses of tool functionality. By compiling and analyzing these tools, this study not only advances the field of genomic research but also contributes to the broader scientific community by facilitating informed decision-making in the selection of SSR analysis tools. Researchers seeking to understand SSRs and select the most appropriate tools for their projects will benefit from this comprehensive guide. Overall, this study enhances our understanding of SSR analysis tools, paving the way for more efficient and effective SSR research in various fields of study.

Developing Strain-Specific Simple Sequence Repeat (SSR) Markers for Chlorella sorokiniana

Chlorella sorokiniana green microalga offers many environmentally friendly applications, including wastewater treatment, biofertilizers, animal feed, and biofuel production. Different strains of C. sorokiniana have unique properties that may suit one application but not another. There is a need to distinguish between the many available strains of C. sorokiniana to choose the one that best fits the application. Consequently, our research goal was to develop strain-specific simple sequence repeat (SSR) markers to differentiate between the different strains. Seventeen markers spanning ten out of the twelve chromosomes of the C. sorokiniana genome were developed and validated on eight different strains from culture collections and our lab, and were then analyzed by fragment analysis. The results demonstrate the potential of these polymorphic markers to detect the genetic differences between the strains of C. sorokiniana, and to serve as useful tools for the intra-species population genetic analysis and conservation genetics studies of C. sorokiniana.

Genome-wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): Survey and analysis of their abundance and diversity

The cobia Rachycentron canadum, mainly distributed in the warm waters of tropical and subtropical regions around the world, remains a fish of considerable economic importance. Detailed diversity and the number of microsatellite sequences in the cobia genome are still unintelligible. The primary aim of this work was to identify and quantify the miscellaneous SSR sequences in the cobia genome. More than 280,000 sequences were sequenced and screened using next-generation sequencing technology and microsatellite identification. Perfect mononucleotide repeats, dinucleotide microsatellites, and trinucleotide microsatellites contain (A)10 /(T)10 , (AC)6 /(TG)6 , and (AAT)5-32 as the largest number of motifs in each type of microsatellite, respectively. The tetranucleotide and pentanucleotide microsatellites (TTM and PTM) consist of the largest number of motifs of both (ATCT)5-32 and (TCAT)5-31 in TTMs, and (CTCTC)5-9 in PTMs, whereas the hexanucleotide microsatellites are rarely observed in the cobia genome. All c. 38000 sequences of composite microsatellites are extremely diverse, including compound (11.71%), interrupted compound (71.77%), complex (0.45%), and interrupted complex (16.07%). In this study, we developed a convenient and useful recording system for writing down and categorizing diverse composite microsatellite types. This system will provide great support for exploring repeat origins, evolutionary mechanisms, and the application of polymorphic microsatellites.

Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.

Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas (Vicugna pacos) in Southern Peru

The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each population, respectively. A total of 168 alpaca biological samples were outsourced to Peruvian laboratories for DNA extraction and genotyping. For genetic diversity, observed heterozygosity (H_o), expected heterozygosity (H_e), polymorphism information content (PIC), and fixation indices values were estimated. An admixture analysis was performed for the population structure analysis. Different programs were used for these estimations. In total, 133 (Ajoyani) and 129 (Quimsachata) alleles were found, with a range of 4 to 17 by locus. The mean H_O, H_E, and PIC per marker for Ajoyani were 0.764 ± 0.112, 0.771 ± 0.1, and 0.736; for Quimsachata, they were 0.783 ± 0.087, 0.773 ± 0.095, and 0.738, respectively. The population structure showed no structure with K = 2. This study provides useful indicators for the creation of appropriate alpaca conservation programs.

Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook

A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.

Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers

Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields under limited water supplies. A candidate gene approach was used to develop functional simple sequence repeat (SSR) markers for association studies in potato with the aim to enhance breeding for drought tolerance. SSR primer combinations, mostly surrounding interrupted complex and compound repeats, were derived from 103 candidate genes for drought tolerance. Validation of the SSRs was performed in an association panel representing 34 mainly starch potato cultivars. Seventy-five out of 154 SSR primer combinations (49%) resulted in polymorphic, highly reproducible banding patterns with polymorphic information content (PIC) values between 0.11 and 0.90. Five SSR markers identified allelic differences between the potato cultivars that showed significant associations with drought sensitivity. In all cases, the group of drought-sensitive cultivars showed predominantly an additional allele, indicating that selection against these alleles by marker-assisted breeding might confer drought tolerance. Further studies of these differences in the candidate genes will elucidate their role for an improved performance of potatoes under water-limited conditions.

Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep

Simple Summary

Parentage misassignments directly affect genetic gain in traditional breeding programs. The use of genetic markers facilitates parentage verification. In sheep, microsatellite markers and single nucleotide polymorphism (SNP) markers have been proposed by the International Society of Animal Sciences (ISAG) for parentage testing. Since the implementation of genomic selection, the microsatellite information used for parental testing in previous generations is gradually being replaced by SNPs. However, parentage verifications should all be performed using the same technology. A strategy for transitioning from microsatellites to SNP markers, while avoiding extra genotyping costs, is the imputation of microsatellite alleles from SNP haplotypes. This study aims to identify the optimum approach, using a minimum number of SNPs to accurately impute microsatellite markers and developing a low-density SNP chip for parentage verification in the Assaf sheep breed. The imputation approach described here reached high accuracies using a low number of SNP markers, which supports the development of a low-density SNP chip that could avoid the problems of genotyping with both technologies, being a cost-effective method for parentage testing. This study will help sheep breeders to perform parentage verification when different genotyping platforms have been used across generations.

Abstract

Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r²), and allelic dosage (allelic r²), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r²), and 0.75 (allelic r²), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.

Implications of genome simple sequence repeats signature in 98 Polyomaviridae species

The analysis of simple sequence repeats (SSRs) in 98 genomes across four genera of the family Polyomaviridae was performed. The genome size ranged from 3962 (BM87) to 7369 bp (BM85) but maximum genomes were in the range of 5-5.5 kb. The GC% had an average of 42% and ranged between 34.69 (BM95) and 52.35 (BM81). A total of 3036 SSRs and 223 cSSRs were extracted using IMEx with incident frequency from 18 to 56 and 0 to 7, respectively. The most prevalent mono-nucleotide repeat motif was "T" (48.95%) followed by "A" (33.48%). "AT/TA" was the most prevalent dinucleotide motif closely followed by "CT/TC". The distribution was expectedly more in the coding region with 77.6% SSRs of which nearly half were in Large T Antigen (LTA) gene. Notably, most viruses with humans, apes and related species as host exhibited exclusivity of mono-nucleotide repeats in AT region, a proposed predictive marker for determination of humans as host in the virus in course of its evolution. Each genome has a unique SSR signature which is pivotal for viral evolution particularly in terms of host divergence.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02583-w.

Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome

Genome-wide in-silico identification of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036-1,181 microsatellites per strain. The further screening revealed the presence of 83-107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6-8.4 and 53.0-59.5 bp/kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6-0.8 and 12.1-17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD significantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-significantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)-x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. Finally, in-silico polymorphism was assessed, followed by in-vitro validation using PCR analysis and sequencing. The thirteen polymorphic SSR markers developed in this study were further characterized by mapping with the sequence present in the database. The results of the present study indicate that these SSRs could be a useful tool for identification, analysis of genetic diversity, and understanding the evolutionary status of the virus.

Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation

Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect's DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.

Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis

Chinese sturgeon (Acipenser sinensis) has been listed as a critically endangered species on the IUCN Red List and is an endemic fish of China. Five sets of duplex polymerase chain reactions (PCR) assays were developed with 10 tetranucleotide microsatellites for Chinese sturgeon. The size of CS57, ZHX43, ZHX69, AS105, ZHX51, AS074, ZHX2, AS078, AS026 and AS073 products in 184 Chinese sturgeon individuals ranged from 257-305, 191-241, 251-285, 172-244, 236-260, 169-209, 194-234, 92-176, 165-257 and 120-164, respectively. The observed allele number of the 10 microsatellites ranged from 7 to 16, and the total number of alleles was 106. The number of alleles per individual in CS57, ZHX43, AS105, AS074, AS078 and AS026 was 1-4. The number of alleles per individual in ZHX69, ZHX51, ZHX2 and AS073 was 2-4. The mean number of alleles per locus per individual ranged from 2.01-3.76. The expected heterozygosity (H_E), observed heterozygosity (H_O), polymorphic information content (PIC) and Shannon-Weiner diversity index (H') ranged from 0.582 to 0.899, from 0.676 to 1, from 0.518 to 0.886 and from 1.034 to 2.34, respectively. Despite many advantages, the use of microsatellites as genetic analysis tools can be limited by the cost of the associated experiment. To solve this problem, this set of five duplex PCRs will provide tools that are more helpful, less expensive and less time consuming than others used for genetic analyses in Chinese sturgeon.

Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia

Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.

Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family

The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono- to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (∼78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.

Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes

As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3′-untranslated regions (3′UTRs), 5′UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3′UTRs, TEs, and intergenic regions. Trifold P-SSRs had more GC-contents in the 5′UTRs and coding regions than that in the introns, 3′UTRs, TEs, and intergenic regions, whereas mononucleotide P-SSRs had the least GC-contents in all genomic regions. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs showed significantly different distributions in different regions (P < 0.01). Except for the coding regions, mononucleotide P-SSRs had the most RCNs, followed by the pattern: di- > tri- > tetra- > penta- > hexanucleotide P-SSRs in the same regions. The analysis of coefficient of variability (CV) of SSRs showed that the CV variations of RCN of the same mono- to hexanucleotide SSRs were relative higher in the intronic and intergenic regions, followed by the CV variation of RCN in the TEs, and the relative lower was in the 5′UTRs, 3′UTRs, and coding regions. Wide SSR analysis of different genomic regions has helped to reveal biological significances of their distributions.

A genome-wide investigation of microsatellite mismatches and the association with body mass among bird species

Mutation rate is usually found to covary with many life history traits of animals such as body mass, which has been readily explained by the higher number of mutation opportunities per unit time. Although the precise reason for the pattern is not yet clear, to determine the universality of this pattern, we tested whether life history traits impact another form of genetic mutation, the motif mismatches in microsatellites. Employing published genome sequences from 65 avian species, we explored the motif mismatches patterns of microsatellites in birds on a genomic level and assessed the relationship between motif mismatches and body mass in a phylogenetic context. We found that small-bodied species have a higher average mismatches and we suggested that higher heterozygosity in imperfect microsatellites lead to the increase of motif mismatches. Our results obtained from this study imply that a negative body mass trend in mutation rate may be a general pattern of avian molecular evolution.

A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae"

Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions. The GC-contents varied greatly among different intragenic and intergenic regions: 5'UTRs > CDSs > 3'UTRs > TEs > introns > intergenic regions, and high GC-content was frequently distributed in exon-rich regions. Our results also showed that in the same intragenic and intergenic regions, the distribution of GC-contents were great similarity in the different primates. Tri- and hexanucleotide P-SSRs had the most GC-contents in the 5'UTRs and CDSs, whereas mononucleotide P-SSRs had the least GC-contents in the six genomic regions of these primates. The most frequent motifs for different length varied obviously with the different genomic regions.

