Application Of Molecular Genetics Research Articles

Genetic and Genomic Pathways to Improved Wheat (Triticum aestivum L.) Yields: A Review

Wheat (Triticum aestivum L.) is a fundamental crop essential for both human and animal consumption. Addressing the challenge of enhancing wheat yield involves sophisticated applications of molecular genetics and genomic techniques. This review synthesizes current research identifying and characterizing pivotal genes that impact traits such as grain size, number, and weight, critical factors influencing overall yield. Key genes including TaSPL17, ABP7, TaGNI, TaCKX6, TaGS5, TaDA1, WAPO1, TaRht1, TaTGW-7A, TaGW2, TaGS5-3A, TaSus2-2A, TaSus2-2B, TaSus1-7A, and TaSus1-7B are examined for their roles in these traits. The review also explores genes responsive to environmental changes, which are increasingly significant under current climate variability. Multi-trait regulatory genes and quantitative trait loci (QTLs) that contribute to these traits are discussed, highlighting their dual influences on grain size and yield. Furthermore, the paper underscores the utility of emerging technologies such as CRISPR/Cas9, Case13, and multi-omics approaches. These innovations are instrumental for future discoveries and are poised to revolutionize wheat breeding by enabling precise genetic enhancements. Facing unprecedented challenges from climate change, the identification and utilization of these candidates is crucial. This review aims to be a comprehensive resource for researchers, providing an integrative understanding of complex traits in wheat and proposing new avenues for research and crop improvement strategies.

Construction and functional verification of size-reduced plasmids based on TMP resistance gene dfrB10.

Antibiotic resistance screening is crucial in the construction of recombinant plasmids. The dfrB10 gene, a short-size trimethoprim (TMP)-resistance type B dihydrofolate reductase gene, is a promising antibiotic drug screening marker for plasmid construction in molecular genetic research. Currently, available plasmid backbones (without the resistance gene) were amplified using PCR, and then we ligated these products with dfrB10 gene fragments via homologous recombination to construct new plasmid vectors with TMP resistance. The cloning, expression, and gene editing functions of the new plasmids based on their different purposes were verified. By successfully replacing the original resistance genes of pUC19, pET28a, pcDNA3.1, and pX330 plasmids with dfrB10, we constructed a series of plasmids with TMP resistance. The change of the resistance selection marker to TMP did not affect the function of the plasmids compared to the original ones. Furthermore, a short (988 bp) TMP-resistant miniature tool plasmid, pTMi, was constructed based on the pUC19 plasmid. With the use of the dfrB10 gene as a resistance marker under TMP drug screening, various size-reduced tool plasmids can be routinely constructed. These plasmids have similar functions to the original ones and can be used for research applications in molecular genetics.IMPORTANCEPlasmid size is one of the factors affecting transfection efficacy in most of the molecular genetic research studies. One effective approach for reducing plasmid size is to replace relatively large, conventional antibiotic resistance genes with the short-size dfrB10 gene. The successful construct of a series of dfrB10-based tool plasmids and their functional validation, via comparison with original plasmids, suggest that dfrB10 is a potent drug resistance selection marker. The antibiotic trimethoprim offers convenient usage comparable to that of ampicillin or kanamycin. Additionally, fluorescence analysis has demonstrated the compatibility of TMP with protein expression in various host cells. Based on these findings, TMP-dfrB10 could be an alternative choice for future use in molecular genetic research studies that require miniature plasmids to achieve optimal results.

Genes and Sales

This paper presents one of the first marketing applications of molecular genetics. We report evidence that salespeople’s genetic variants linked to educational attainment predict sales performance. Both genetics and selling effort contribute to sales performance, whereas genetics contribute more than personality traits. We further show that adaptive learning, as captured in salespeople’s customer orientation and opportunity recognition skills, may explain the gene-sales relationship. We discuss the implications of these findings for sales management and the value of genetic research for the marketing field. This paper was accepted by Matthew Shum, marketing. Funding: S. Gong acknowledges financial support from the NSFC [Grant 71972040] and Fundamental Research Funds for the Central Universities [2022NTSS43]. Q. Li acknowledges financial support from the NSFC [Grant 72072014] and Young Talent Program of Beijing Foreign Studies University. S. Su acknowledges financial support from the NSFC [Grant 71872016]. Supplemental Material: The data files and online appendix are available at https://doi.org/10.1287/mnsc.2023.4879 .

