Microsatellite Research Articles

De novo assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat‐mediated recombination

Phellodendron amurense Rupr., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of P. amurense, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between P. amurense and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.

Global Presence and Penetrance of CSF1R-Related Disorder.

To highlight the worldwide presence of CSF1R-related disorder (CSF1R-RD), discuss its penetrance, and provide the first haplotype analysis. Data on patients worldwide were collected, including demographics, genotype, family history, and clinical status. For haplotype analysis, polymorphisms of short tandem repeats in 3 distinct families with CSF1R p.Ile794Thr variant were examined. Nineteen new patients were included, at a mean age of 38.7 years (ranging from 11 to 74 years), from 14 families from the Americas, Asia, Australia, and Europe, including the first from Mexico, North Macedonia, and Ukraine. Fifteen CSF1R variants were found, including 8 novel. Three patients were compound heterozygotes with disease onset at 1, 4, and 22 years. Patients with heterozygous CSF1R variants developed symptoms at a mean of 39.0 years (range 8-71 years). Four patients died at a mean of 3.3 years from onset (range 2-5 years). Negative family history was noted in 7 patients. In haplotype analysis, 2 families exhibited shared haplotype encompassing ∼6-Mb region downstream of the CSF1R while the third family displayed a different haplotype. CSF1R-RD has a global prevalence. The reasons for negative family history include de novo variants (as shown by the haplotype analysis), mosaicism, and incomplete penetrance, which are possibly modulated by environmental and genetic factors.

Squamous cell carcinoma of the cervix associated with choriocarcinomatous differentiation: a case report and review of the literature.

The morphology of the choriocarcinomatous variant of cervical squamous cell carcinoma (SCC) suggests an undifferentiated aggressive biological behaviour and a poor outcome, for which standard treatment has not been established. In addition, cases are rarely reported, with only five cases of patients with cervical carcinoma with choriocarcinoma reported previously in the literature. This current case report describes in detail a patient who was diagnosed with cervical SCC mixed with choriocarcinomatous differentiation. The case report includes details of the diagnosis, pathology, short tandem repeat genotyping, treatment and follow-up of this patient. As there is no standard treatment for this variant, the patient underwent surgery followed by radiotherapy. Unfortunately, 4 months after therapy discontinuation, radiological evaluation and laboratory tests documented a recurrence of the disease and the patient died. This report also systematically reviews the literature on cervical cancer associated with choriocarcinomatous differentiation and the five previous cases. It provides the most up-to-date summary of this disease, including its clinical manifestations, histopathology, diagnosis, treatment and prognosis.

Nuclear DNA Markers to Distinguish between Salix caprea, Salix gracilistyla, and Their Interspecific Hybrids

The Salix genus of the Salicaceae family has advantages such as rapid initial growth, a high germination rate, and asexual reproduction; therefore, it is used as a short-rotation energy crop for biomass production. The National Institute of Forest Science created new interspecific hybrid cultivars with superior biomass production by artificially interbreeding Salix caprea L. and Salix gracilistyla Miq. Identifying these hybrids during the seedling stage is challenging because their separate reproductive and vegetative growth stages necessitate prolonged observation of their morphological characteristics. Consequently, a reliable identification method is required to overcome these limitations. This study aimed to develop nuclear DNA markers to distinguish between S. caprea, S. gracilistyla, and their interspecific hybrids. An evaluation of 35 nuclear simple-sequence repeat (nSSR) markers in the Salix genus revealed two markers that distinguish these parent species and their hybrids. A sequence analysis confirmed the presence of insertion-deletion (InDel) regions within the nSSR markers that differed between S. caprea and S. gracilistyla. To effectively identify hybrids, a primer set comprising the InDel region, which exhibited only interspecies differences and no intraspecies differences, was developed. The results of this study will facilitate the genetic resource management of interspecific hybrids between S. caprea and S. gracilistyla, thus allowing for early identification and improved management of hybrids.