Dating the beginning of the Roman viticultural model in the Western Mediterranean: The case study of Chianti (Central Italy)

Although domestication of the grapevine (Vitis vinifera L.) has been extensively documented, the history of genotype selection and evolution of vineyard management remain relatively neglected fields of study. The find of 454 waterlogged grapevine pips from a well-dated Etrusco-Roman site in the Chianti district (Tuscany, Central Italy) is an extraordinary chance to gain insights into the progress of viticulture occurring in a key historical period in one of the world's most famous wine regions. The molecular and geometrical analyses of grape seeds showed (a) the presence in the site of different grapevine individuals and (b) a sudden increase in pip size, occurring at around 200 BC, whic explainable by the selection and introduction of new varieties. In this period, the Etruscans settlers in Chianti were stimulated by northward-expanding Roman culture to use novel vineyard management practices. We hypothesize that one of the most important innovations may have been the introduction of pruning, inducing vine physiological conditions more favorable to pip growth. Such changes were the consequence of specific entrepreneurial choices made by the Romans in a period of economic investment in grape cultivation and wine making to satisfy the increased trade demand after the conquest of the Central-Western Mediterranean basin.

The human ovarian cancer cell line CABA I: A peculiar genetic evolution

The objective of this study was to study the human ovarian cancer cell line CABA I by means of short tandem repeats (STR) profiling and cytogenetic analysis in order to prevent future misidentification or cross-contamination and verify its stability during in vitro cultivation. To this end, cells at passages 18 and 38 were analyzed using cytogenetic techniques in order to verify possible chromosomal aberrations and the karyotypic evolution of this cell line; GTG-banding and FISH were also performed. For STR analysis, DNA was extracted using the automated extractor MagNA pure and analyzed by means of PowerPlex 16 HS. STR profiles were analyzed by GeneMapper 3.2.1 software. Whereas comparative cytogenetic analysis of CABA I cells at passage 18 and 38 has demonstrated considerable genetic instability, we found that STR profiles were essentially unaltered in both analyzed passages, suggesting that the STR profile is reliable and could be used for the regular authentication of CABA I over time. It should be emphasized, however, that of the 16 loci generally used in human STR profiles, only 3 were properly detectable in CABA I. The data highlight that the CABA I cell line demonstrates an anomalous STR profile that does not fully adjust the criteria currently used for the identification of human cells; in spite of this, it remains stable during the in vitro maintainance. Moreover, the genetic instability of the CABA I cell line overlaps with those observed in vivo in tumor cells, making it a suitable candidate to analyze, in vitro, the peculiar genetic evolution of ovarian cancer cells.

Microsatellites in Pursuit of Microbial Genome Evolution

Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.

Evolution of Nine Microsatellite Loci in the Fungus Fusarium oxysporum

The evolution of nine microsatellites and one minisatellite was investigated in the fungus Fusarium oxysporum and sister taxa Fusarium redolens and Fusarium verticillioides. Compared to other organisms, fungi have been reported to contain fewer and less polymorphic microsatellites. Mutational patterns over evolutionary time were studied for these ten loci by mapping changes in core repeat numbers onto a phylogeny based on the sequence of the conserved translation elongation factor 1-α gene. The patterns of microsatellite formation, expansion, and interruption by base substitutions were followed across the phylogeny, showing that these loci are evolving in a manner similar to that of microsatellites in other eukaryotes. Most mutations could be fit to a stepwise mutation model, but a few appear to have involved multiple repeat units. No evidence of gene conversion was seen at the minisatellite locus, which may also be mutating by replication slippage. Some homoplastic numbers of repeat units were observed for these loci, and polymorphisms in the regions flanking the microsatellites may provide better genetic markers for population genetics studies of these species.

Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrephafraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area.

Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same nucleotide SSR type showed great similarity among different chromosomes of B. taurus, O. aries, and C. hircus.