Notes from the Anatolian underground: two new mole taxa from Eastern Turkey, together with a revised phylogeny of the genus Talpa (Mammalia: Eulipotyphla: Talpidae)

Abstract Subterranean life is associated with strong adaptive constraints, leading to the frequent occurrence of morphologically cryptic lineages. This is true of most small mammals, including moles (Eulipotyphla: Talpidae), where a number of species have been recognized recently, particularly following the application of molecular genetics. Here, we use mitochondrial and nuclear DNA sequence data and geometric morphometrics to explore the systematics and evolution of some of the least-known Western Palaearctic moles: the Talpa davidiana group of Eastern Anatolia/Iran. We show that T. davidiana includes four taxa, two of which we describe herein: T. hakkariensissp. nov.,T. davidiana davidiana, T. davidiana tatvanensisssp. nov., and T. streetorumvalid species. For the first time, we apply molecular species delimitation analyses to Talpa, confirming taxonomic hypotheses and suggesting the existence of further morphologically cryptic lineages. These analyses also support the recognition of T. transcaucasica as a valid species distinct from T. levantis. We present a revised phylogeny for Eurasian Talpa and increase the number of known extant taxa to 18, most of which are found in Anatolia, the global hotspot of diversity in this genus. This probably results from the isolation of suitable habitats by a combination of climatic and topographical heterogeneity.

The multifarious role of callose and callose synthase in plant development and environment interactions.

Callose is an important linear form of polysaccharide synthesized in plant cell walls. It is mainly composed of β-1,3-linked glucose residues with rare amount of β-1,6-linked branches. Callose can be detected in almost all plant tissues and are widely involved in various stages of plant growth and development. Callose is accumulated on plant cell plates, microspores, sieve plates, and plasmodesmata in cell walls and is inducible upon heavy metal treatment, pathogen invasion, and mechanical wounding. Callose in plant cells is synthesized by callose synthases located on the cell membrane. The chemical composition of callose and the components of callose synthases were once controversial until the application of molecular biology and genetics in the model plant Arabidopsis thaliana that led to the cloning of genes encoding synthases responsible for callose biosynthesis. This minireview summarizes the research progress of plant callose and its synthetizing enzymes in recent years to illustrate the important and versatile role of callose in plant life activities.

One fits all: a highly sensitive combined ddPCR/pyrosequencing system for the quantification of microchimerism after hematopoietic and solid organ transplantation.

A combined digital droplet PCR (ddPCR)/pyrosequencing assay system was developed that demonstrated advantages applicable to multiple qualitative and quantitative molecular genetic diagnostic applications. Data for characterizing this combined approach for hematologic stem cell transplantation (HSCT) and allele quantification from graft-derived cell-free (cf) DNA in solid organ transplantation (SOT) is presented. ddPCR and pyrosequencing assays targeting 32 SNPs/markers were established. ddPCR results from 72 gDNAs of 55 patients after allogeneic HSCT and 107 plasma-cfDNAs of 25 liver transplant recipients were compared with established methods/markers, i.e.short-tandem-repeat PCR and ALT, respectively. The ddPCR results were in good agreement with the established marker. The limit of detection was 0.02 % minor allele fraction. The relationship between ddPCR andSTR-PCR was linear with R2=0.98 allowing to transfer previously established clinical STR-PCR cut-offs to ddPCR; 50-fold higher sensitivity and a variation coefficient of <2 % enable the use of low DNA concentrations (e.g. pre-sorted cells). ddPCR detected liver allograft injury at least as sensitive as ALT suggesting that ddPCR is a reliable method to monitor the transplant integrity, especially when other biomarkers are lacking (e.g. kidney). Combining pyrosequencing for genotyping and ddPCR for minor allele quantification enhances sensitivity and precision for the patient after HSCT and SOT. Theassay is designed for maximum flexibility. It is expected to be suitable for other applications (sample tracking, prenatal diagnostics, etc.).

