Microsatellite Research Articles

Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense.

Citrus huanglongbing (HLB) is a major challenge that impacts the flourishing of the citrus industry. Therefore, analyzing the genomic information of HLB-resistant or tolerant citrus resources is crucial for breeding HLB-resistant citrus varieties. The Carrizo citrange, a hybrid of Citrus sinensis and Poncirus trifoliata, plays a pivotal role in citrus cultivation. However, its genetic explorations are difficult due to the absence of a reference genome or full-length transcriptome. In order to enhance our understanding of the genetic information of citrange, we conducted a full-length transcriptomic sequencing of multiple tissues from the Carrizo citrange using the PacBio Sequel II platform. Moreover, we performed gene ontology (GO) annotation, gene functional annotation, simple sequence repeats (SSR) types analysis, as well as identification of lncRNAs, alternative splicing events, and analysis of pathogen defense-related genes. Results showed that a total of 43,452 isoforms were generated, with 43,307 of them being annotated. GO annotation indicated the involvement of these isoforms in various biological processes, cellular components, and molecular functions. The coding sequence length of the isoforms ranged from 1,000 to 4,000 base pairs (bp). Moreover, we have discovered 54 varieties of transcription factors and regulators, along with 16 classifications of genes associated with resistance. Among all types of SSRs, trimer type SSRs were the most abundant. 130 lncRNAs were predicted to be highly reliable in the isoforms of the Carrizo citrange, with alternative splicing events identified, and the most frequent being retained intron. The analysis of gene family expansion and contraction revealed a significant increase in pathogen defense-related genes within the Carrizo citrange. The results of this study will be of great value for future investigations into gene function in citrange and for expanding the genetic pool for breeding citrus varieties resistant or tolerant to HLB.

Genetic Diversity and Forensic Utility of X-STR Loci in Punjabi and Kashmiri Populations: Insights into Population Structure and Ancestry

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

“CLADE-FINDER”: Candida auris Lineage Analysis Determination by Fourier Transform Infrared Spectroscopy and Artificial Neural Networks

In 2019, Candida auris became the first fungal pathogen included in the list of the urgent antimicrobial threats by the Centers for Disease Control (CDC). Short tandem repeat (STR) analysis and whole-genome sequencing (WGS) are considered the gold standard, and can be complemented by other molecular methods, for the genomic surveillance and clade classification of this multidrug-resistant yeast. However, these methods can be expensive and require time and expertise that are not always available. The long turnaround time is especially not compatible with the speed needed to manage clonal transmission in healthcare settings. Fourier transform infrared (FTIR) spectroscopy, a biochemical fingerprint approach, has been applied in this study to a set of 74 C. auris isolates belonging to the five clades of C. auris (I-V) in combination with an artificial neural network (ANN) algorithm to create and validate “CLADE-FINDER”, a tool for C. auris clade determination. The CLADE-FINDER classifier allowed us to discriminate the four primary C. auris clades (I-IV) with a correct classification for 96% of the samples in the validation set. This newly developed genotyping scheme can be reasonably applied for the effective epidemiological monitoring and management of C. auris cases in real time.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Comprehensive genome analysis and variant detection at scale using DRAGEN.

Research and medical genomics require comprehensive, scalable methods for the discovery of novel disease targets, evolutionary drivers and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size or location. Here we present DRAGEN, which uses multigenome mapping with pangenome references, hardware acceleration and machine learning-based variant detection to provide insights into individual genomes, with ~30 min of computation time from raw reads to variant detection. DRAGEN outperforms current state-of-the-art methods in speed and accuracy across all variant types (single-nucleotide variations, insertions or deletions, short tandem repeats, structural variations and copy number variations) and incorporates specialized methods for analysis of medically relevant genes. We demonstrate the performance of DRAGEN across 3,202 whole-genome sequencing datasets by generating fully genotyped multisample variant call format files and demonstrate its scalability, accuracy and innovation to further advance the integration of comprehensive genomics. Overall, DRAGEN marks a major milestone in sequencing data analysis and will provide insights across various diseases, including Mendelian and rare diseases, with a highly comprehensive and scalable platform.