Multiplexing with three-primer PCR for rapid and economical microsatellite validation

The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs were tested, resulting in 73 polymorphic markers. Of these, 55 loci were combined in six multiplex panels each containing between six and eleven markers. Variability of the loci was assessed on G. morhua from the Celtic Sea (n = 46) and the Scotian Shelf (n = 46), two locations that have shown genetic differentiation in previous studies. Multilocus F(ST) between the two samples was estimated at 0.067 (P = 0.001). After three loci potentially under selection were excluded, the global F(ST) was estimated at 0.043 (P = 0.001). Our technique combines three-primer and multiplex PCR techniques, allowing simultaneous screening and validation of relatively large numbers of microsatellite loci.

Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.

Microsatellite polymorphism among Chrysanthemum sp. polyploids: the influence of whole genome duplication

Polyploidy is common among flowering plants, including the Asteraceae, a relatively recent angiosperm group. EST-SSRs were used to characterize polymorphism among 29 Chrysanthemum and Ajania spp. accessions of various ploidy levels. Most EST-SSR loci were readily transferable between the species, 29 accessions were separated into three groups in terms of the number of fragments. It inferred that the formation from tetraploid to hexaploid and from octoploid to decaploid may be a recent event, while from the diploid to the tetraploid may be an ancient one in the Chrysanthemum lineage. EST-SSR polymorphism was found and some transcripts containing an SSR were transcribed differently in the de novo autotetraploid C. nankingense and C. lavandulifolium than in their progenitor diploid. EST-SSR could provide a potential molecular basis of adaptation during evolution, while whole genome duplication has a major effect on the mutational dynamics of EST-SSR loci, which could also affect gene regulation.

In- silico exploration of thirty alphavirus genomes for analysis of the simple sequence repeats

The compilation of simple sequence repeats (SSRs) in viruses and its analysis with reference to incidence, distribution and variation would be instrumental in understanding the functional and evolutionary aspects of repeat sequences. Present study encompasses the analysis of SSRs across 30 species of alphaviruses. The full length genome sequences, assessed from NCBI were used for extraction and analysis of repeat sequences using IMEx software. The repeats of different motif sizes (mono- to penta-nucleotide) observed therein exhibited variable incidence across the species. Expectedly, mononucleotide A/T was the most prevalent followed by dinucleotide AG/GA and trinucleotide AAG/GAA in these genomes. The conversion of SSRs to imperfect microsatellite or compound microsatellite (cSSR) is low. cSSR, primarily constituted by variant motifs accounted for up to 12.5% of the SSRs. Interestingly, seven species lacked cSSR in their genomes. However, the SSR and cSSR are predominantly localized to the coding region ORFs for non structural protein and structural proteins. The relative frequencies of different classes of simple and compound microsatellites within and across genomes have been highlighted.

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This is the first analysis of SSR and cSSR in alphaviruses.

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We analysed differential frequency and distribution patterns of SSRs and cSSRs.

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We studied localization of SSR and cSSR in alphaviruses proteomics

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This study would help in better understanding of evolutionary biology of alphaviruses.

De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis

Background

Algae in the order Trentepohliales have a broad geographic distribution and are generally characterized by the presence of abundant β-carotene. The many monographs published to date have mainly focused on their morphology, taxonomy, phylogeny, distribution and reproduction; molecular studies of this order are still rare. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus.

Methods/Principal Findings

Illumina HiSeq 2000 sequencing generated 55,007,830 Illumina PE raw reads, which were assembled into 41,328 assembled unigenes. Based on NR annotation, 53.28% of the unigenes (22,018) could be assigned to gene ontology classes with 54 subcategories and 161,451 functional terms. A total of 26,217 (63.44%) assembled unigenes were mapped to 128 KEGG pathways. Furthermore, a set of 5,798 SSRs in 5,206 unigenes and 131,478 putative SNPs were identified. Moreover, the fact that all of the C4 photosynthesis genes exist in T. jolithus suggests a complex carbon acquisition and fixation system. Similarities and differences between T. jolithus and other algae in carotenoid biosynthesis are also described in depth.

