Genome Annotation Research Articles

BindCompare: A Novel Integrated Protein-Nucleic Acid Binding Analysis Platform

Abstract Summary Advanced genomic technologies have generated thousands of protein-nucleic acid binding datasets that have the potential to identify testable gene regulatory network (GRNs) models governed by combinatorial associations between factors. Transcription factors (TFs) and RNA binding proteins (RBPs) are nucleic-acid binding proteins regulating gene expression and are key drivers of GRN function. However, the combinatorial mechanisms by which the interactions between specific TFs and RBPs regulate gene expression remain largely unknown. To identify possible combinations of TFs and RBPs that may function together, developing a tool that compares and contrasts the interactions of multiple TFs and RBPs with nucleic acids to identify their common and unique targets is necessary. Therefore, we introduce BindCompare, a user-friendly tool that can be run locally to predict new combinatorial relationships between TFs and RBPs. BindCompare can analyze data from any organism with known annotated genome information and outputs files with detailed genomic locations and gene information for targets for downstream analysis. Overall, BindCompare is a new tool that identifies TFs and RBPs that co-bind to the same DNA and/or RNA loci, generating testable hypotheses about their combinatorial regulation of target genes. Availability and Implementation BindCompare is an open-source package that is available on the Python Packaging Index (PyPI, https://pypi.org/project/bindcompare/) with the source code available on GitHub (https://github.com/pranavmahabs/bindcompare). Complete documentation for the package can be found at both links. Supplementary information Supplementary data are available at Bioinformatics online.

Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding

We report the construction and analysis of a new reference genome assembly forRattus norvegicus, the laboratory rat, a widely used experimental animal model organism. The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same strain and from the same colony as the prior reference assembly, mRatBN7.2. The assembly is at chromosome level with 98.7% of the sequence assigned to chromosomes. All chromosomes have increased in size compared with the prior assembly andk-mer analysis indicates that the subject animal is fully inbred and that the genome is represented as a single haploid assembly. Notable increases are observed in Chromosomes 3, 11, and 12 in the prospective rDNA regions. In addition, Chr Y has increased threefold in size and is more consistent with the rat karyotype than previous assemblies. Several other chromosomes have grown by the incorporation of sizable discrete new blocks. These contain highly repetitive sequences and encode numerous previously unannotated genes. In addition, centromeric sequences are incorporated in most chromosomes. Genome annotation has been performed by NCBI RefSeq, which confirms improvement in assembly quality and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.

Characterization and complete genome sequence of highly lytic phage active against methicillin-resistant Staphylococcus aureus (MRSA) isolated from Egypt

BackgroundMethicillin-Resistant Staphylococcus aureus (MRSA) is one of the most resistant bacteria to antibiotics. S. aureus is an important, widespread pathogen that can cause a variety of infectious diseases in humans and animals. Phages have been recognized as natural, safe, highly specific and effective alternatives agents to antibiotics for preventing and treating bacterial infections caused by MRSA. Therefore, this study aims at the characterization of a novel isolated lytic phage, vB_SauP_ASUmrsa123.MethodsIsolates of Staphylococcus aureus MRSA were obtained on Mannitol Salt Agar and Baird Parker Agar plates and confirmed using VITEK 2. Sewage and clinical samples were used to isolate specific phages for S. aureus MRSA, and plaque assays were used for host range determination on Luria-Bertani (LB) media. The phage morphology of the isolated phage was determined by transmission electron microscopy. The phage’s whole genome sequencing was identified.ResultsA total of 25 isolates of Staphylococci were obtained from different clinical sources and showed typical colonies on Baird-Parker and Mannitol Salt Agar plates. The VITEK 2 automated system revealed that all 25 isolates were confirmed as S. aureus (MRSA). Two of the most antibiotics-resistant isolates were further confirmed using 16S ribosomal RNA sequencing. A lytic phage was detected against the MRSA isolates tested In Vitro, namely vB_SauP_ASUmrsa123. The phage belonged to Rountreeviridae family based on morphological properties observed by TEM and the host range of the isolated phage was tested on the 25 clinical MRSA isolates in Vitro. The one-step growth curve of the isolated phage showed that the latent period was about 55 min, and the burst size was estimated at 167 PFU. The whole genome sequencing and annotation of genes revealed that phage vB_SauP_ASUmrsa123 contained a linear dsDNA with a size of about 17,155 bp with predicted 24 ORFs. Analysis of its genome provides valuable information approximately the variety of phages belonging to the staphylococcal phages class I.ConclusionA lytic Podo Phage vB_SauP_ASUmrsa123 was identified against S. aureus MRSA isolates and its genome was sequenced. The phage was found to be eligible for potential application in biocontrol.

