Genomic Analysis Research Articles

OysterDB: A Genome Database for Ostreidae.

The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters ( http://oysterdb.com.cn/ ).

A novel liquid biopsy assay with an 88% detection rate of genomic alterations across CNS tumors.

2077 Background: Diagnosis and treatment decisions for CNS tumors rely upon imaging with subsequent histological and genomic analyses of tissue to identify appropriate courses of therapy. Genomic profiling of tumor tissue for informative alterations is used to guide treatment, however contemporaneous tissue can sometimes be unavailable, inconclusive or overlook possible actionable alterations given the high amount of spatial heterogeneity in certain tumor types such as glioblastomas GBMs. Liquid biopsies may pose a possible solution, as they are readily accessible and provide a holistic snapshot of the tumoral genomic landscape. However, detection of ctDNAs from CNS tumors is impeded by its inherently low shedding biology and poor permeability across the BBB resulting in low plasma variant allele fractions (VAFs), with alteration detection rates ranging 27-55%. Thus, current assays do not yet have the sensitivity to be clinically useful in aiding decision making for CNS tumors. Methods: 62 cases of primary CNS tumors were submitted commercially for assessment with Northstar Select, a tumor-naive, plasma-based ctDNA liquid biopsy assay. Cases were obtained from a single clinic dating from January-December 2023. Results: See table. Conclusions: There remains an unmet clinical need for a highly sensitive liquid biopsy assay for use in determining the genomic landscape of CNS tumors to aid in clinical decision making. Current assays do not have a low enough limit of detection (LoD) to accurately detect ctDNAs at low VAFs. Herein, we demonstrate that Northstar Select has a detection rate of 88.7% in all cases and 91.4% in GBMs, nearly doubling current rates. This is due to the assay’s uniquely low LoD of 0.13-0.16% VAF, which is below the 0.17% median VAF demonstrated across CNS tumors in this study, allowing for more low-abundance alterations to be detected. Given the increased total variant detection rate, nearly 50% of which were actionable when alterations were detected, these data support the clinical utility of Northstar Select to inform clinical decisions either as a complement to imaging and tissue analyses or independently when tissue biopsies are infeasible. These data further suggest that the clinical utility of Northstar Select may be expanded into metastatic brain disease and other low ctDNA shedding tumors. [Table: see text]

EXPRESS study: A trial exploring the association of low level of genomic alteration with exceptional and unexpected response to targeted therapies in patients with advanced solid tumors.

e15140 Background: Small subsets of pts treated with targeted therapies (TT) present exceptional and unexpected response (1-10%), which could be driven and correlated by a low level of genomic alterations in genes identified as causally implicated in cancer. Conversely, the multiplication of the genomic alterations in such genes would decrease the oncogenic de-addiction process. Methods: EXPRESS is an exploratory, multicenter, prospective trial conducted in pts with locally advanced or metastatic solid tumors, who presented an exceptional and unexpected response to an antineoplastic TT. This research aimed to explore whether tumors with a low level genomic alteration (mutation, amplification, deletion) as assessed by whole exome sequencing (WES) are associated with exceptional and unexpected response. Secondary endpoints including the identification of novel candidate somatic molecular profiles and host immunologic characteristics susceptible to drive exceptional and unexpected response will be reported later. Results: 439 pts were identified over 32 centres from December 2016 to April 2021. Out of 270 pts confirmed with an exceptional response by our review committee of cases, 183 were included in the EXPRESS study. Exceptional responder population is summarised (Table). Out of 183, WES analysis was performed for 103 pts (56.3%). Genomic analysis failure was predominant in the breast and lung cohort (60.9% and 52.5%). The number of genomic alterations in the EXPRESS cohort was lower than in the TCGA control cohort (median[Q1-Q3]: 11[7-17] vs 19 [11-32], p<0.001). A lower number of genomic alterations was also reported in the melanoma (8[5-13] vs 33[17-51], p<0.001) and lung cancer cohort (8[5-17] vs 22[13-34], p<0.001) but not in the breast and kidney cohorts (13[10-21] vs 17[10-29], p=0.41 and 12[9-14] vs 11[7-17], p=0.89). Conclusions: Compared to the TCGA cohort, a low level of genomic alteration is associated with exceptional response in pts with lung cancer and melanoma. A comparison with a matched population based on genomic criteria in the TCGA is undergoing and will be presented at the conference. Clinical trial information: NCT02701907 . [Table: see text]

Genomic alterations in DNA damage response (DDR) genes in HR+/HER2- metastatic breast cancer (mBC) and impact on clinical efficacy with sacituzumab govitecan (SG): Biomarker results from TROPICS-02 study.