Diversity of Improved Diploids and Commercial Triploids from Musa spp. via Molecular Markers

Banana breeding consists of obtaining diploid, triploid, and tetraploid intra- and interspecific hybrids by conventional breeding methods with the objective of aggregating characteristics of agronomic and commercial interest. Given the narrow genetic base of bananas, Embrapa’s Banana Genetic Breeding Program (BGBP) aims at crosses between improved diploids (ID) (ID × ID) and between improved diploids (ID) and commercial triploids (ID × CTP) and tetraploids (ID × CTT), in order to increase the genetic base and variability in bananas regarding agronomic traits of interest and resistance to main biotic and abiotic factors. These improved diploids are resistant to main fungal diseases such as yellow (YSD) and black Sigatoka (BSD) disease and Fusarium wilt (race 1 and subtropical race 4), the latter being one of the most devastating diseases in bananas. The genetic diversity between 22 improved diploids and seven commercial banana triploids was analyzed using DNA molecular markers. Five IRAP (Inter-Retrotransposon Amplified Polymorphism, 7 ISSR (Inter-Simple Sequence Repeats) and 12 SSR (Simple Sequence Repeat) markers were used. The genetic dissimilarity matrix was based on the Jaccard dissimilarity index; clusters were separated using the UPGMA (Unweighted Pair Group Method With Arithmetic Mean) method and cophenetic correlation of 0.8755. This study of the genetic diversity between improved diploids and commercial triploids, based on the genetic dissimilarity matrix, revealed that the most dissimilar diploids were DM23 and DM15 (74%) and DM16 and DM15 (74%). The smallest genetic distances between the improved diploids and commercial triploids were between TCGN25 and DM17 (50%) and TCN26 and DM17 (50%). The genetic distance matrix also revealed important genotypes to be used in crosses in order to maintain good characteristics in commercial triploids when crossed with improved diploids. The results of our study provide better breeding strategies for one of the largest banana-breeding programs worldwide focused on the development of banana varieties resistant to main biotic and abiotic factors.

The genetic diversity and population structure of wild and cultivated Avena species in Ethiopia using a SSR markers

Oats are grains that can be consumed by both animals and humans. They have thrived in Ethiopia, where certain oat species are considered native to the region. This work represents the first investigation of the population structure and genetic diversity of Ethiopian and other country oats. This led the scientists to explore the genetic diversity and population structure of wild and cultivated Ethiopian oats (Avena) species as well as oat cultivated in USA, the Netherlands and Austria. This study's main objective looks to be to investigate the variation in genetic makeup of cultivated and wild oat species. Studying the population structure of the oat species in the germplasm of Ethiopia, USA, the Netherlands and Austria. We used nineteen fluorescent SSR (simple sequence repeat) markers since previous research had indicated that these markers had high PIC (polymorphism information content) values. Five species of Avena were studied among the 176 oat accessions: A. sativa (cultivated oats) and four wild oats, such as A. abyssinica, A. vaviloviana, A. fatua, and A. sterilis. The AMOVA investigation revealed significant genetic distinctions among populations, individuals, and within individuals, explaining 18 % of the variance within populations, 4 % among populations, and 78 % within individuals. The AMOVA analysis of Avena species demonstrated extensive variance, with 33 % variation among species and 67 % within each species, underscoring robust species differentiation. The study also discovered gene interchange between wild oat and cultivated populations, defining two Avena species: domesticated oats and wild oats. Using the STRUCTURE software at K = 2, PCoA, and UPGMA, a distinct genetic structure was displayed in the dataset. Despite variations in ploidy levels and genomes, A. sterilis and A. vaviloviana were determined to be more closely linked, whereas A. abyssinica and A. fatua demonstrated a close association. This research delivers valuable insights for scientists and can be employed in oat breeding programs to improve future oat yield and productivity.

Assessment of Genetic Diversity and Population Structure of Exotic Sugar Beet (Beta vulgaris L.) Varieties Using Three Molecular Markers

Sugar beet (Beta vulgaris L.) is a biennial herb belonging to the Amaranthaceae family. It contributes to approximately 30% of the world’s total sucrose production and is an economically important crop. In this study, we analyzed the genetic diversity and population structure of 132 exotic sugar beet varieties using three molecular makers: four pairs of simple sequence repeat (SSR) primers, three pairs of insertion–deletion sequence (InDel) primers, and 20 cis-element amplification polymorphism (CEAP) primers. The results indicated that the number of alleles (Na) was 298, among which the number of effective alleles (Ne) was 182.426 (accounting for approximately 61.2%). The mean value of the genetic diversity index was 0.836. The polymorphic information content (PIC) was 0.639–0.907 (mean = 0.819), indicating a high level of polymorphism. These sugar beet varieties were classified into six clusters using the UPGMA method of cluster analysis. Population structure analysis revealed that the most ideal K value was 6. This indicated that the test materials could be divided into six categories, consistent with the clustering results. The clustering results indicated that most sugar beet varieties from the same breeding company clustered together, and the genetic distance between them was small, indicating that they may share the same male and/or female parent. Some varieties from different companies clustered together, indicating a narrow genetic base and potential exchange of germplasm resources between breeding companies. This study revealed the genetic differences among exotic sugar beet varieties and characteristics of the population structure. It provided a scientific basis for the identification of sugar beet varieties and markers-assisted breeding in China in the future.

Comparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium

‘Boju’ and ‘Huaiju’ are cultivars of the Chrysanthemum (Chrysanthemum morifolium Ramat.) in the family Asteraceae, valued for their medicinal, tea, and ornamental properties, and valued by individuals. However, the yield and quality of medicinal chrysanthemums are limited by the characteristics of the germplasm resources, including the identification at the varieties and cultivation levels. Currently, research characterizing the chloroplast genomes of medicinal Chrysanthemum flowers is relatively limited. This study conducted chloroplast whole-genome sequencing on two cultivars of Chrysanthemum, ‘Boju’ and ‘Huaiju’, and compared them with the previously published chloroplast genomes of ‘Hangbaiju’ and ‘Gongju’. The study analyzed the chloroplast genome structures of these four medicinal Chrysanthemums, identifying mutation hotspots and clarifying their phylogenetic relationships. The chloroplast genome sizes of four medicinal Chrysanthemum cultivation products ranged from 151,057 to 151,109 bp, with GC content ranging from 37.45% to 37.76%. A total of 134 genes were identified, including 89 protein-coding genes, 37 ribosomal RNA genes, and 8 transfer RNA genes. Comparative genomic analysis revealed 159 large repeat sequences, 276 simple sequence repeats, 1 gene, and 8 intergenic regions identified as highly variable regions. Nucleotide diversity (Pi) values were high (≥ 0.004) for the petN-psbM, trnR-UCU-trnT-GGU, trnT-GGU-psbD, ndhC-trnV-UCA, ycf1, ndhI-ndhG, trnL-UGA-rpl32, rpl32-ndhF, and ndhF-ycf1 fragments, aiding in variety identification. Phylogenetic analysis revealed consistent results between maximum likelihood and Bayesian inference trees, showing that the four medicinal Chrysanthemum cultivars, along with their wild counterparts and related species, evolved as a monophyletic group, forming a sister clade to Artemisia and Ajania. Among the six Chrysanthemum species, the wild Chrysanthemum diverged first (Posterior probability = 1, bootstrap = 1,000), followed by Ajania, while C. indicum and C. morifolium clustered together (Bootstrap = 100), indicating their closest genetic relationship. The chloroplast whole-genome data and characteristic information provided in this study can be used for variety identification, genetic conservation, and phylogenetic analysis within the family Asteraceae.

Characterization of a gene conferring resistance to US Russian wheat aphid biotypes in the Iranian wheat landrace PI 625139

AbstractRussian wheat aphid (RWA, Diuraphis noxia Kurdjumov) is a highly invasive and destructive wheat pest evolving rapidly to overcome host resistance. Novel genes conferring resistance to multiple RWA biotypes are needed to sustain wheat production. The Iranian landrace PI 625139 is resistant to all five US RWA biotypes. To map the RWA resistance gene in PI 625139, both F2 and F2:3 populations were developed from cross PI 625139 × Smith's Gold, and the F2:3 population was evaluated for responses to five RWA biotypes, RWA1, RWA2, RWA3/7, RWA6, and RWA8. RWA assays identified a single gene in PI 625139, designated Dn625139, conditioning resistance to all five US RWA biotypes. Selective genotyping of a subset of F2 plants using genotyping‐by‐sequencing (GBS) revealed a set of single‐nucleotide polymorphism (SNP) markers on the short arm of chromosome 7D that are closely associated with RWA resistance. Kompetitive allele‐specific PCR (KASP) markers were developed from selected GBS‐SNPs in 7DS. Genetic analysis using the new KASP and simple sequence repeat (SSR) markers placed Dn625139 to a 2.6 cM interval. Dn625139 was 1.2 cM proximal to the KASP marker Stars‐KASP1007 (169.57 Mb) and 1.4 cM distal to the SSR marker Stars1039 (195.27 Mb) in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.1 reference sequence, and co‐segregated with the SSR marker Stars1029 (180.82 Mb). Dn625139 is a valuable gene conferring resistance to multiple RWA biotypes, and the molecular markers developed in this study can facilitate its rapid introgression into locally adapted cultivars to enhance wheat RWA resistance.