Assembly and comparative analysis of the first complete mitochondrial genome of Astragalus membranaceus (Fisch.) Bunge: an invaluable traditional Chinese medicine

BackgroundAstragalus membranaceus (Fisch.) Bunge is one of the most well-known tonic herbs in traditional Chinese medicine, renowned for its remarkable medicinal value in various clinical contexts. The corresponding chloroplast (cp) and nuclear genomes have since been accordingly sequenced, providing valuable information for breeding and phylogeny studies. However, the mitochondrial genome (mitogenome) of A. membranaceus remains unexplored, which hinders comprehensively understanding the evolution of its genome.ResultsFor this study, we de novo assembled the mitogenome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P. K. Hsiao using a strategy integrating Illumina and Nanopore sequencing technology and subsequently performed comparative analysis with its close relatives. The mitogenome has a multi-chromosome structure, consisting of two circular chromosomes with a total length of 398,048 bp and an overall GC content of 45.3%. It encodes 54 annotated functional genes, comprising 33 protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. An investigation of codon usage in the PCGs revealed an obvious preference for codons ending in A or U (T) bases, given their high frequency. RNA editing identified 500 sites in the coding regions of mt PCGs that exhibit a perfect conversion of the base C to U, a process that tends to lead to the conversion of hydrophilic amino acids into hydrophobic amino acids. From the mitogenome analysis, a total of 399 SSRs, 4 tandem repeats, and 77 dispersed repeats were found, indicating that A. membranaceus possesses fewer repeats compared to its close relatives with similarly sized mitogenomes. Selection pressure analysis indicated that most mt PCGs were purifying selection genes, while only five PCGs (ccmB, ccmFc, ccmFn, nad3, and nad9) were positive selection genes. Notably, positive selection emerged as a critical factor in the evolution of ccmB and nad9 in all the pairwise species comparisons, suggesting the extremely critical role of these genes in the evolution of A. membranaceus. Moreover, we inferred that 22 homologous fragments have been transferred from cp to mitochondria (mt), in which 5 cp-derived tRNA genes remain intact in the mitogenome. Further comparative analysis revealed that the syntenic region and mt gene organization are relatively conserved within the provided legumes. The comparison of gene content indicated that the gene composition of Fabaceae mitogenomes differed. Finally, the phylogenetic tree established from analysis is largely congruent with the taxonomic relationships of Fabaceae species and highlights the close relationship between Astragalus and Oxytropis.ConclusionsWe provide the first report of the assembled and annotated A. membranaceus mitogenome, which enriches the genetic resources available for the Astragalus genus and lays the foundation for comprehensive exploration of this invaluable medicinal plant.

The genome sequence of the long-horned nomad bee, Nomada hirtipes Pérez, 1884

We present a genome assembly from an individual female Nomada hirtipes (the long-horned nomad bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 316.5 megabases. Most of the assembly (90.79%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 29.88 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,693 protein-coding genes.

High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crabs

BackgroundEvolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood.ResultsHere, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation.ConclusionsOur findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism.

Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration

The vast majority of gecko species are capable of tail regeneration, but singular geckos of Correlophus, Uroplatus, and Nephrurus genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (Correlophus ciliatus) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make C. ciliatus particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of C. ciliatus with a total size of 1.65 Gb, 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Our assembly of the crested gecko genome provides a valuable resource for future comparative genomic studies between non-regenerative and regenerative geckos and other squamate reptiles. Findings We report genome sequencing, assembly, and annotation for the crested gecko, Correlophus ciliatus.

Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos.