1075 Background: In the phase 3 TROPiCS-02 study, SG, a Trop-2–directed antibody-drug conjugate coupled to SN-38 as the payload, demonstrated clinically meaningful improvement in survival outcomes over chemotherapy in patients (pts) with pretreated HR+/HER2- mBC. SN-38 leads to double-stranded DNA damage, therefore we hypothesized that in tumors with defective DDR machinery, SG may provoke synthetic lethality. We report on comprehensive genomic analysis of DDR gene variants and the impact on SG clinical efficacy in this patient population. Methods: Pts with HR+/HER2– mBC who received prior taxane, endocrine therapy (ET), CDK4/6 inhibitor, and 2-4 prior lines of chemotherapy were randomized to receive SG (10 mg/kg IV days 1 and 8, every 21 days) or treatment of physician’s choice (TPC) until disease progression or unacceptable toxicity. DDR gene deleterious variants were identified using whole exome sequencing (WES) on archival or screening tumor tissues based on 142 DDR pathway genes annotated in the Kyoto Encyclopedia Genes and Genomes (KEGG) database and Human DNA Repair Gene database; association between these variants and clinical outcomes was evaluated using Cox regression model as Hazard Ratio (HR) with 95% Confidence Intervals (CI). Results: Of 543 patients included in the intent-to-treat (ITT) population, WES data was available for 195 (36%) – clinicopathological features were similar between ITT and WES dataset (median age = 57 vs 58 for SG and 55 vs 55 for TPC; prior lines of chemotherapy >2 lines = 59% vs 57% for SG and 58% vs 55% for TPC). Estrogen Receptor (ER)>10% and prior lines of chemotherapy were comparable between WT and MUT in SG arm and in TPC arm. Overall, 114 (58%) of tumor samples had ≥1 deleterious alteration with BRCA2, PRKDC, ATM being the most common alterations. The primary results are included (Table). Although all patients demonstrated improved efficacy with SG vs TPC, patients with DDR mutant MBC had numerically greater benefit in PFS vs WT (MUT HR= 0.61; WT HR= 0.76) and OS (MUT HR = 0.68; WT HR= 0.82). Conclusions: While SG benefit over TPC was observed in both DDR WT and DDR MUT HR+/HER2– mBC, numerically greater benefit was observed for patients with DDR deficient tumors, suggesting possible synergy between the DDR pathway and SG’s anti-tumor effect. Further study of the synergistic effects of SG in combination with agents targeting DDR pathway are warranted. Clinical trial information: NCT03901339 . [Table: see text]

The Gundersen Precision Oncology Cohort: A biospecimen resource for mutation characterization and target discovery.

e15184 Background: The generation and widespread sharing of large somatic mutation datasets has revolutionized our understanding of genetic mechanisms driving cancer initiation and progression. For well-understood mutations, this has created the opportunity for individualized therapeutic intervention in a wide range of malignancies. Beyond these well-characterized mutations, there exists a wide range of alterations that remain poorly understood and which require some kind of functional genomics analysis to determine whether such patients are eligible for the targeted therapy used for more typical mutations in that gene, whether these alterations are passenger mutations that don’t affect throughput on the associated signaling pathway, or reflect another more nuanced phenomenon. Whether using ectopic overexpression in cell lines or generation of genetically modified mice, addressing this problem at scale using functional genomics approaches is challenging. A key limitation is the absence of the original tissue context in which that variant co-evolved with other genetic alterations as well as data on the clinical response of the patient to successive lines of therapy. This can be addressed, in part, by the banking of tissue from patient cohorts who have had comprehensive genomic profiling as part of their routine clinical care. For this purpose, we have established the Gundersen Precision Oncology Cohort. Methods: The Gundersen Precision Oncology Cohort is a retrospective collection of tissue specimens, NGS reports and associated clinical data from deceased patients who received cancer care at the Gundersen Health System. The cohort is updated twice per year and banked tissue specimens are available for collaborative research studies. Results: At November 20, 2023 there were data from 780 patients in the cohort, with specimens tested between 2015 and 2023. 54 tumor types were represented, of which lung (n = 196), colorectal (n = 79), pancreas (n = 65), esophageal (n = 58) and breast (n = 46) were most common. The most common diagnostic companies were STRATA Oncology (n = 463) and Tempus (n = 248). Most patients had testing at a single timepoint, but longitudinal testing is available for 13 patients. We present data from some of the studied subgroups, including atypical point mutations in BRAF as well as fusions affecting BRAF and ROS1. Conclusions: This cohort, available for collaborative studies via the Gundersen Cancer Biobank, illustrates the value of banking well-annotated biospecimens to address outstanding questions in oncology.

