Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing

A mutation associated with resistance to synthetic pyrethroids is widespread in US populations of the tropical lineage of Rhipicephalus sanguineus s.l

The brown dog tick, Rhipicephalus sanguineus sensu lato (s.l.), is an important vector for Rickettsia rickettsii, causative agent of Rocky Mountain spotted fever. Current public health prevention and control efforts to protect people involve preventing tick infestations on domestic animals and in and around houses. Primary prevention tools rely on acaricides, often synthetic pyrethroids (SPs); resistance to this chemical class is widespread in ticks and other arthropods. Rhipicephalus sanguineus s.l. is a complex that likely contains multiple unique species and although the distribution of this complex is global, there are differences in morphology, ecology, and perhaps vector competence among these major lineages. Two major lineages within Rh. sanguineus s.l., commonly referred to as temperate and tropical, have been documented from multiple locations in North America, but are thought to occupy different ecological niches. To evaluate potential acaricide resistance and better define the distributions of the tropical and temperate lineages throughout the US and in northern Mexico, we employed a highly multiplexed amplicon sequencing approach to characterize sequence diversity at: 1) three loci within the voltage-gated sodium channel (VGSC) gene, which contains numerous genetic mutations associated with resistance to SPs; 2) a region of the gamma-aminobutyric acid-gated chloride channel gene (GABA-Cl) containing several mutations associated with dieldrin/fipronil resistance in other species; and 3) three mitochondrial genes (COI, 12S, and 16S). We utilized a geographically diverse set of Rh sanguineus s.l. collected from domestic pets in the US in 2013 and a smaller set of ticks collected from canines in Baja California, Mexico in 2021. We determined that a single nucleotide polymorphism (T2134C) in domain III segment 6 of the VGSC, which has previously been associated with SP resistance in Rh. sanguineus s.l., was widespread and abundant in tropical lineage ticks (>50 %) but absent from the temperate lineage, suggesting that resistance to SPs may be common in the tropical lineage. We found evidence of multiple copies of GABA-Cl in ticks from both lineages, with some copies containing mutations associated with fipronil resistance in other species, but the effects of these patterns on fipronil resistance in Rh. sanguineus s.l. are currently unknown. The tropical lineage was abundant and geographically widespread, accounting for 79 % of analyzed ticks and present at 13/14 collection sites. The temperate and tropical lineages co-occurred in four US states, and as far north as New York. None of the ticks we examined were positive for Rickettsia rickettsii or Rickettsia massiliae.

Establishment of Parentage Identification Method for Sea Urchin Strongylocentrotus intermedius Based on SSR-seq Technology

To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was used for gene frequency statistics, simulated analysis, and parentage identification analysis. The results showed that, in validation population, using 15 microsatellite loci, the highest success rate of parent pairs identification was 86%, the highest success rate of female parent identification was 93%, and the highest success rate of male parent identification was 90%. The simulated population was analyzed using 12-15 loci, and the identification rate was up to 90%. In cases where accurate parentage was not achieved, individuals could exhibit genetic similarities with 1-3 male or female parents. Individuals identified as lacking a genetic relationship can be selected as parents to prevent inbreeding. This study shows that parent pairs or single parents of most offspring can be identified successfully using these 15 selected loci. The results lay a foundation for the establishment of a parentage identification method for S. intermedius.

Barriers to chimpanzee gene flow at the south-east edge of their distribution

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.

Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations

Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.

Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.

Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea

Developing new varieties in fruit and tea breeding programs is very costly and labor-intensive. Thus, establishing a variety discrimination system is important for protecting breeders’ rights and producers’ profits. Simple sequence repeat (SSR) databases that can be utilized for both next-generation sequencing (SSR-GBS) and polymerase chain reaction–capillary electrophoresis (PCR-CE) would be very useful in variety discrimination. In the present study, SSRs with tri-, tetra- and pentanucleotide repeats were examined in apple, pear and tea. Out of 37 SSRs that showed clear results in PCR-CE, 27 were suitable for SSR-GBS. Among the remaining markers, there was allele dropout for some markers that caused differences between the results of PCR-CE and SSR-GBS. For the selected 27 markers, the alleles detected by SSR-GBS were comparable to those detected by PCR-CE. Furthermore, we developed a computational pipeline for automated genotyping using SSR-GBS by setting a value “α” for each marker, a criterion whether a genotype is homozygous or heterozygous based on allele frequency. The set of 27 markers contains 10, 8 and 9 SSRs for apple, pear and tea, respectively, that are useful for both PCR-CE and SSR-GBS and suitable for automation. The databases help researchers discriminate varieties in various ways depending on sample size, markers and methods.

