The Ensembl gene annotation system

lncRNA CARINH regulates expression and function of innate immune transcription factor IRF1 in macrophages

The discovery of long non-coding RNAs (lncRNAs) has provided a new perspective on the centrality of RNA in gene regulation and genome organization. Here, we screened for lncRNAs with putative functions in the host response to single-stranded RNA respiratory viruses. We identify CARINH as a conserved cis-acting lncRNA up-regulated in three respiratory diseases to control the expression of its antisense gene IRF1, a key transcriptional regulator of the antiviral response. CARINH and IRF1 are coordinately increased in the circulation of patients infected with human metapneumovirus, influenza A virus, or SARS-CoV-2, and in macrophages in response to viral infection or TLR3 agonist treatment. Targeted depletion of CARINH or its mouse ortholog Carinh in macrophages reduces the expression of IRF1/Irf1 and their associated target gene networks, increasing susceptibility to viral infection. Accordingly, CRISPR-mediated deletion of Carinh in mice reduces antiviral immunity, increasing viral burden upon sublethal challenge with influenza A virus. Together, these findings identify a conserved role of lncRNA CARINH in coordinating interferon-stimulated genes and antiviral immune responses.

Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution

Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with cis-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.

Whole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population

BACKGROUND

Keratoconus (KC) is a prevalent corneal condition with a modest genetic basis. Recent studies have reported significant genetic associations in multi-ethnic cohorts. However, the situation in the Chinese population remains unknown. This study was conducted to identify novel genetic variants linked to KC and to evaluate the potential applicability of a polygenic risk model in the Han Chinese population.

METHODS

A total of 830 individuals diagnosed with KC and 779 controls from a Chinese cohort were enrolled and genotyped by whole-genome sequencing (WGS). Common and rare variants were respectively subjected to single variant association analysis and gene-based burden analysis. Polygenic risk score (PRS) models were developed using top single-nucleotide polymorphisms (SNPs) identified from a multi-ethnic meta-analysis and then evaluated in the Chinese cohort.

RESULTS

The characterization of germline variants entailed correction for population stratification and validation of the East Asian ancestry of the included samples via principal component analysis. For rare protein-truncating variants (PTVs) with minor allele frequency (MAF) < 5%, ZC3H11B emerged as the top prioritized gene, albeit failing to reach the significance threshold. We detected three common variants reaching genome-wide significance (P ≤ 5 × 10-8), all of which are novel to KC. Our study validated three well known predisposition loci, COL5A1, EIF3A and FNDC3B. Additionally, a significant correlation of allelic effects was observed for suggestive SNPs between the largest multi-ethnic meta-genome-wide association study (GWAS) and our study. The PRS model, generated using top SNPs from the meta-GWAS, stratified individuals in the upper quartile, revealing up to a 2.16-fold increased risk for KC.

CONCLUSIONS

Our comprehensive WGS-based GWAS in a large Chinese cohort enhances the efficiency of array-based genetic studies, revealing novel genetic associations for KC and highlighting the potential for refining clinical decision-making and early prevention strategies.

From Gene to Whole Cell: Modeling, Visualization, and Analysis

Proteogenomics combines proteomic and genetic data to gain new insights in molecular mechanisms. Here, we extend this approach toward structural biology from a tool perspective. The chapter starts with tools which can be used to explore genetic information and then enrich those with proteomic data. Based on the corresponding identifiers, three-dimensional structures of proteins are identified and used to embed them in their molecular environment, here the surrounding membrane. This membrane is then mapped onto the surface of an interpretative three-dimensional cell model. Then, the embedded protein and the cell environment are associated with a metabolic pathway, again based on the identifiers provided by biomedical databases. Accompanying the different chapters, related work is discussed which can alternatively be used. Finally, an outlook toward immersive analytics is given.