The effect of resting dendritic cells on overall survival in the hepatocellular carcinoma tumor microenvironment.

e14559 Background: Hepatocellular carcinoma (HCC) continues to have a poor prognosis even in the advent of new immunotherapy regimens. An area of growing interest in HCC is its tumor immune microenvironment. Classifying the immune microenvironment based on available genomics can lead to insights on prognosis and treatment, especially regarding the role of immunotherapy. Methods: RNA sequencing data was extracted from The Cancer Genome Atlas (TCGA), specifically from the hepatocellular carcinoma section (n = 366). CIBERSORT was utilized to organize the immune cell fractions present for each patient sample. Radiant by Shiny was used to perform a linear regression elucidating the relationship between overall survival and several other variables including: age, gender, tumor stage, race, ethnicity, B-cells naïve, B-cells memory, plasma cells, CD8 T-cells, CD4 T-cells, T-cells follicular, T-cells regulatory, natural killer activated and resting cells, monocytes, macrophages (M0, M1, M2), dendritic cells activated and resting, mast cells activated and resting, eosinophils, and neutrophils. Subgroup analyses were also performed via radiant regarding gender, race, and resting dendritic counts. Results: Resting dendritic cells were independently prognostic of overall survival on multivariable analysis (p = 0.041). The coefficient of correlation was +164.53 showing a positive association between the number of resting dendritic cells and the overall survival. Subgroup analysis showed no difference in resting dendritic counts between males and females (p = 0.526). Also, there was no difference seen in resting dendritic counts between populations of Asians and African Americans (p = 0.873), Asians and Whites (p = 0.223), and between Whites and African Americans (p = 0.811). Conclusions: Patients with a higher number of resting dendritic cells in their tumor immune microenvironment had a better overall survival. There was no difference between males and females in the resting dendritic counts. Likewise, there was no difference in the resting dendritic counts between Asian, African American, and white populations. Resting dendritic cells have been shown to be enriched in hepatocellular carcinomas with a low tumor mutational burden. This is a paradigm that should be explored further in the context of immunotherapy. Resting dendritic cells are also in a state of plasticity as they go from resting to active. Future genomic analysis of the tumor microenvironment regarding this plasticity could also lead to enhancing treatment options.

Impact of genome build on RNA-seq interpretation and diagnostics.

Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.

Association of a germline single nucleotide polymorphism (SNP) in the interleukin-7 (IL7) gene with immune-related adverse events (irAEs) in the CheckMate 025 trial.