Clinical application of molecular genetics in acute myeloid leukemia

With the increasing application of genetic testing, we have gradually understood the heterogeneous molecular nature of acute myeloid leukemia (AML). We have been able to identify a large number of translocations and single gene mutations to go with the previously known karyotypic abnormalities associated with this disease. This has led to a refinement in the way we diagnose, prognosticate, and treat this disease. The newer classification systems proposed by the World Health Organization and the International Consensus Classification systems show an increasing reliance on molecular genetics for the diagnosis and classification of AML. This has also generated situations where molecular genetics assume preference over morphologic assessment, namely, in the case of recurring genetic abnormalities where the standard 20% of blast count is not required, and in AML with underlying myelodysplasia where the disease shall be defined not by morphologic dysplasia but by the presence of certain cytogenetic and molecular abnormalities. The new prognostic system proposed by the European LeukemiaNet also places an emphasis on genetic mutations along with the previously known cytogenetic abnormalities. Similarly, the assessment of measurable residual disease (MRD) is recommended to be done by quantitative polymerase chain reaction (PCR) for core-binding factor and NPM1 mutated AML. In the future, next-generation sequencing is also expected to play a prominent role in the assessment of MRD alongside flow cytometry and PCR. Finally, precision oncology is supplementing conventional treatment regimens and patients with FLT3 and isocitrate dehydrogenase mutations are recommended to be offered the respective targeted agents. This review shall discuss the clinical implications of molecular genetics in the current management of AML.

Persepsi Peternak tentang Ayam IPB D-1 sebagai Ayam Lokal Unggul (Kasus Sinar Harapan Farm Jampang Tengah Sukabumi)

IPB D-1 chickens were produced from research on the application of molecular genetics with the aim of increasing the productivity and quality of Indonesian local chickens. This study aims to determine the perception of farmers at Sinar Harapan Farm Jampang Tengah Sukabumi about IPB D-1 chickens, which is viewed from the characteristics of innovations in IPB D-1 chickens. The research was conducted at Sinar Harapan Farm (SHF) which was located in Jampang Tengah District, Sukabumi Regency. Data collection was carried out in August 2020. Data collection was carried out by interviewing all 18 member farmers of Sinar Harapan Farm. SHF farmers’ perceptions of IPB D-1 chickens were measured from five characteristics of innovations in IPB D-1 chickens which included: relative advantage, compatibility, complexity, trialability, and observability. The results showed that the perception score for the aspect of relative advantage was 4.34, compatibility was 4.38, compatibility was 4.25, trialability was 4.13, and observability was 4.15. The farmers of Sinar Harapan Farm Jampang Tengah Sukabumi showed a good perception about IPB-D1 chickens.

Review on Animal Diseases Resistance and Adaptation Improvement through Molecular Genetics

This review is conducted to highlight the application of molecular genetics for improvement of diseases resistance in livestock. Diseases prevention is a serious issue to restrict economic damage due to economically important diseases outbreaks worldwide. Over the last decades, the excessive use of drugs has been criticised because of the possible development of drug-resistant zoonotic organisms and the potential dangers of drug residues in food animal products for human consumption. To prevent this problem following the ways for host resistance improvement to disease is a low cost and sustainable approach. So, this literature review was done on the theory of how to use molecular markers to select for quantitative trait loci (QTL) in genetic improvement programs, both within populations and for introgression of QTL from one population to another. If the effect of each marker is known, then an animal with no available phenotype for disease can be genotyped and its direct genomic value can be estimated based on its genotype only. The advantage of such a method is that accurate estimates of genetic merit can be achieved exploiting knowledge of the genotype of the animal even if the animal is very young. So, it is possible to put recommendation for further research on the generation of phenotypes that are resistant to diseases and development accurate bio-markers that can be readily measured in large numbers of animals at a relatively low cost.

Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development.

The application of molecular genetics has reinvigorated and improved how species are defined and investigated scientifically, especially for morphologically cryptic micro-organisms. Here we show how species recognition improves understanding of the ecology and evolution of mutualisms between reef-building corals and their mutualistic dinoflagellates (i.e. Symbiodiniaceae). A combination of genetic, ecological, and morphological evidence defines two sibling species of Cladocopium (formerly Symbiodinium Clade C), specific only to host corals in the common genus Pocillopora, which transmit their obligate symbionts during oogenesis. Cladocopium latusorum sp. nov. is symbiotic with P. grandis/meandrina while the smaller-celled C. pacificum sp. nov. associates with P. verrucosa. Both symbiont species form mutualisms with Pocillopora that brood their young. Populations of each species, like their hosts, are genetically well connected across the tropical and subtropical Pacific Ocean, indicating a capacity for long-range dispersal. A molecular clock approximates their speciation during the late Pliocene or early Pleistocene as Earth underwent cycles of precipitous cooling and warming; and corresponds to when their hosts were also diversifying. The long temporal and spatial maintenance of high host fidelity, as well as genetic connectivity across thousands of kilometers, indicates that distinct ecological attributes and close evolutionary histories will restrain the adaptive responses of corals and their specialized symbionts to rapid climate warming.