Characterization of Intsia spp. from Indonesia using microsatellite markers

Microsatellite DNA markers are known to have a high level of genetic diversity and can be used for various purposes. These include population genetic analysis, gene flow assessment, pollen distribution, parent analysis, and accurate distinction between types and varieties. Despite the potential application of microsatellite markers, their development process often requires high costs, energy, and time. To overcome the limitations, several studies have proposed the use of cross-species amplification, which has proven to be a cost and time-efficient method for obtaining species-specific DNA markers. Therefore, this study aimed to identify three species of Merbau in Indonesia, namely Intsia bijuga, I. palembanica, and I. acuminata using cross-species amplification. The three species are known to exhibit similarities in all taxonomical characteristics except for minor differences in the number of leaf pairs per twig and the tip shape of the leaflets. These species also have different levels of economic value and conservation status due to variations in the type of wood produced. Several studies have shown that identification errors can affect the economic value of their wood and logging mistakes can lead to a decrease in the genetic diversity. To address the concerns, Intsia bijuga and I. acuminata from Indonesia were selected as test samples for the cross-amplification of microsatellite markers created for I. palembanica. Due to their taxonomical similarities, the diagnostic characteristics of each Intsia species were assessed based on microsatellite markers. Leaf samples were obtained from three species of Intsia that had been verified and identified based on morphological characteristics by taxonomists from the Bogor Botanical Garden Indonesia. In addition, a total of 10 polymorphic I. palembanica microsatellite markers from the previous literature were used in this study. The results showed that the cross-species amplification of microsatellite locus was successful in all markers. Certain alleles were also observed to be shared by the three species of Intsia, while some were specific to a particular species. These specific alleles could also serve as a diagnostics characteristic for Intsia spp. In addition, a set of polymorphic microsatellites showing a successful transfer across species of Intsia could serve as a valuable tool for comparative studies among related taxa species and breeding and conservation programs.

The Characteristics of Microsatellites and Development of SSR Markers in the Genome of Periplaneta americana

The research was to analyze the number and pattern of microsatellites in Periplaneta americana’s genome, and also developed tetranucleotide SSR markers. We thoroughly scrutinized and dissected the inherent traits that govern the allocation of microsatellite sequences within the profound domain of P. americana’s genome, software MSDBv2 allowed for the utilization of 2.67 Gb. There were precisely 1,498,458 flawless microsatellite sequences, encompassed approximately 1.57%. The cumulative length of microsatellites was 45,076,707 bp, and the abundance of microsatellites was 16889.577 loci/Mb. Out of all the microsatellite repeat variations, the trinucleotide repeats accounted for 44.83% of the total, with a count of 671,830, which were the most abundant type. The tetranucleotide, mononucleotide, pentanucleotide, dinucleotide, and hexanucleotide repeats accounted for 29.01%, 13.62%, 8.37%, 3.70% and 0.47%, respectively. The numbers of different repeat copy categories in each repeat type were also quite different, such as the A in mononucleotide repeat type, the AT in dinucleotides, the AAT in trinucleotides, and AAAT in tetranucleotide were the most of each categories. 143 primers were designed. After undertaking the arduous task of enhancing the initial PCR conditions to perfection, we successfully determined and analyzed a gargantuan number of 38 different polymorphic tetranucleotide microsatellite markers with utmost precision, employed the assistance of two-color fluorescence markers and ingenious genotyping scaned for their comprehensive characterization. The genetic variation in P. americana population involved analyzing the diversity of microsatellite loci, which exhibited varying numbers of alleles per locus ranging from 4 to 21 among the 32 individuals studied. Among them, there were 24 microsatellite loci whose alleles were greater than 10, accounted for 63.16% of the total number of polymorphic microsatellite. The calculated degrees of genetic diversity varied between 0 and 1, the observed heterozygosities was between 0.219 and 1.0, with a mean of 0.6391. The expected heterozygosities was between 0.312 and 0.942, with a mean of 0.7663. The PIC was between 0.296 and 0.923, with a mean of 0.7294, and there were 36 microsatellite loci whose PIC was greater than 0.5, accounted for 94.74%. This study indicated that new development of microsatellite markers for P. americana was feasible. Furthermore, these new development microsatellite markers will provide adequate and reliable molecular genetics data for carrying out the research of molecular ecology and conservation genetics for P. americana.