Characterization of Bread Wheat Genotypes Using SSR Markers for Terminal Heat Tolerance

Wheat is a major global food crop, but its productivity is increasingly threatened by terminal heat stress due to climate change. This study aimed to characterize the genetic diversity and heat tolerance of widely grown bread wheat genotypes using SSR markers to identify heat-tolerant cultivars adaptable to various regions in Bangladesh. A total of 15 genotypes were screened, and 13 polymorphic SSR (Simple Sequence Repeats) markers were used to determine the genetic similarity and categorize genotypes based on their heat tolerance. The molecular analysis revealed 13 polymorphic SSR markers that produced distinct PCR (Polymerase Chain Reaction) bands across the different genotypes. By the conclusion of the study, bread wheat genotypes were categorized as either tolerant or sensitive to heat, and the genetic similarity among the varieties was assessed using molecular markers. The genetic similarity coefficients obtained from the SSR primer screening ranged from 0.00 to 0.925. The lowest genetic distance (0.000) was found in Nadi 2 vs BAW1147 variety pair indicating that they are genetically similar to each other. Comparatively higher genetic distance (0. 925) was observed between BAW 1290 vs BARI Gom 28. The dendrogram divided the fifteen genotypes into two main groups, A and B, both formed at a similar coefficient of 0.05. Group A included seven genotypes and was further divided into two clusters, while Group B comprised eight genotypes, which were also divided into two clusters. The categorization of the genotypes was based on the average Heat Susceptibility Index (HSI), Thousand Grain Weight (TGW), grain yield, and the relative reduction in TGW and grain yield under stress conditions compared to timely sown conditions, aligning with the molecular data. Among the fifteen genotypes, BARI Gom 25, BARI Gom 26, BARI Gom 27, BARI Gom 28, BARI Gom 29, BARI Gom 30, and BARI Gom 31 demonstrated their adaptability to late sown conditions. The heat tolerance observed in these genotypes, as indicated by their SSR marker scores, is anticipated to provide valuable insights for molecular breeding studies focused on heat resistance.

Isolated Lateralized Overgrowth - Phenotypic Spectrum and Molecular Alterations.

To evaluate the molecular aberrations at 11p15.5 locus in thirty-two patients with isolated lateralized overgrowth (ILO). Among selected 32 cases of ILO, methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed initially followed by short tandem repeats (STR) marker analysis to confirm uniparental disomy (UPD). In those patients with normal MLPA reports, cyclin dependent kinase inhibitor 1C (CDKN1C) gene and whole exome sequencing was performed. Molecular analysis by MS-MLPA showed methylation aberrations in 28% (9/32) of patients. Gain of methylation at IC1 imprinting center (H4, H7) and loss of methylation at IC2 (H6, H9) was observed in 2 patients each. Uniparental disomy was observed in 9% cases. Except one, all patients with methylation aberration had more than one limb hypertrophy. Two patients (H22/H29) also had loss of methylation at IC1. Though this molecular alteration is specifically associated with Silver Russel syndrome (SRS), but the affected children did not completely fulfill the diagnostic criteria for SRS. In a recent study, a discrepancy was reported between the diagnosis of Beckwith-Wiedemann syndrome (BWS)/SRS and the molecular findings in the patients. Many times, it is very difficult to differentiate between hemi hypertrophy/hemi hypotrophy. Patients, in whom no aberrations were detected on MS-MLPA, whole exome sequencing (WES) was performed and no pathogenic variant was identified. Thus, ILO may be considered as a mild presentation on the extreme edge of BWS spectrum with methylation aberration and UPDin one thirdof cases which has implications in follow up.