Order-Stability in Complex Biological, Social, and AI-Systems from Quantum Information Theory.

This paper is our attempt, on the basis of physical theory, to bring more clarification on the question “What is life?” formulated in the well-known book of Schrödinger in 1944. According to Schrödinger, the main distinguishing feature of a biosystem’s functioning is the ability to preserve its order structure or, in mathematical terms, to prevent increasing of entropy. However, Schrödinger’s analysis shows that the classical theory is not able to adequately describe the order-stability in a biosystem. Schrödinger also appealed to the ambiguous notion of negative entropy. We apply quantum theory. As is well-known, behaviour of the quantum von Neumann entropy crucially differs from behaviour of classical entropy. We consider a complex biosystem S composed of many subsystems, say proteins, cells, or neural networks in the brain, that is, We study the following problem: whether the compound system S can maintain “global order” in the situation of an increase of local disorder and if S can preserve the low entropy while other increase their entropies (may be essentially). We show that the entropy of a system as a whole can be constant, while the entropies of its parts rising. For classical systems, this is impossible, because the entropy of S cannot be less than the entropy of its subsystem . And if a subsystems’s entropy increases, then a system’s entropy should also increase, by at least the same amount. However, within the quantum information theory, the answer is positive. The significant role is played by the entanglement of a subsystems’ states. In the absence of entanglement, the increasing of local disorder implies an increasing disorder in the compound system S (as in the classical regime). In this note, we proceed within a quantum-like approach to mathematical modeling of information processing by biosystems—respecting the quantum laws need not be based on genuine quantum physical processes in biosystems. Recently, such modeling found numerous applications in molecular biology, genetics, evolution theory, cognition, psychology and decision making. The quantum-like model of order stability can be applied not only in biology, but also in social science and artificial intelligence.

Molecular genetics of medicinal plants, past achievement, and new era

Unraveling the genetic basis of medicinal plant metabolism and developmental traits is a long-standing goal for pharmacologists and plant biologists. This paper discusses the definition of molecular genetics of medicinal plants, which is an integrative discipline with medicinal plants as the research object. This discipline focuses on the heredity and variation of medicinal plants, and elucidates the relationship between the key traits of medicinal plants(active compounds, yield, resistance, etc.) and genotype, studies the structure and function, heredity and variation of medicinal plant genes mainly at molecular level, so as to reveal the molecular mechanisms of transmission, expression and regulation of genetic information of medicinal plants. Specifically, we emphasize on three major aspects of this discipline.(1)Individual and population genetics of medicinal plants, this part mainly highlights the genetic mechanism of the domestication, the individual genomics at the species level, and the formation of genetic diversity of medicinal plants.(2)Elucidation of biosynthetic pathways of active compounds and their evolutionary significance. This part summarizes the biosynthesis, diversity and molecular evolution of active compounds in medicinal plants.(3) Molecular mechanisms that shaping the key agronomic traits by internal and external factors. This part focuses on the accumulation and distribution of active compounds within plants and the regulation of metabolic network by environmental factors. Finally, we prospect the future direction of molecular genetics of medicinal plants based on the rapid development of multi-omics technology, as well as the application of molecular genetics in the future strategies to achieve conservation and breeding of medicinal plants and efficient biosynthesis of active compounds.

A fast, flexible and inexpensive protocol for DNA and RNA extraction for forest trees

Aim of the study: DNA and RNA extraction are still one of the most important and challenging steps of many molecular genetics applications such as Next-Generation Sequencing technologies. In this study, traditional laboratory preparation protocols and commercially available nucleic acids extraction kits’ features were combined into a procedure suitable for extraction of either DNA or RNA in 96-well plate format at high throughput.Area of study: The study covers forest tree species from the United States of America.Materials and methods: The DNA and RNA protocol were tested on 27 species, including especially recalcitrant forest tree species, from five angiosperm and three gymnosperm families. DNA was also extracted from stored (from 2 to 6 years) silica-dried samples of 11 species of Pinaceae.Main results: The spectrophotometric analysis of DNA and RNA showed that gymnosperms yielded lower quantity, but higher quality nucleic acids than angiosperms which have variable results among species. The quantity and quality of DNA from stored samples were generally lower than fresh silica-dried samples. The RNA results showed high-enough yield (6.6 to 8.8 RIN) for downstream analyses.Research highlights: It was demonstrated that high quality and high molecular weight nucleic acids for Next-Generation Sequencing applications can be isolated from hundreds of samples from a wide range of taxonomic groups. The new protocol has features similar to both traditional laboratory and commercial extraction kits; is easy to set up in any molecular research laboratory, can be applied to a large number of samples (hundreds) in a working day, uses inexpensive reagents and supplies, and is compatible with automation.Key words: Angiosperms; gymnosperms; isolation protocol; nucleic acids.