Quantifying Genetic Diversity Based on Morphological and Molecular Analysis in Pearl millet [<i>Pennisetum glaucum</i> (L.) R. Br.] Inbred Lines

The experiment was carried out with thirty pearl millet inbred lines at Research Farm of ICAR-AICRP on Pearl Millet, Project Coordinating Unit, Mandor-Jodhpur during kharif 2020 in randomized block design (RBD) with three replications. Morphological and molecular diversity was assessed in 30 pearl millet inbred lines by Mahalanobis D2 analysis and Simple Sequence Repeats (SSR) molecular marker, respectively. Total five clusters were formed from D2 analysis and seven clusters were generated from SSR markers data analysis. The character viz. panicle girth, number of effective tillers per plant and 1000 seed weight contributed maximum to morphological diversity. The clustering pattern based on SSR markers data revealed that genotypes at molecular level had high diversity as compared to that seen at phenotypic level. There was significant differences among the clustering pattern of D2 and SSR molecular marker analysis. The reason may be environmental influence on phenotypic level. This information can be used as selection criteria to have hybridization between diverse parents to exploit heterosis in pearl millet breeding program.

Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host.

Parasites, including pathogens, can adapt to better exploit their hosts on many scales, ranging from within an infection of a single individual to series of infections spanning multiple host species. However, little is known about how the genomes of parasites in natural communities evolve when they face diverse hosts. We investigated how Bartonella bacteria that circulate in rodent communities in the dunes of the Negev Desert in Israel adapt to different species of rodent hosts. We propagated 15 Bartonella populations through infections of either a single host species (Gerbillus andersoni or Gerbillus pyramidum) or alternating between the two. After 20 rodent passages, strains with de novo mutations replaced the ancestor in most populations. Mutations in two mononucleotide simple sequence repeats (SSRs) that caused frameshifts in the same adhesin gene dominated the evolutionary dynamics. They appeared exclusively in populations that encountered G. andersoni and altered the dynamics of infections of this host. Similar SSRs in other genes are conserved and exhibit ON/OFF variation in Bartonella isolates from the Negev Desert dunes. Our results suggest that SSR-based contingency loci could be important not only for rapidly and reversibly generating antigenic variation to escape immune responses but that they may also mediate the evolution of host specificity.

A survey in natural olive resources exposed to high inoculum pressure indicates the presence of traits of resistance to Xylella fastidiosa in Leccino offspring.

The epidemic spread of the harmful bacterium Xylella fastidiosa causing the "olive quick decline syndrome", decimating olive trees in southern Italy, in the region of Apulia, prompted investigations to search for olive genotypes harbouring traits of resistance. A prospecting survey was carried out to identify, in the heavily infected area of Apulia, olive genotypes bearing resistance. Given the limited genetic diversity in the commercial olive groves with few cultivars widely cultivated, surveys targeted predominantly spontaneous olive genotypes in natural and uncultivated areas. Trees, selected for the absence of symptoms, were subjected to diagnostic tests and parentage analysis to disclose their genetic background. Transcriptomic analyses were also employed to decipher the molecular pathways in resistant genotypes. Artificial inoculations were carried out to confirm the resistant phenotypes of four open-pollinated seedlings of the cultivar Leccino. Among the 171 olive collected genotypes, 139 had unique simple sequence repeat (SSR) profiles, with the cultivars Leccino, Cellina di Nardò, and Ogliarola salentina being the most frequent candidate parents. Among the Leccino progeny (n. 61), 67% showed a highly resistant (HR), resistant (R), or tolerant (T) phenotype to infection by X. fastidiosa. The occurrence of such phenotypes among those deriving from Cellina di Nardò and Ogliarola salentina was 32% and 49%, respectively. Analyses of the transcriptomic profiles of three Leccino-bearing genotypes, naturally infected and not showing symptoms, unravelled that a total of 17,227, 13,031, and 4,513 genes were found altered in the expression, including genes involved in photosynthesis, cell wall, or primary and secondary metabolism. Indeed, transcriptomic analyses showed that one of these genotypes (S105) was more resilient to changes induced by the natural bacterial infection than the remaining two (S215 and S234). This study consolidates the evidence on the presence and heritage of resistance traits associated with the cv. Leccino. Moreover, valuable insights were gathered when analysing their transcriptomic profiles, i.e., genes involved in mechanisms of response to the bacterium, which can be used in functional genetic approaches to introduce resistance in susceptible cultivars and initiate strategies in olive-breeding programs through marker-assisted selection.