Conclusions/Significance

This is the first broad transcriptome survey for T. jolithus, increasing the amount of molecular data available for the class Ulvophyceae. As well as providing resources for functional genomics studies, the functional genes and putative pathways identified here will contribute to a better understanding of carbon fixation and fatty acid and carotenoid biosynthesis in T. jolithus.

Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability

Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.

Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas

The triploid Pacific oyster, which is produced by mating tetraploid and diploid oysters, is favored by the aquaculture industry because of its better flavor and firmer texture, particularly during the summer. However, tetraploid oyster production is not feasible in all oysters; the development of tetraploid oysters is ongoing in some oyster species. Thus, a method for ploidy verification is necessary for this endeavor, in addition to ploidy verification in aquaculture farms and in the natural environment. In this study, a method for ploidy verification of triploid and diploid oysters was developed using multiplex polymerase chain reaction (PCR) panels containing primers for molecular microsatellite markers. Two microsatellite multiplex PCR panels consisting of three markers each were developed using previously developed microsatellite markers that were optimized for performance. Both panels were able to verify the ploidy levels of 30 triploid oysters with 100% accuracy, illustrating the utility of microsatellite markers as a tool for verifying the ploidy of individual oysters.

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next-generation sequencing analysis of both the genome and transcriptome from two sibling species, Calanus finmarchicus and Calanus glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species-specific amplicon length. Furthermore, most of the markers were successfully amplified in other Calanus species, allowing the molecular identification of Calanus helgolandicus, Calanus hyperboreus and Calanus marshallae.

Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes

Simple sequence repeats (SSRs) are tandem-repeated sequences ubiquitously present but differentially distributed across genomes. Present study is a systematic analysis for incidence, composition and complexity of different microsatellites in 48 representative Human papillomavirus (HPV) genomes. The analysis revealed a total of 1868 SSRs and 120 cSSRs. However, four genomes (HPV-60, HPV-92, HPV-112 and HPV-136) lacked any cSSR content; while HPV-31 accounted for a maximum of 10 cSSRs. An overall increase in cSSR% with higher dMAX was observed. The SSRs and cSSRs were prevalent in coding regions. Poly(A/T) repeats were significantly more abundant than poly(G/C) repeats possibly due to high (A/T) content of the HPV genomes. Further, higher prevalence of di-nucleotide repeats over tri-nucleotide repeats may be attributed to instability of former because of higher slippage rate. An in-depth study of the satellite sequences would provide an insight into the imperfections and evolution of microsatellites.

DNA fingerprinting in zoology: past, present, future

In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work.

Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus

Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.

Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization

The strategy of bulk DNA sampling has been a valuable method for studying large numbers of individuals through genetic markers. The application of this strategy for discrimination among germplasm sources was analyzed through information theory, considering the case of polymorphic alleles scored binarily for their presence or absence in DNA pools. We defined the informativeness of a set of marker loci in bulks as the mutual information between genotype and population identity, composed by two terms: diversity and noise. The first term is the entropy of bulk genotypes, whereas the noise term is measured through the conditional entropy of bulk genotypes given germplasm sources. Thus, optimizing marker information implies increasing diversity and reducing noise. Simple formulas were devised to estimate marker information per allele from a set of estimated allele frequencies across populations. As an example, they allowed optimization of bulk size for SSR genotyping in maize, from allele frequencies estimated in a sample of 56 maize populations. It was found that a sample of 30 plants from a random mating population is adequate for maize germplasm SSR characterization. We analyzed the use of divided bulks to overcome the allele dilution problem in DNA pools, and concluded that samples of 30 plants divided into three bulks of 10 plants are efficient to characterize maize germplasm sources through SSR with a good control of the dilution problem. We estimated the informativeness of 30 SSR loci from the estimated allele frequencies in maize populations, and found a wide variation of marker informativeness, which positively correlated with the number of alleles per locus.