Abstract B058: Nous-209 off-the-shelf vaccine targets neoantigens mutations well represented both in primary and metachronous incident CRCs from Lynch syndrome patients

Abstract Lynch Syndrome (LS) is the most common hereditary cancer syndrome, caused by germline mutations in one of the four DNA mismatch repair (MMR) genes. LS patients have a high risk to develop microsatellite instable (MSI) colorectal cancers. Tumors developed by LS carriers display high levels of microsatellite instability, which leads to the accumulation of large numbers of mutations, among which frameshift insertion/deletions (indels) within microsatellite (MS) loci are very common and shared among different tumors. When indels occur in coding genes they give rise to frameshift peptides (FSPs) with a very high potential to act as safe and potent neoantigens for a vaccine. NOUS-209 is a genetic vaccine encoding 209 neoantigens, shared across sporadic and hereditary MSI tumors, developed for interception and treatment of MSI tumors. Phase 1b trial evaluating NOUS-209 monotherapy in healthy LS carriers showed the induction of a potent and broad immune response. Here, we characterize indels encoding FSPs in a cohort of 50 incident MSI CRC from LS patients detected during routine screening (38 primary tumors; 22 metachronous tumors) by whole Exomeseq NGS. Overall, primary and metachronous tumors have a similar number of indels in coding genes. The repertoire of detected indels is only partially shared (27%) between the two categories of tumors. The 209 indels selected for the NOUS-209 vaccine are instead highly shared (95%) between primary and metachronous tumors. Moreover, the analysis of 8 patients for which both the primary and the metachronous tumor were available confirmed the presence of the 209 mutations both in the first and the second tumor. Therefore, the NOUS 209 vaccine has the potential to prevent tumor occurrence both in previvors and survivors by inducing a broad T cell immune response against recurrent FSP. Citation Format: Lorenzo De Marco, Elisa Micarelli, Joni Panula, Anna Morena D'Alise, Guido Leoni, Kalle E. Hokkanen, Eija Hämäläinen, Jukka-Pekka Mecklin, Elisa Scarselli, Toni Seppälä. Nous-209 off-the-shelf vaccine targets neoantigens mutations well represented both in primary and metachronous incident CRCs from Lynch syndrome patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2024 Oct 18-21; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2024;12(10 Suppl):Abstract nr B058.

Species delimitations in the Campomanesia xanthocarpa group (Myrtaceae): insights from molecular markers and taxonomy

Different views on recognising taxa associated with the Campomanesia xanthocarpa group (Myrtaceae) demonstrate the difficulties in clearly delimiting species. Studies using Inter Simple Sequence Repeats (ISSR) molecular markers were carried out on 201 individuals from 13 populations of C. xanthocarpa Mart. ex O.Berg, C. adamantium (Cambess.) O.Berg, C. costata M.Ibrahim & Landrum and C. littoralis D.Legrand in an attempt to improve understanding of species boundaries between these species. SplitsTree, analysis of molecular variance (AMOVA), principal component analysis (PCA), Neighbour-Joining (NJ) dendrogram and STRUCTURE showed inconsistencies between morphological and genetic data in these taxa. Therefore C. adamantium and C. xanthocarpa are treated as distinct taxa in this study, as are C. costata, C. littoralis and C. rhombea O.Berg that were previously considered part of C. xanthocarpa. Structured populations in C. adamantium were not congruent with taxonomic data or poorly supported in the data analysed. These were maintained as a single polymorphic species and new integrative approaches are necessary to improve understanding of taxon boundaries. We present a taxonomic treatment based on these decisions. This study contributes to the systematic treatment of Campomanesia and encourages specific delimitation studies to resolve remaining taxonomic issues within the genus.

Genome-wide discovery of polymorphic simple sequence repeat (SSR) markers through comparative analysis of closely related hami melon cultivars

Genome-wide discovery of polymorphic simple sequence repeat (SSR) markers through comparative analysis of closely related hami melon cultivars

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

Variation in SSRs at different genomic regions and implications for the evolution and identification of Armillaria gallica.

Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysis revealed that SSRs were more abundant in the intergenic region than the intron and exon region, as was the SSR density. Compared with other two genomes, SSR density was the lowest in exon region and largest in the intron region of A. gallica, with significant variation in genic region. There were 17 polymorphic markers in A. gallica genome was identified, with 26.7% in genic region, which is higher than that of 18.8% in the intergenic region. Moreover, a total of 50 alleles and 42 polymorphic loci were detected among these A. gallica strains. The averaged polymorphism information content (PIC) was 0.4487, ranged from 0.2577 to 0.6786. Both principal coordinate analysis (PCoA) and population structure analyses based on the genotype data of SSRs divided the strains into two clusters. The cluster I included all the strains from high-altitude G. elata producing areas and some low-altitude areas, while the strains in Cluster II originated from low-altitude G. elata producing areas. These results indicated that substantial genome-specific variation in SSRs within the genic region of A. gallica and provide new insights for further studies on the evolution and breeding of A. gallica.