Genetic and phenotypic evidence suggest the existence of indigenous olive population of wild var. sylvestris in the Carmel coast, southern Levant

BackgroundPopulations of Olea europaea subsp. europaea var. sylvestris, the ancestor of cultivated olives, are scattered across the Mediterranean Basin. However, after millennia of possible hybridization with cultivated varieties, the genetic identity of many of these populations remain questionable. In the southern Levant, the plausible primary domestication center of olives, many of the naturally growing olive (NGOs) are considered feral, having developed from nearby olive groves. Here, we investigated the genetic identity of NGOs population in the Carmel region, hypothesizing that their specific location, which limit anemophily, provided an opportunity for the persistence of genuine var. sylvestris.ResultsWe mapped more than 1,000 NGOs on the Kurkar ridge along the Carmel coast, within and outside the residential area of Atlit and used simple sequence repeats of 14 loci to assess the spatial genetic structure of 129 NGOs. Genetic diversity parameters and genetic distances between NGO and cultivated olives, as well as phenotypic and morphometric analyses of their oil content and pits, respectively, indicated the presence of a genuine var. sylvestris population. However, NGOs within the residential area of Atlit and old settlements showed an intermediate admix genetic structure, indicating on hybridization with local varieties, a consequence of their proximity to cultivated trees.ConclusionsIntegrating the results of genetic and phenotypic analyses we provide crucial evidence of the presence of a genuine var. sylvestris population in the southern Levant, in close geographical proximity to archaeological sites with the earliest evidence of olive exploitation in the ancient world. We supplement the results with recommendations for a conservation program that combines municipal requirements and the urgent need to preserve the largest population of var. sylvestris in the southern Levant.

Forensic characteristics of 38 Y-STR loci in the Hui population from Shaanxi Province, Northwest China

In this study, we genotyped 939 unrelated healthy individuals to investigate the genetic polymorphisms of 38 Y chromosome short tandem repeats(Y-STRs) loci included in the Yfiler™ Platinum kit in the Hui population of Shaanxi Province. Comprehensive population comparisons were performed using analysis of molecular variance(AMOVA), multidimensional scaling(MDS), and molecular evolutionary genetics analysis(MEGA) to explore population relationships. The allele frequencies of the single-copy loci ranged from 0.001 to 0.940 (DYS645), while those of the multi-copy loci ranged from 0.001 to 0.138 (DYS527). The highest genetic diversity (GD) value was observed for DYS385 (0.9723), and the lowest for DYS645 (0.1138). A total of 849 distinct haplotypes were identified among the 939 Hui individuals, with 808 (95.2 %) being unique. Haplotype diversity (HD), haplotype match probability, and discriminatory power (DC) in the Shaanxi Hui population were 0.9996, 0.0015, and 0.9041, respectively. Interpopulation comparisons based on Rst genetic distance values, phylogenetic trees, and MDS indicated that the Shaanxi Hui population has a close genetic relationship with the Ningxia Hui, Qinghai Hui, Xinjiang Hui, and Yunnan Hui populations. The population genetic stratification largely coincides with geographic distribution and language families. Our study revealed that the 38 Y-STR loci exhibit high genetic polymorphisms in the Hui population from Shaanxi Province.

Patterns of Ecological Specialisation Among Multiple Piscivorous Morphs of a Diverse Assemblage of Salvelinus Fishes

ABSTRACTAdaptive radiation is considered to be a major source of biodiversity in charrs of the genus Salvelinus. These fishes demonstrate numerous examples of diversification in postglacial lakes and rivers resulting in the emergence of different ecomorphs, including piscivorous. Usually, the number of fish feeders does not exceed two, suggesting the existence of ecological and/or internal factors that prevent further diversification. Under these circumstances, rare instances of increases in the number of piscivorous morphs are of particular interest. Here, we present a comprehensive study of the piscivorous charr assemblage in Lake Kronotskoe, residence of the most diverse species flock of Salvelinus fishes. To unravel the diversity and ecological relationships of piscivorous charrs, we analysed their morphology and microsatellite DNA polymorphism, distribution within the lake, trophic preferences and parasite load, as well as trace element accumulation, stable isotope and free fatty acid ratios. We revealed that, apart from a few strictly benthivorous morphs, the lake is inhabited by four closely related but morphologically and genetically distinct morphs that exhibit a range of piscivorous specialisation: from opportunistic secondary predation to ultra‐specialised primary piscivory. They effectively exploit the spatiotemporal structure of the ecosystem and experience diversifying selection due to niche discordance. Each piscivorous morph develops specific phenotypic, ecological and life history traits that allow it to terminate weakly overlapping branches of the trophic chain and share the energy flows of the lake ecosystem. Our data suggest that Lake Kronotskoe facilitates high level of ecological opportunity that favours niche expansion and allows the piscivorous lineage to simultaneously realise the archetypical modes of ecological diversification available to fishes in cold‐water freshwaters.