Investigation of the Effects of Micromeria congesta Essential Oil Extract on Wound Healing in Rabbits and Molecular Genetics Applications

Background: The chemical composition and antimicrobial and antioxidant properties of Micromeria congesta (M. congesta) have been previously revealed, but their effect on wound healing has not been investigated. This study aimed to investigate the effects of M. congesta extract in rabbits where full-thickness skin wounds were used. Methods: Twentyone New Zealand rabbits that were used in the study were divided into 3 groups as Group I (M. congesta’s essential oil extract), Group II (Centella asiatica (C. asiatica) extract in pomade form) and Group III (control). Two wounds of 2.8 cm in size were created at the caudal border of the scapula. While the unhealed wound areas were measured on the 7th, 14th, 21st and 28th days. Result: It was observed histopathologically and immunohistochemically that the healing was more noticeable in Group II in comparison to the others and the wound healing in Group I was more limited. In the genetic analysis, the expression levels of all the target genes in Group I and Group II were significantly higher than those in the control group on the 7th day (p less than 0.05). The results demonstrate that topical application of the oily form of M. congesta results in significant improvements on wound healing in rabbits.

Highlights of the Genetics and Importance of Bacillus subtilis Spore Formation

Bacillus species are important producers of essential biomolecules such as antibiotics, insecticides and enzymes. However, the immense potential for commercial scale production of these biomolecules still remain largely unexplored. Optimization of the exploitation of these species has, therefore, become the major preoccupation of many laboratories worldwide. Success in this regard depends on a thorough understanding of the species gene regulatory mechanisms, metabolism and secretary pathways. Bacillus subtilis by virtue of its relatively simple cellular organization, experimental tractability and excellent genetics has become the principal paradigm for the study of the cellular processes of the Bacillus genus. The bacteria survive adverse environmental conditions by undergoing a complex process of spore formation termed sporulation. The process of spore formation involves cellular differentiation of an asymmetrically dividing mother cell, with each compartment undergoing distinct cell-specific gene expression. These processes eventually culminate in the formation of resistant spores. The molecular genetics, importance and industrial applications of these species as well as the historical perspective of Bacillus research have been reviewed. Furthermore, scientific advancements in the study of the spore formation process in B. subtilis have been presented with emphasis on the basic genetic regulatory mechanisms.

Application of immunophenotypic analysis and molecular genetics in the diagnosis of acute promyelocytic leukemia

目的研究免疫表型分析及分子遗传学在急性早幼粒细胞白血病（APL）诊断中的应用价值。方法对2012年5月–2017年12月门诊或住院的798例APL患者的流式细胞术（FCM）免疫分型、染色体核型及染色体荧光原位杂交（FISH）进行回顾性分析，并深入研究FCM免疫表型及分子遗传学在APL诊断中的应用价值。结果FCM诊断APL敏感性为91.9%，特异性为98.7%。APL具有独特免疫表型特点：典型APL的表型为侧向（SSC）偏大，CD34和HLA-DR表达缺失，表达或强表达CD33，均一表达CD13、CD9、CD123，可伴有CD56、CD7、CD2的表达。约10%的患者为非典型APL表型，一般伴有CD34和（或）HLA-DR表达，SSC减小，经常伴有CD2表达，而FCM免疫分型很难明确诊断为APL，需要依赖遗传学或者分子生物学检查结果。约1/3的患者除存在t（15;17）（q22;q21）外，还存在额外染色体异常；伴有t（15；17）的复杂核型、变异易位或者t（11;17）、t（5;17）等变异型的APL，FCM表型与单纯t（15；17）APL差异无统计学意义（P>0.05）。结论FCM能够快速诊断APL，伴有额外染色体异常患者和单纯t（15；17）患者FCM免疫表型没有明显差异。遗传学是诊断APL的金标准，免疫分型中约10%的患者依赖于分子遗传学来确诊。