12140 Background: Immune checkpoint inhibitors (ICIs) have dramatically improved outcomes of patients (pts) with metastatic renal cell carcinoma (mRCC). Unfortunately, adverse events (AEs) can limit treatment efficacy and worsen patient outcomes. Recently, a germline IL7 SNP (rs16906115) was identified as a potential biomarker for prediction of irAEs. We aimed to characterize the association between a germline IL7 SNP (rs16906115) and AEs in a prospective clinical trial of patients with mRCC treated with nivolumab (NIVO) or everolimus (EVE). Methods: Whole-exome sequencing (WES) data of tumor and peripheral blood samples from CheckMate 025 (NCT01668784) were used to infer somatic alterations using the Cancer Genome Analysis pipeline, as well as SNP carrier status using the STITCH pipeline. Within each treatment arm, time to incident adverse events (AEs) were compared between carriers (SNP+) and non-carriers (SNP-) via multivariable Cox regression, controlling for age, sex and sample purity, followed by a SNP´treatment interaction term in the whole cohort. Overall survival (OS) and progression-free survival (PFS) were also assessed. Finally, a recurrent event analysis for AEs was conducted using the Andersen-Gill model, controlling for the same variables. Results: In total, 382 pts were included (NIVO: n=189, EVE: n=193), among which 56 (14.7%) were SNP+. There were no differences in clinical and pathological characteristics between SNP+ and SNP-, except for sex (SNP+ 16.1% vs. SNP- 30.1% females, P=0.046). Similarly, no differences in somatic alterations, including single nucleotide and copy number variants were seen between SNP+ and SNP-. SNP carrier status had no effect on OS nor PFS in both treatment arms (all P≥0.47). Regarding AEs, 63 pts (33.3%) in the NIVO arm experienced at least 1 grade 2+ AE, compared to 78 pts (40.4%) in the EVE arm. The most common types of grade 2+ AEs were cutaneous (21.0%), hepatobiliary (16.8%) and endocrine (15.8%) in the NIVO arm, and respiratory (30.1%), cutaneous (22.3%) and gastrointestinal (19.4%) in the EVE arm. The rate of grade 2+ AEs was significantly higher in SNP+ vs. SNP- in the NIVO arm (HR=2.91[1.48-5.72]), but not in the EVE arm (HR=0.63[0.3-1.29], SNP´treatment Pinteraction=0.002). The rate of recurrent grade 2+ AEs was also significantly higher in SNP+ vs. SNP- in the NIVO arm (HR=3.43[1.83-6.43]), whereas a trend for fewer recurrent grade 2+ AEs was seen in SNP+ vs. SNP- in the EVE arm (HR=0.46[0.17-1.25], SNP´treatment Pinteraction=0.0005). Conclusions: The IL7 SNP (rs16906115) is associated with significantly higher rates of grade 2+ AEs, including recurrent events, in pts with mRCC treated with NIVO but not with EVE, with no effect on survival outcomes. These results affirm the SNP’s predictive potential as a biomarker for irAEs to guide therapeutic decisions in pts treated with ICIs.

Genomic analysis of the tumor microenvironment in Asian and Native Hawaiian and Pacific Islander patients with triple negative breast cancer.

e12644 Background: Triple negative breast cancer (TNBC) accounts for approximately 10- 20% of breast cancer cases and has the worst overall survival and prognosis compared to other subtypes. Unlike other subtypes, patients with TNBC are responsive to neoadjuvant therapy. A higher percent of stromal tumor infiltrating lymophocytes (sTILs) in the tumor microenvironment of TNBC correlates with an improved prognosis. Previous studies demonstrate that Native Hawaiians and Pacific Islanders (NHPIs) and Asians have equivocal percent of sTILs. Yet NHPIs have a higher mortality rate at 24.9% compared to Asians at 11%. Our study aims to molecularly characterize the tumor microenvironment in a diverse population of patients with TNBC who received neoadjuvant therapy. Methods: Retrospective chart review was conducted on 12 Asians and 12 NHPI patients with early stage TNBC from 2015 to 2022 from a medical oncology clinic within the Hawai’i Pacific Health system. Patient data collected include age at diagnosis of breast cancer, histology, BMI, clinical stage, sTILs, residual cancer burden, neoadjuvant treatment, and pathologic complete response. Core biopsy samples were processed and analyzed using the nCounter Breast Cancer 360 Panel. Further analysis was obtained using the nSolver Advanced Analysis Module. Results: Patient characteristics are listed in the table. Most patients had the basal-like immunosuppressed TNBC subtype. Among differentially expressed genes between races, 31 genes were statistically significant. NHPIs expressed more IL12RB2 and MYC, and Asians expressed more FGFR4 and MLPH. Among responders compared to non-responders, 5 genes were statistically significant. Responders expressed more STC1 and PTGER3, and non-responders expressed more CRAYAB, TMPRSS2, and CHAD. Among old and young patients, 132 genes were statistically significant. Older patients expressed more FUT3 and CKMT1, and younger patients expressed more MMP7 and MIA. Conclusions: In this pilot study, the molecular and genetic differences suggest that the tumor microenvironment may play a role in treatment outcomes between NHPIs and Asians. Further analysis will be conducted to determine the differences in immune cell infiltration. [Table: see text]

Structure–function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus

BackgroundManganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure–function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule.ResultsTwo MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD—referred to as Ape-MnP1 and Cst-MnP1, respectively—were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation.ConclusionsUnderstanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure–function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.