Embryonic genome activation (EGA) is a critical step in early embryonic development, as it marks the transition from relying on maternal factors to the initiation of transcription from embryo's own genome. The factors associated with EGA are not well understood and need further investigation. PRD-like (PRDL) homeodomain transcription factors (TFs) are considered to play crucial roles in this early event during development but these TFs have evolved differently, even within mammalian lineages. Different numbers of PRDL TFs have been predicted in bovine (Bos taurus); however, their divergent evolution requires species-specific confirmation and functional investigations. In this study, we conducted molecular cloning of mRNAs for the PRDL TFs ARGFX, DUXA, LEUTX, NOBOX, TPRX1, TPRX2, and TPRX3 in bovine oocytes or in vitro fertilized (IVF) preimplantation embryos. Our results confirmed the expression of PRDL TF genes in early bovine development at the cDNA level and uncovered their structures. For each investigated PRDL TF gene, we isolated at least one homeodomain-encoding cDNA fragment, indicative of DNA binding and thus potential role in transcriptional regulation in developing bovine embryos. Additionally, our cDNA cloning approach allowed us to reveal breed-related differences in bovine, as evidenced by the identification of a high number of single nucleotide variants (SNVs) across the PRDL class homeobox genes. Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. We supported this finding by identifying a shared set of genes between our and published bovine early embryo development datasets. Providing full-length cDNA evidence for previously predicted homeobox genes that belong to PRDL class improves the annotation of the bovine genome. Updating the annotation with seven developmentally-important genes will enhance the accuracy of RNAseq analysis with datasets derived from bovine preimplantation embryos. In addition, the absence of TPRX3 in humans highlights the species-specific and TF-specific regulation of biological processes during early embryo development.

Synergistic Epistasis and Systems Biology Approaches to Uncover a Pharmacogenomic Map Linked to Pain, Anti-Inflammatory and Immunomodulating Agents (PAIma) in a Healthy Cohort

The global public health addiction crisis has been stark, with over 932,400 deaths in the USA and Canada from opioid overdose since 1999–2020, surpassing the mortality rates at the top of the HIV/AIDS epidemic. Both nations exhibit opioid consumption rates significantly above the norm for developed countries. Analgesic type of opioids present both therapeutic benefits and substantial health risks, necessitating balanced drug regulation, careful prescribing, and dedicated opioid stewardship. The role of the cytochrome P450 2D6 (CYP2D6) system (Enzymatic functions) in metabolizing opioids highlights the potential of genotype-guided analgesia. By integrating Pharmacogenomics (PGx), this approach aims to optimize pain management, enhance safety, and reduce addiction risks. This understanding prompted the utilization of multifactor dimensionality reduction (MDR) to explore a range of phenotypes including PGx and gene–gene interactions (GGI) in a healthy cohort, thereby personalizing pain management strategies. The study sampled 100 unrelated healthy Western Iranians and 100 individuals from the 1000 Genome Project. Pre-testing involved searching for PGx annotations (variants associated with drug-gene-diseases) related to pain sensitivity and inflammation using the PharmGKB database, which identified 128 relevant genes. A questionnaire helped select 100 participants who had never used potent opioids but also other psychoactive agents (e.g., nicotine, amphetamines, etc.) and disease-related drugs. Whole-exome sequencing (WES) was then employed to analyze these genes in an Iranian cohort. Further analyses included MDR for identifying synergistic gene annotations and GGI for exploring complex gene interactions through the Visualization of Statistical Epistasis Networks (ViSEN). The study identified a Pain, Anti-Inflammatory, and Immunomodulating agents (PAIma) panel from the 128 genes, resulting in 55,590 annotations across 21 curated pathways. After filtering, 54 significant structural or regulatory variants were identified. This research also highlighted novel gene relationships involving the CYP3A5 gene, hsa-miR-355-5p, Paliperidone, and CYP2D6, which warrant further investigation. This study offers a novel pharmacogenetic framework that could potentially transform opioid prescribing practices to mitigate misuse and enhance personalized pain management. Further validation of these findings from multi countries and ethnic groups could guide clinicians in implementing DNA-based opioid prescribing, aligning treatment more closely with individual genetic profiles.Graphical abstract

The genome sequence of the Common Wainscot moth, Mythimna pallens Linnaeus, 1758

We present a genome assembly from an individual male Mythimna pallens (the Common Wainscot moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 719.10 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,343 protein-coding genes.