Structural insights into the recognition of purine-pyrimidine dinucleotide repeats by zinc finger protein ZBTB43.

Purine-pyrimidine repeats (PPRs) can form left-handed Z-form DNA and induce DNA double-strand breaks (DSBs), posing a risk for genomic rearrangements and cancer. The zinc finger (ZF) and BTB domain-containing protein 43 (ZBTB43) is a transcription factor containing two Cys2-His2 (C2H2) and one C3H1 zinc fingers and plays a crucial role in maintaining genomic and epigenomic integrity by converting mutagenic Z-form PPRs to the B-form in prospermatogonia. Despite its importance, the molecular mechanism underlying the recognition of PPRs by ZBTB43 remains elusive. In this study, we determined the X-ray crystal structure of the ZBTB43 ZF1-3 in complex with the B-form DNA containing the CA repeats sequence. The structure reveals that ZF1 and ZF2 primarily recognize the CACA sequence through specific hydrogen-bonding and van der Waals contacts via a quadruple center involving Arg389, Met411, His413, and His414. These interactions were further validated by fluorescence-based DNA-binding assays using mutated ZBTB43 variants. Our structural investigation provides valuable insights into the recognition mechanism of PPRs by ZBTB43 and suggests a potential role for ZBTB43 in the transformation of Z-DNA to B-DNA, contributing to the maintenance of genomic stability.

In-silico identification of simple sequence repeat (SSR) markers and phylogenetic analysis from chloroplast genomes of the genus Bambusa

Microsatellites or simple sequence repeats (SSRs), are short DNA sequences composed of repetitive units typically 1 to 6 base pairs long. These highly variable sequences are found in both protein-coding and noncoding DNA regions and exhibit a high degree of polymorphism. In the present study, chloroplast genomes of five species of Bambusa viz. B. bambos, B. multiplex, B. teres, B. vulgaris, and B. tulda, along with three outgroup species viz. Sorghum timorense, Hordeum vulgare, and Triticum aestivum were retrieved from NCBI in FASTA and GenBank formats and screened for chloroplast SSRs (cpSSRs) using MISA Perl script. The sequence analysis of the chloroplast genomes of different species of Bambusa confirmed the presence of 144 cpSSRs. The number of cpSSRs varied among the five bamboo species, with B. vulgaris exhibiting the highest count (31) and B. multiplex showing the lowest (27). Tetranucleotides were the most observed repeats in Bambusa, followed by mono-, di- and trinucleotides. Of the 144 SSR markers identified, only 16 (11.11 %) were suitable for primer design since the remaining sequences failed to produce acceptable primer pairs. An unweighted pair-group method with an arithmetic mean (UPGMA) dendrogram was constructed to analyze the genetic relationships among the genotypes. This analysis revealed three distinct clusters among the genotypes. SSR markers were found to be informative in differentiating the species of Bambusa and were likely to find potential applications in genetic fingerprinting, population genetics, conservation, and phylogenetics.

Fusobacterium Nucleatum Promotes Microsatellite Instability in Colorectal Carcinoma Through Up-regulation of miRNA-155-5p-Targeted Inhibition of MSH6 via the TLR4/NF-κB Signaling Pathway.