Prokrustean Graph: A substring index supporting rapid enumeration across a range of k-mer sizes.

2012Applied computing → Computational biology. 10.4230/LIPIcs.WABI.2024.YY. https://github.com/KoslickiLab/prokrustean.

Actinobacteria diversity associated with marine sediments and a wetland system, Agulhas-South Africa

BackgroundSouth Africa is known for its great biodiversity. The Agulhas Plain represents one such unique environment where low-gradient topography has resulted in extensive wetland formation. It is fed by two major river systems, bringing in brackish, alkaline water. It has been exposed to major marine transgression and regression events, and harbours great Fynbos diversity as well as a Mediterranean-type climate, thereby creating unique ecosystems. It is therefore surprising that little is known about the bacterial diversity associated with the Agulhas Plain and associated marine ecosystems.MethodsIn this study, we focused on the actinobacterial diversity (Phylum Actinomycetota) associated with an emerging peatland on the Agulhas Plain (SF; Areas 1–3) and a marine site (ANP; Ocean, Rocky, Dry) located 10 km away from SF. A combined metataxanomics and isolation approach was taken to evaluate the actinobacterial diversity of the sampling sites and to determine the effect of environmental physicochemical parameters on these populations. Various genome analyses were performed on an Sva0096 marine bin to gain insight into its ecological role.ResultsMetataxanomics showed that the two sites shared defined major taxa, including Blastococcus, Geodermatophilus, Microbacterium, Mycobacterium, Nocardioides, Streptomyces, and the Sva0996 marine group. Analysis of the biosynthetic potential of an Sva0996 marine bin134 (obtained from GenBank) provided insights into the potential ecological role of this group of bacteria in both the marine and terrestrial environments. Higher actinobacterial diversity (Shannon index > 5) was observed for Areas 2 and 3 (SF), as well as the ANP Dry samples. The actinobacterial population composition was found to be driven by salinity, pH, Mn, and Ca, with certain areas of SF exhibiting similar (and even higher) salinity (SF: 70–100 Ω vs. ANP: 100–160 Ω) and lower pH levels (SF: 6.3-8.0 vs. ANP: 8.6–8.9) to that of the marine environment.ConclusionThis snapshot study has provided some insights into the actinobacterial diversity of the two sites studied. Analysis of an Sva0096 marine bin134 provided further insights into the potential ability of the Sva0096 marine group to survive in a unique terrestrial environment that is periodically exposed to environmental pressures that mimic the marine environment.

High Level Immunoglobulin Gene Expression and Reduced Intra-tumoral Bacteria Associated With the Transition from Initial to Progressive Diffuse Intrinsic Pontine Glioma.

In the past decade, diffuse intrinsic pontine glioma (DIPG), the most common childhood brainstem glioma, has benefitted from an increase in tissue-based research because of improved biopsy collection techniques. However, the adaptive immune receptor (IR) features represented by tumor material and tumor infiltrating lymphocytes have remained poorly understood. Herein, we characterized the adaptive immune parameters of DIPG through the recovery of IR recombination reads from RNAseq files representing initial and progressive DIPG samples. An elevated level of immunoglobulin gene expression in the progressive DIPG sample files and a reduced number of bacterial sequencing read recoveries in comparison to RNAseq files representing the initial form of DIPG, was found. Furthermore, the RNAseq files representing both initial and progressive DIPG samples had significant numbers of reads representing Cutibacterium acnes, a bacterium previously linked to prostate cancer development. Results also indicated an opportunity to distinguish overall survival probabilities based on IGL complementarity determining region-3 amino acid sequence physicochemical parameters. Genomics analyses allow for a better understanding of adaptive IR features and bacterial infections in the DIPG setting.

Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens)

Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.