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

Early blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( {\overline{r}_{d} } \right)$$\end{document}r¯d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

Muskrats as a bellwether of a drying delta

Wetlands worldwide are under threat from anthropogenic impacts. In large protected North American areas such as Yellowstone and Wood Buffalo National Parks, aquatic habitats are disappearing and wetland-dependent fauna are in decline^1-3. Here we investigate population dynamics of an indicator species in Canada's Peace-Athabasca Delta ("the delta"), a World Heritage Site. Based on population surveys, habitat mapping and genetic data from 288 muskrats, we use agent-based modeling and genetic analyses to explain population expansion and decline of the semi-aquatic muskrat (Ondatra zibethicus). Simulations quantify a large population (~500,000 individuals) following flood-induced habitat gains, with decreased size (~10,000 individuals) during drying. Genetic analyses show extremely low long-term effective population size (N_e: 60-127), supporting a legacy of population bottlenecks. Our simulations indicate that the muskrat population in the delta is a metapopulation with individuals migrating preferentially along riparian pathways. Related individuals found over 40 km apart imply dispersal distances far greater than their typical home range (130 m). Rapid metapopulation recovery is achieved via riparian corridor migration and passive flood-transport of individuals. Source-sink dynamics show wetland loss impacts on the muskrat metapopulation's spatial extent. Dramatic landscape change is underway, devastating local fauna, including this generalist species even in a protected ecosystem.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

Background

In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics.

Results

Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands.

Conclusions

Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01862-1.

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

The use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

Population abundance in arctic grayling using genetics and close-kin mark-recapture

Arctic Grayling (Thymallus arcticus) are among the most widely distributed and abundant freshwater fish in the Yukon Territory of Canada, yet little information exists regarding their broad and fine-scale population structures or the number and size of these populations. The estimation of population abundance is fundamental for robust management and conservation, yet estimating abundance in the wild is often difficult. Here, we estimated abundance of an Arctic Grayling population using multiple genetic markers and the close-kin mark-recapture (CKMR) method. A total of N = 1,104 Arctic Grayling collected from two systems in Yukon were genotyped at 38 sequenced microsatellites. We first identified structure and assessed genetic diversity (effective population size,N ^ e ). Collections from one of the systems (Lubbock River) comprised adults and young-of-the-year sampled independently allowing the identification of parent-offspring pairs (POPs), and thus, the estimation of abundance using CKMR. We used COLONY and CKMRsim to identify POPs and both provided similar results leading to indistinguishable estimates (95% CI) of census size, that is,N ^ c ( C O L O N Y ) = 1858 (1259-2457) andN ^ c ( C K M R s i m ) = 1812 (1229-2389). The accuracy of the population abundance estimates can in the future be improved with temporal sampling and more precise age or size-specific fecundity estimates for Arctic Grayling. Our study demonstrates that the method can be used to inform management and conservation policy for Arctic Grayling and likely also for other fish species for which the assumption of random and independent sampling of adults and offspring can be assured.

Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe

BACKGROUND

Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts.

RESULT

To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east-west differentiations in Middle-Europe.

CONCLUSION

We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.

The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)

The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.

Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (n= 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, Structure) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.

Fast sequence-based microsatellite genotyping development workflow

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.

Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-throughput genotyping approaches

Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.

Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management

The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.

Molecular analysis of hemoglobinopathies in a large ethnic Hakka population in southern China