Insights into Adaption and Growth Evolution: Genome–Wide Copy Number Variation Analysis in Chinese Hainan Yellow Cattle Using Whole–Genome Re–Sequencing Data

Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re–sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate the resources of population genetic variation. We conducted whole–genome sequencing on 30 Chinese Hainan yellow cattle, thus generating 814.50 Gb of raw data. CNVs were called using CNVnator software, and subsequent filtering with Plink and HandyCNV yielded 197,434 high–quality CNVs and 5852 CNV regions (CNVRs). Notably, the proportion of deleted sequences (81.98%) exceeded that of duplicated sequences (18.02%), with the lengths of CNVs predominantly ranging between 20 and 500 Kb This distribution demonstrated a decrease in CNVR count with increasing fragment length. Furthermore, an analysis of the population genetic structure using CNVR databases from Chinese, Indian, and European commercial cattle breeds revealed differences between Chinese Bos indicus and Indian Bos indicus. Significant differences were also observed between Hainan yellow cattle and European commercial breeds. We conducted gene annotation for both Hainan yellow cattle and European commercial cattle, as well as for Chinese Bos indicus and Indian Bos indicus, identifying 206 genes that are expressed in both Chinese and Indian Bos indicus. These findings may provide valuable references for future research on Bos indicus. Additionally, selection signatures analysis based on Hainan yellow cattle and three European commercial cattle breeds identified putative pathways related to heat tolerance, disease resistance, fat metabolism, environmental adaptation, candidate genes associated with reproduction and the development of sperm and oocytes (CABS1, DLD, FSHR, HSD17B2, KDM2A), environmental adaptation (CNGB3, FAM161A, DIAPH3, EYA4, AAK1, ERBB4, ERC2), oxidative stress anti–inflammatory response (COMMD1, OXR1), disease resistance (CNTN5, HRH4, NAALADL2), and meat quality (EHHADH, RHOD, GFPT1, SULT1B1). This study provides a comprehensive exploration of CNVs at the molecular level in Chinese Hainan yellow cattle, offering theoretical support for future breeding and selection programs aimed at enhancing qualities of this breed.

A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.

The Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary. Herein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes. Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.

GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data.

Microbial culture collections play a crucial role in the collection, maintenance, and distribution of quality-assured living microbial strains, along with their associated phenotypic and omics data. To enhance the find-able, accessible, interoperable, and re-usable (FAIR) data utilization of microbial resources, the World Data Center for Microorganisms (WDCM) has developed the Global Catalogue of Microorganisms (GCM) and the Global Catalogue of Type Strains (gcType). These platforms provide interactive interfaces for cataloging the holdings of collections, along with detailed annotations of type strain genomes and curated metadata, including ecosystems, growth conditions, and collection locations. The system maximizes the scientific impact of microbial resources and culture collections through an integrated data mining tool that links strain- and species-related information from various public resources. Currently, the GCM and gcType include 574422 strains from 154 culture collections across 51 countries and regions, along with 25980 genomes from type species. Additionally, 2702655 articles and 103337 patents are integrated with these microbial resources.The system supports microbial taxonomic research and provides evidence for implementing the Nagoya Protocol in the field of microbial resources and their digital sequence information (DSI). Access is freely available at gcm.wdcm.org and gctype.wdcm.org.

Genetic Variation Study of Several Romanian Pepper (Capsicum annuum L.) Varieties Revealed by Molecular Markers and Whole Genome Resequencing

Numerous varieties of Capsicum annuum L. with multiple valuable traits, such as adaptation to biotic and abiotic stress factors, can be found in south-east Romania, well known for vegetable cultivation and an important area of biodiversity conservation. To obtain useful information about sustainable agriculture, management, and conservation of local pepper varieties, we analyzed the genetic diversity and conducted deep molecular characterization using whole genome resequencing (WGS) for variant/mutation detection. The pepper varieties used in the present study were registered by VRDS in the ISTIS catalog between 1974 and 2019 and maintained in conservative selection; however, no studies have been published yet using WGS analysis in order to characterize this specific germplasm. The genome sequences, annotation, and alignments provided in this study offer essential resources for genomic research as well as for future breeding efforts using the C. annuum local varieties.

Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: genome-wide polymorphisms, differential gene expression, and drug resistance