Comparison of transduction efficiency among various cell types by a lentivector containing CMV promoter

Due to their unique biological characteristics, mesenchymal stem cells (MSCs) are useful in developing cell-based therapies, tissue regeneration, and many other applications of cellular and molecular genetics. Use of lentiviral system allows the integration of specific nucleic acid sequence into a target cell genome near an active transcription site in such a way that it is stable and heritable. The aim of the present study was to evaluate the gene transduction efficiency on the cells of different species using lentivirus along with cytomegalovirus in a lentiviral shuttle vector. In this study, the third-passage isolated MSCs from four different species, including ovine and goat cardiac fibroblasts, HEK293T, and L929 cell line were transduced by concentrated virus particles. Then, transduction percentage was detected by flow cytometry. The findings showed different transduction efficiencies for various cells of one species or other species, indicating that differentiated and undifferentiated cells had different transduction percentages. Different degrees of transduction observed in differentiated and undifferentiated cells might be the result of various lentiviral receptors on the plasma membrane, site of integration, and activity of CMV promoter. Further, other regulatory factors involved in cell transduction and target gene expression can cause different percentages of transduction.

Clinical application of molecular genetics in lymphatic malformations.

ObjectivesTo describe the clinical presentation of lymphatic malformations (LM) and genotypically associated disorders and to summarize the recent literature regarding the genetic etiology of LM and provide a biologic correlation to medical and surgical management.ResultsLM are congenital lesions derived from a developmental abnormality of the lymphatic vessels. The severity of disease varies widely and complications can occur with higher staged disease and those associated with a known constellation of symptoms. Somatic mutations of the PIK3CA gene have been found to be an etiologic factor in the development of LM and associated overgrowth syndromes. Sirolimus is a mammalian target of rapamycin (mTOR) inhibitor that inhibits the pathway downstream of PIK3CA. Preliminary studies in select groups of patients suggest that sirolimus has a role in the medical management of certain aspects of this disease.ConclusionsDiscovery of LM molecular genetics has led to the possibility of targeted therapies and highlights the importance of precision medicine in rare diseases. Identifying genetic mutations in larger cohorts of patients with LM will lead to additional insights. Knowledge of the genetic basis for disease can then lead to discovery of directed medical therapy. A specific molecular diagnosis can also help families understand better why their child is different and provide accurate counseling for subsequent pregnancies.Level of Evidence6

Unique sympatric quartet of limnetic, benthic, profundal and piscivorous brown trout populations resolved by 3D sampling and focused molecular marker selection

Abstract The full extent of sympatric intraspecific population diversity (SIPD) i.e. structuring into multiple genetically distinct Mendelian populations, remains uncertain for most lacustrine fish species, particularly in northern lakes. However, increasing application of molecular genetics is advancing understanding and has shown both that many known intraspecific sympatric lacustrine morphological and behavioural polymorphisms represent SIPD, and resolved the existence of phenotypically cryptic structuring. Uncertainty remains as only a few northern lakes have been comprehensively surveyed and existing studies focus on known phenotypic polymorphisms or exploit ad hoc field sampling, marker selection and data analysis methods. Such unfocused approaches constrain resolving power and increase the likelihood of failing to detect SIPD when present. Brown trout (Salmo trutta L.) in a previously unstudied Scottish lake were collected by 3D stratified random netting. They were screened with both an arbitrary set of molecular markers and markers pre‐selected for their ability to resolve regional allopatric brown trout population structuring and data analysed by both Bayesian and non‐Bayesian approaches. Depth clines for mitochondrial and microsatellite markers variation were observed and found to arise from different, but overlapping, depth distributions of four genetically distinct piscivorous, limnetic, shallow benthic, and profundal benthic populations. This is the highest number of ecologically and phenotypically distinct sympatric brown populations identified in any lake to date, and includes the first reported profundal benthic form. The detection of the SIPD in Loch Laidon depended critically on the random 3D sampling and using markers preselected for their power to differentiate regional allopatric populations of trout, as well as aided by using both Bayesian and non‐Bayesian analytical approaches. The findings support the view that the extent of ecologically and evolutionarily significant SIPD is probably underestimated in brown trout and other fish species, and probably is a significant component of the biodiversity in many northern hemisphere lakes.

Dante: genotyping of known complex and expanded short tandem repeats

Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays. We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases. Dante is open source software, freely available for download at https://github.com/jbudis/dante. Supplementary data are available at Bioinformatics online.