Integrated analysis of genomics and transcriptomics revealed the genetic basis for goaty flavor formation in goat milk

Goat milk exhibits a robust and distinctive “goaty” flavor. However, the underlying genetic basis of goaty flavor remains elusive and requires further elucidation at the genomic level. Through comparative genomics analysis, we identified divergent signatures of certain proteins in goat, sheep, and cow. MMUT has undergone a goat-specific mutation in the B12 binding domain. We observed the goat FASN exhibits nonsynonymous mutations in the acyltransferase domain. Structural variations in these key proteins may enhance the capacity for synthesizing goaty flavor compounds in goat. Integrated omics analysis revealed the catabolism of branched-chain amino acids contributed to the goat milk flavor. Furthermore, we uncovered a regulatory mechanism in which the transcription factor ZNF281 suppresses the expression of the ECHDC1 gene may play a pivotal role in the accumulation of flavor substances in goat milk. These findings provide insights into the genetic basis underlying the formation of goaty flavor in goat milk. Statement of significanceBranched-chain fatty acids (BCFAs) play a crucial role in generating the distinctive “goaty” flavor of goat milk. Whether there is an underlying genetic basis associated with goaty flavor is unknown. To begin deciphering mechanisms of goat milk flavor development, we collected transcriptomic data from mammary tissue of goat, sheep, cow, and buffalo at peak lactation for cross-species transcriptome analysis and downloaded nine publicly available genomes for comparative genomic analysis. Our data indicate that the catabolic pathway of branched-chain amino acids (BCAAs) is under positive selection in the goat genome, and most genes involved in this pathway exhibit significantly higher expression levels in goat mammary tissue compared to other species, which contributes to the development of flavor in goat milk. Furthermore, we have elucidated the regulatory mechanism by which the transcription factor ZNF281 suppresses ECHDC1 gene expression, thereby exerting an important influence on the accumulation of flavor compounds in goat milk. These findings provide insights into the genetic mechanisms underlying flavor formation in goat milk and suggest further research to manipulate the flavor of animal products.

CFPG: Creating a Common Fungal Pathogenic Genes Database through Data Mining

Fu ngal pathogenicity is one of the most vigorously tackled ecological and medicinal issues facing many scientists. Comparative genomics is an extremely important methodology and tool used to understand fungal pathogenicity, and it allows the development of early diagnostic tools for fungal-inflicted diseases across different host organisms. However, comparative genomics depends heavily on readily available fungal pathogenic gene databases to enable downstream genomics study and the development of new diagnosis and detection methods. Here, we have developed the Common Fungal Pathogenic Genes Database through comparative genomic analysis using 86 publicly available fungal genomic data against fungal pathogenicity-related databases, such as Pathogenic-Host Interaction Database (PHI-base), Carbohydrate-Active enZymes Database (CAZy), and Database of Fungal Virulence Factory (DFVF).

Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics.

Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.

Integrative genomic and transcriptomic analysis of Xanthomonas oryzae pv. oryzae pathotype IV, V, and IX in China reveals rice defense-responsive genes

Bacterial blight of rice is a devastating disease caused by the gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo). Chinese Xoo strain pathotypes IV, V, and IX are the major virulent Xoo strain types in South China sequentially from the 1990s to the present. Here, we report the isolation of GD0201 and GD0202, which belong to pathotypes IV and IX, respectively, and the complete genome sequence and transcriptomic analysis of GD0201 (IV), GD1358 (V), and GD0202 (IX). We found that resistance genes xa5, Xa23, and Xa27 confer strong resistance to all three Xoo strains, indicating that they are currently good choices for resistance rice breeding. The genome analysis reveals fewer TAL and non-TAL effector coding genes in GD0202 than in the other two strains, potentially contributing to its strong virulence. Transcriptomic analysis of ZH11 inoculated with the three Xoo strains strongly suggests that three Xoo strains for better infection repress the ethylene response factor (ERF) gene family members. Furthermore, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis revealed 14 hub genes potentially associated with rice response to the three Xoo strains. The expression of several hub genes was validated to be induced by all three Xoo strains, suggesting its role in bacterial blight disease response to Xoo strains. Genomic analysis of the Xoo strains belonging to pathotypes IV, V, and IX, identification of effectors and genes related to Xoo virulence in rice plants will provide insights into understanding the molecular mechanism underlying rice-Xoo interaction and the gene expression pattern in response to Xoo infection.

Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov.

Quorum quenching refers to any mechanism that inhibits quorum sensing processes. In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11T, which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11T could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37T, and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15T and Reyranella massiliensis 521T, respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11T had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11T. Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11T. Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11T could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11T = KCTC 82780T = LMG 32365T).

Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient

BackgroundEnterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. MethodsThe bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. ResultsThe results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. ConclusionsThe study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.