BackgroundThe study of rodent malaria parasites has significantly advanced our understanding of malaria parasite biology and host responses to parasite infections. There are four well-characterized rodent malaria parasite species (Plasmodium yoelii, P. chabaudi, P. berghei, and P. vinckei). Each species also has multiple strains that cause different disease phenotypes. P. yoelii nigeriensis N67C and N67, two isogenic parasites, are particularly intriguing as they differ in virulence and incite different immune responses in mice. The genome of the N67 parasite has been assembled recently, but not that of N67C. This study used PacBio HiFi sequencing data to assemble the N67C genome, compared the two genomes, and performed RNA sequencing to identify polymorphisms and differentially expressed genes (DEGs).ResultsThe assembled N67C parasite genome consisted of 16 scaffolds and three contigs of approximately 22.5 Mb with 100% and 96.6% completeness based on well-characterized single-copy orthologs specific to the Apicomplexa phylum and the Plasmodium genus, respectively. A comparison between the annotated N67C and N67 genomes revealed 133 single nucleotide polymorphisms (SNPs) and 75 indels. Among the polymorphic sites, an S (N67) to N (N67C) amino acid substitution at position 114 (S114N) in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) confers resistance to pyrimethamine in mice. Additionally, 60 differentially expressed single-copy genes (DEGs) were detected after comparing mRNA levels between the two parasites. Starting with the predicted and annotated 5,681 N67C and 5,749 N67 genes, we identified 4,641 orthogroups that included at least one gene from the four P. yoelii parasites (N67, N67C, 17X, and YM), whereas 758 orthogroups showed subspecies or strain-specific patterns.ConclusionThe identification of polymorphic sites between the N67 and N67C genomes, along with the detection of the DEGs, may provide crucial insights into the variations in parasite drug responses and disease severity between these two isogenic parasites. The functional characterization of these genetic differences and candidate genes will deepen our understanding of disease mechanisms and pave the way for developing more effective control measures against malaria.

The genome sequence of the Shoulder-striped Wainscot moth, Leucania comma Linnaeus, 1761

We present a genome assembly from an individual female Leucania comma (the Shoulder-striped Wainscot moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 751.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,477 protein-coding genes.

The genome sequence of the Large Beech Piercer moth, Cydia fagiglandana (Zeller, 1841)

We present a genome assembly from an individual male Cydia fagiglandana (Large Beech Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 555.10 megabases. Most of the assembly (99.91%) is scaffolded into 28 chromosomal pseudomolecules, including the sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,783 protein-coding genes.

The genome sequence of a soliderfly, Stratiomys singularior (Harris, 1776)

We present a genome assembly from an individual female solidierfly, Stratiomys singularior (Arthropoda; Insecta; Diptera; Stratiomyidae). The genome sequence has a total length of 715.20 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,614 protein-coding genes.

The genome sequence of the Clouded Drab moth, Orthosia incerta Hufnagel, 1766

We present a genome assembly from an individual male Orthosia incerta (the Clouded Drab; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 946.20 megabases. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,327 protein-coding genes.

Evaluation of Bayesian Linear Regression models for gene set prioritization in complex diseases.

Genome-wide association studies (GWAS) provide valuable insights into the genetic architecture of complex traits, yet interpreting their results remains challenging due to the polygenic nature of most traits. Gene set analysis offers a solution by aggregating genetic variants into biologically relevant pathways, enhancing the detection of coordinated effects across multiple genes. In this study, we present and evaluate a gene set prioritization approach utilizing Bayesian Linear Regression (BLR) models to uncover shared genetic components among different phenotypes and facilitate biological interpretation. Through extensive simulations and analyses of real traits, we demonstrate the efficacy of the BLR model in prioritizing pathways for complex traits. Simulation studies reveal insights into the model's performance under various scenarios, highlighting the impact of factors such as the number of causal genes, proportions of causal variants, heritability, and disease prevalence. Comparative analyses with MAGMA (Multi-marker Analysis of GenoMic Annotation) demonstrate BLR's superior performance, especially in highly overlapped gene sets. Application of both single-trait and multi-trait BLR models to real data, specifically GWAS summary data for type 2 diabetes (T2D) and related phenotypes, identifies significant associations with T2D-related pathways. Furthermore, comparison between single- and multi-trait BLR analyses highlights the superior performance of the multi-trait approach in identifying associated pathways, showcasing increased statistical power when analyzing multiple traits jointly. Additionally, enrichment analysis with integrated data from various public resources supports our results, confirming significant enrichment of diabetes-related genes within the top T2D pathways resulting from the multi-trait analysis. The BLR model's ability to handle diverse genomic features, perform regularization, conduct variable selection, and integrate information from multiple traits, genders, and ancestries demonstrates its utility in understanding the genetic architecture of complex traits. Our study provides insights into the potential of the BLR model to prioritize gene sets, offering a flexible framework applicable to various datasets. This model presents opportunities for advancing personalized medicine by exploring the genetic underpinnings of multifactorial traits.