Thalassemia is an inherited autosomal recessive disorder with microcytic hypochromic anemia resulting from reduced or absent synthesis of 1 or more of the globin chains of hemoglobin. This study provided the insight into prevalence and molecular characterization of thalassemia in Hakka population. 14,524 unrelated subjects were included in our study from January 2015 to November 2017. All the subjects were detected by hematological analysis, hemoglobin electrophoresis analysis, and molecular diagnosis (gap-polymerase chain reaction and flow-through hybridization technology). Data analysis was used to compare allele frequencies between the Hakka populations. Seven thousand four hundred twenty-two cases of microcytosis were found. The percentage of microcytosis in Meizhou, Ganzhou, and Heyuan was 50.91% (6738/13,236), 51.27% (445/868), and 56.90% (239/420), respectively. A total of 5516 mutant chromosomes were identified, including 3775 α-thalassemia and 1741 β-thalassemia. --/αα was the most common α-thalassemia genotype, followed by -α/αα and -α/αα, accounted for 84.92% of α-thalassemia genotypes. Twelve kinds of mutations and 26 genotypes in β-thalassemia were found. IVS-II-654(C→T), CD41-42(-TCTT), -28(A→G), and CD17(A→T) alleles accounted for 92.65% of these mutations. IVS-II-654/N, CD41-42/N, -28/N, CD17/N genotypes accounted for 91.53% of β-thalassemia genotypes. 27 fetuses with at-risk pregnancies were subjected to prenatal diagnosis. Five fetuses were Bart's hydrops syndrome and 2 fetuses with β-thalassemia major. There were some differences in molecular characterization of thalassemia among Hakka people in different areas of southern China. Our results enriched the related information of thalassemia in the region, which provided valuable references for the prevention and control of thalassemia.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

BACKGROUND

Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and unstable nature, making them a major source of genomic variation between individuals. Despite recent advances in high throughput sequencing, analysis of tandem repeats in the context of complex diseases is still hindered by technical limitations. We report a novel targeted sequencing approach, which allows simultaneous analysis of hundreds of repeats. We developed a Bayesian algorithm, namely - GtTR - which combines information from a reference long-read dataset with a short read counting approach to genotype tandem repeats at population scale. PCR sizing analysis was used for validation.

RESULTS

We used a PacBio long-read sequenced sample to generate a reference tandem repeat genotype dataset with on average 13% absolute deviation from PCR sizing results. Using this reference dataset GtTR generated estimates of VNTR copy number with accuracy within 95% high posterior density (HPD) intervals of 68 and 83% for capture sequence data and 200X WGS data respectively, improving to 87 and 94% with use of a PCR reference. We show that the genotype resolution increases as a function of depth, such that the median 95% HPD interval lies within 25, 14, 12 and 8% of the its midpoint copy number value for 30X, 200X WGS, 395X and 800X capture sequence data respectively. We validated nine targets by PCR sizing analysis and genotype estimates from sequencing results correlated well with PCR results.

CONCLUSIONS

The novel genotyping approach described here presents a new cost-effective method to explore previously unrecognized class of repeat variation in GWAS studies of complex diseases at the population level. Further improvements in accuracy can be obtained by improving accuracy of the reference dataset.

Molecular prenatal diagnosis of alpha and beta thalassemia in pregnant Hakka women in southern China

BACKGROUND

To date, there has been no systematic study of DNA-based prenatal diagnosis of thalassemia in pregnant Hakka women in southern China.

METHODS

A total of 279 pregnant Hakka women with confirmed cases of thalassemia who had been treated at the Meizhou People's Hospital in China's Guangdong Province from January 2014 to December 2016 were here enrolled. Genomic DNA was extracted from peripheral blood of couples and villus, amniotic fluid, or fetal cord blood. DNA-based diagnosis was performed on the tissues of fetuses whose parents had tested positive for α- and β-globin gene mutations were found using polymerase chain reaction (PCR) and flow-through hybridization technique. Follow-up visits were performed 6 months after the fetuses were born. Prenatal diagnosis was performed on 279 fetuses in at-risk pregnancies.

RESULTS

Here, 211 α-thalassemia fetuses were confirmed, including 41 (19.43%) that tested positive for Bart's hydrops syndrome and 15 (7.11%) for Hb H disease. There were 103 (48.81%) heterozygotes. β-thalassemia was confirmed in 68 fetuses, including 23 (33.82%) with severe thalassemia and 27 (39.71%) heterozygotes. Another 12 cases were confirmed with α+β-thalassemia, including three cases of severe β-thalassemia. DNA-based testing prenatal diagnosis of thalassemia was found to be highly reliable.

CONCLUSIONS

Our findings provide key information for clinical genetic counseling of prenatal diagnosis for major thalassemia in pregnant Hakka women in southern China.

Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper)

The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (Capros aper) across the species' range. Microsatellite loci were developed de novo and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies-a crucial element for assessment, sustainable management and conservation of valuable biological resources.