Fusobacterium nucleatum (Fn) is significantly associated with poor prognosis in colorectal carcinoma (CRC), however, mechanisms of Fn in DNA mismatch repair (MMR) and microsatellite instability (MSI) in CRC have not been fully elucidated. Clinical samples are collected to analyze the relationship between Fn abundance and microsatellite stability. Tumor cells are treated with Fn to detect the expression of proteins related to toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (Myd88), mutS homolog 6 (MSH6), and nuclear factor-κB (NF-κB) signaling pathways, respectively. Combined with the prediction results from TargetScan, the regulatory role of microRNA upstream of MSH6 is demonstrated. The effect of this regulatory axis on CRC development is demonstrated using a nude mouse tumor model. Compared with microsatellite stability (MSS)-type CRC patients, MSI-type showed higher Fn abundance. Fn treatment of CRC cells activated TLR4/Myd88/NF-κB signaling pathway, transcriptionally activating miRNA-155-5p expression, thereby negatively regulating MSH6. Fn treatment accelerated the malignant progression of CRC in mice, and this process is inhibited by miRNA-155-5p antagomir. Fn in CRC upregulated miRNA-155-5p by activating TLR4/NF-κB signaling to inhibit MSH6, and this regulatory pathway may affect MSS of cancer cells.

Association between microsatellite instability status, clinicopathological features and mitochondrial DNA amplification in patients with colorectal cancer.

The relationship between BRAF-V600E mutations, mitochondrial DNA amplification and microsatellite instability-high (MSI-H) in colorectal cancer (CRC) has yet to be fully elucidated. The aim of the present study was to assess the association between the MSI status and BRAF-V600E gene mutations/clinicopathological features/mitochondrial DNA amplification in CRC. A non-interventional study analysis was performed using the clinicopathological features of 455 patients with CRC. Immunohistochemistry was used to evaluate four mismatch repair proteins (MutS homolog 2, MutS homolog 6, MutL homolog 1 and postmeiotic segregation increased 2), Ki-67 index, and programmed cell death protein 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) expression. Additionally, PCR coupled with capillary electrophoresis were used to ascertain the MSI status. Moreover, amplification refractory mutation system-PCR was used to detect BRAF-V600E gene mutation and fluorescence in situ hybridization analysis was used to assess mitochondrial DNA. A total of 455 patients were divided into the MSI high (MSI-H) group (n=52) and microsatellite stability (MSS) group (n=403) based on their MSI status. Compared with the results of immunohistochemistry of four mismatch repair proteins, the consistency rate between mismatch repair protein deficiency and MSI was 94.23%. There were significant differences in PD-L1, primary tumor site, clinical stage, degree of differentiation, tumor size, lymph node metastasis and the occurrence of multiple primary tumors between the MSI-H group and MSS group (P<0.05 or P<0.001). However, there were no significant differences for sex, age, PD-1, Ki-67 expression and BRAF-V600E. The 24-60-month survival rate of the patients in the MSI-H group was significantly higher than that of those in the MSS group (P<0.05). Furthermore, the number of mitochondrial DNA was significantly amplified in the MSI-H group. In conclusion, the present study demonstrated that the combined detection of PD-L1 and MSI in patients with CRC can provide more accurate and effective guidance for personalized treatment.

Development of microsatellite markers and evaluation of the genetic diversity of the edible sea anemone Paracondylactissinensis (Cnidaria, Anthozoa) in China.

Paracondylactissinensis Carlgren, 1934 is a sea anemone with economic value in China. The wild population of P.sinensis has been shrinking due to overfishing and environmental pollution, which have caused price instability. In winter, the price of P.sinensis can reach 25 USD per kilogram. Up to now, there are no genetic markers developed for P.sinensis, preventing a further exploration of their population genetic diversity. In this study, the full-length transcriptome of P.sinensis was sequenced and microsatellite DNA markers (simple sequence repeats [SSRs]) were developed from those transcripts. A total of 52 primer pairs, which can amplify specific polymorphic bands in PCR experiments, were designed for the SSR markers. Genetic diversity and population genetics were analysed for P.sinensis populations collected from the coasts of Taizhou and Rizhao using six microsatellite DNA loci. While inbreeding was detected in both populations (Fis > 0), the overall number of alleles (Na = 11.3) and bottleneck analysis suggested that the genetic diversity of P.sinensis has not been greatly impacted. Clustering analyses using STRUCTURE, principal coordinate analysis and unweighted pair group method with arithmetic mean tree revealed that the Taizhou population diverged from the Rizhao population; however, the genetic differentiation between the populations was moderate. Human-mediated commercial activities may be the principal reasons for the gene flow between the populations. Our study provides the first evaluation of the genetic resources of wild P.sinensis populations in China, which can serve as a useful reference for future comparative studies on population genetics and may guide policy-makers in initiating strategies for germplasm conservation and artificial breeding.