The Importance of Pathogenesis: A Molecular Investigation on A Solitary Choriocarcinoma Lung Lesion with No Primary Lesion

Abstract Introduction/Objective We present an exceedingly rare case of metastatic choriocarcinoma to the lung with no primary lesion. Notably, this is the only case where STR molecular studies have been conducted. Methods/Case Report A 43-year-old G1P1001 female with no past medical history presents with severe shortness of breath, left-sided back, and chest pain for severe shortness of breath, left sided back and chest pain. Patients pregnancy test was positive with a B-hCG of 17944 u/L. Transvaginal ultrasound was negative for IUP. CTAP showed no masses in the uterine cavity or ovaries. D-dimer was elevated at 623 ng/ml. However, CTA chest was negative for pulmonary emboli but revealed a RLL mass measuring 2.6 x 2.5 cm x 2.9 cm with lobulated areas suspicious for vascular structures and connection to the right pulmonary vein. Patient was treated with a complete right lower lobectomy. An endometrial biopsy was performed and was negative for malignancy with no significant findings. Grossly, the mass was well-circumscribe, hemorrhagic, and necrotic, measuring 3.5 cm. Microscopically, the malignant cells had highly pleomorphic and hyperchromatic nuclei. There were also multiple multinucleated cells and mitotic figures present. Some of the cells had nested architecture leading to us to suspect a pleomorphic lung adenocarcinoma with choriocarcinomatous differentiation. We performed IHC staining that demonstrated strong positivity of AE1/AE3, CK7, hCG and a high Ki-67 index. The neoplastic cells also had focal p63 and p40 positivity. Furthermore, TTF1 and SALL4 were both negative. This staining pattern as well as patient’s clinical history of no gynecological lesion, lead us to favor lung adenocarcinoma with choriocarcinomatous differentiation. However, due to the abundance of syncytiotrophoblastic and trophoblastic cells, metastatic choriocarcinoma could not be ruled out. Therefore, the case was sent out for external consultation and Short Tandem Repeat (STR) molecular testing. Surprisingly, the STR testing results showed some STR of paternal origin indicating a metastatic gestational choriocarcinoma. The patient’s surgery was highly successful and lead to a down trending of b-hCG from 17944 to 1768 after removal. Results (if a Case Study enter NA) NA Conclusion Performing STR testing was pivotal in this case as it revealed the presence of DNA of paternal origin, providing crucial evidence that the tumor was of gestational origin, guiding the diagnosis towards metastatic gestational choriocarcinoma.

Comparison of commercial targeted amplicon sequencing assays for human remains identification casework.

Targeted amplicon sequencing (TAS) facilitates the genotyping of forensically informative single nucleotide polymorphisms (SNPs) using massively parallel sequencing (MPS). For human remains identification, where any extracted DNA is likely to be degraded, TAS may succeed when short tandem repeat (STR) profiling using capillary electrophoresis fails. Further, as well as yielding identity information, SNPs can provide information about ancestry, phenotype, kinship and paternal lineage (Y chromosome haplotypes). Two TAS platforms were compared in this study: Ion AmpliSeq™ panels coupled with Ion Torrent sequencing on an Ion GeneStudio™ S5 Plus System, manufactured by Thermo Fisher Scientific, and the ForenSeq® Kintelligence Kit coupled with Illumina sequencing on the MiSeq FGx® Sequencing System, manufactured by QIAGEN. Four Ion AmpliSeq™ panels (Precision ID Identity, Precision ID Ancestry, DNA Phenotyping and HID Y-SNP) share 177 SNPs with the ForenSeq® Kintelligence Kit and all five were used to profile the DNA extracted from the petrous part of the temporal bone from six skeletonised cadavers. Of the 6 × 177 = 1,062 SNP genotype comparisons, 1,055 (99%) were concordant between the Ion AmpliSeq™ panels and Kintelligence Kit. Of the seven (< 1%) non-concordant SNPs, only three of them (0.3%) would have resulted in erroneous genotypes being reported as a result of allele dropout by either assay, using our optimised relative variant frequency windows for allele calling. We conclude that both the Ion AmpliSeq™ panels and the ForenSeq® Kintelligence Kit were suitable for TAS applied to the human remains in this study.