Identification of Genetic Diversity of Taro White Cattle Using Microsatellite DNA Markers

Taro white cattle have a small population found in Taro Village, Tegalalang, and Gianyar, Bali, which must be protected as one of the most valuable biological resources for the Hindu community in Bali. White cattle require conservation efforts, with morphometric characterization and genetics providing the first phases of an animal conservation program. The purpose of this study was to identify the genetic diversity of Taro white cattle based on allele frequency, heterozygosity, and fixation index (FIT) using different microsatellite DNA loci so that it can be used as a study and reference in determining policies for the conservation of Taro white cattle in Indonesia, particularly in Bali. This cross-sectional observational study utilized ETH 185, INRA 035, and INRA 037 microsatellite DNA markers. Polymerase chain reaction amplified a total of 22 Taro white cattle blood samples with an average of 4.33 alleles; the average observed heterozygosity and expected heterozygosity were 0.288 and 0.637, respectively, with an average fixation index value of 0.55. In conclusion, there is a significant deviation from the Hardy-Weinberg equilibrium with the likelihood of inbreeding, as indicated by the Hardy-Weinberg balance. The microsatellite loci used in this study can be further used to evaluate the genetic diversity of Taro white cattle.

Relationships between crayfish population genetic diversity, species richness, and abundance within impounded and unimpounded streams in Alabama, USA.

Understanding the relationship between multi-scale processes driving community- and population-level diversity can guide conservation efforts. While the importance of population-level genetic diversity is widely recognized, it is not always assessed for conservation planning, and positive correlations with community-level diversity are sometimes assumed, such that only the latter is measured. We surveyed species richness and cumulative multispecies abundance of crayfishes in impounded and unimpounded streams in the southern Appalachian Mountains (Alabama, USA). We simultaneously assessed levels of population genetic diversity within two focal crayfishes (Faxonius validus and F. erichsonianus) using nuclear (nDNA; inter-simple sequence repeat (ISSR)) and mitochondrial DNA (mtDNA; mitochondrial DNA cytochrome oxidase subunit I (mtCOI)) markers. We then tested for species-genetic diversity correlations (SGDCs), species diversity-abundance correlations (i.e., more individuals hypothesis, MIH), and abundance-genetic diversity correlations (AGDCs) across sites. We also examined the relationship between each of the three different types of correlation (i.e., species richness, cumulative multispecies abundance, and population genetic diversity) and stream habitat characteristics and fragmentation. Surprisingly, based on F. validus mtDNA data, sites with the greatest multispecies abundance had the lowest genetic diversity, indicating a negative AGDC. However, no AGDC was evident from nDNA. There was no evidence of SGDCs for F. validus based on either of the two genetic data types. For F. erichsonianus, there was no evidence for SGDC or AGDC. When considering the community-level data only, there was no support for the MIH. Stream width was positively correlated with F. validus genetic diversity, but negatively correlated with multispecies abundance. Similarly, species richness was positively correlated with stream width in unimpounded streams but negatively correlated with width in impounded streams. These findings indicate that community-level diversity cannot be indiscriminately used as a proxy for population-level diversity without empirically testing this correlation on the focal group. As such, community- and population-level assessments for multiple crayfish species are needed to better understand drivers of diversity and eco-evolutionary processes which will aid in the conservation of this vulnerable taxonomic group.

NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm.

Short-tandem repeats (STRs) are the type of genetic markers extensively utilized in biomedical and forensic applications. Due to sequencing noise in nanopore sequencing, accurate analysis methods are lacking. We developed NASTRA, an innovative tool for Nanopore Autosomal Short Tandem Repeat Analysis, which overcomes traditional database-based methods' limitations and provides a precise germline analysis of STR genetic markers without the need for allele sequence reference. Demonstrating high accuracy in cell line authentication testing and paternity testing, NASTRA significantly surpasses existing methods in both speed and accuracy. This advancement makes it a promising solution for rapid cell line authentication and kinship testing, highlighting the potential of nanopore sequencing for in-field applications.