Oncolytic immunotherapy with nivolumab in muscle-invasive bladder cancer: a phase 1b trial

There is a critical unmet need for safe and efficacious neoadjuvant treatment for cisplatin-ineligible patients with muscle-invasive bladder cancer. Here we launched a phase 1b study using the combination of intravesical cretostimogene grenadenorepvec (oncolytic serotype 5 adenovirus encoding granulocyte-macrophage colony-stimulating factor) with systemic nivolumab in cisplatin-ineligible patients with cT2-4aN0-1M0 muscle-invasive bladder cancer. The primary objective was to measure safety, and the secondary objective was to assess the anti-tumor efficacy as measured by pathologic complete response along with 1-year recurrence-free survival. No dose-limiting toxicity was encountered in 21 patients enrolled and treated. Combination treatment achieved a pathologic complete response rate of 42.1% and a 1-year recurrence-free survival rate of 70.4%. Pathologic response was associated with baseline free E2F activity and tumor mutational burden but not PD-L1 status. Although T cell infiltration was broadly induced after intravesical oncolytic immunotherapy, the formation, enlargement and maturation of tertiary lymphoid structures was specifically associated with complete response, supporting the importance of coordinated humoral and cellular immune responses. Together, these results highlight the potential of this combination regimen to enhance therapeutic efficacy in cisplatin-ineligible patients with muscle-invasive bladder cancer, warranting additional study as a neoadjuvant therapeutic option. ClinicalTrials.gov identifier: NCT04610671 .

The genome sequence of Radford's Flame Shoulder, Ochropleura leucogaster (Freyer, 1831)

We present a genome assembly from an individual male Ochropleura leucogaster (Freyer, 1831) (Radford's Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 545.70 megabases. Most of the assembly (99.93%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,155 protein-coding genes.

The genome sequence of the pear, Pyrus communis L

We present a genome assembly from a specimen of Pyrus communis (the pear; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence has a total length of 487.30 megabases. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 443.53 kilobases and 159.93 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 37,713 protein-coding genes.

The genome sequence of the Brown Heath Robberfly, Tolmerus cingulatus (Fabricius, 1781)

We present a genome assembly from an individual male Tolmerus cingulatus (Brown Heath Robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 280.00 megabases. Most of the assembly (88.86%) is scaffolded into 6 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 20.2 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,047 protein-coding genes.

Augmenting Transcriptome Annotations through the Lens of Splicing Evolution

Alternative splicing (AS) is a ubiquitous mechanism in eukaryotes. It is estimated that 90% of human genes are alternatively spliced. Despite enormous efforts, transcriptome annotations remain, nevertheless, incomplete. Conventional means of annotation were largely driven by experimental data such as RNA-seq and protein sequences, while little insight was shed on understanding transcriptomes and alternative splicings from the perspective of evolution. This study addresses this critical gap by presenting TENNIS (Transcript EvolutioN for New Isoform Splicing), an evolution-based model to predict unannotated isoforms and refine existing annotations without requiring additional data. The model of TENNIS is based on two minimal premises-AS isoforms evolve sequentially from existing isoforms, and each evolutionary step involves a single AS event. We formulate the identification of missing transcripts as an optimization problem and parsimoniously find the minimal number of novel transcripts. Our analysis showed approximately 80% of multi-transcript groups from six transcriptome annotations satisfy our evolutionary model. At a high confidence level, 40% of isoforms predicted by TENNIS were validated by deep long-read RNA-seq. In a simulated incomplete annotation scenario, TENNIS dramatically outperforms two randomized baseline approaches by a 2.25-3 fold-change in precision or a 3.5-3.9 fold-change in recall, after controlling the same level of recall or precision of the baseline methods. These results demonstrate that TENNIS effectively identifies missing transcripts by complying with minimal propositions, offering a powerful approach for transcriptome augmentations through the lens of alternative splicing evolutions. TENNIS is freely available at https://github.com/Shao-Group/tennis .

The genome sequence of the Scalloped Hook-tip moth, Falcaria lacertinaria (Linnaeus, 1758)

We present a genome assembly from an individual female Falcaria lacertinaria (the Scalloped Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 300.20 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.07 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,709 protein-coding genes.

The genome sequence of a cranefly Tipula ( Lunatipula) vernalis Meigen, 1804

We present a genome assembly from an individual female cranefly Tipula vernalis (Arthropoda; Insecta; Diptera; Tipulidae). The genome sequence has a total length of 1,272.30 megabases. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.01 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,911 protein-coding genes.

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 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 a tachinid fly, Linnaemya vulpina (Fallén, 1810)

We present a genome assembly from an individual male tachinid fly, Linnaemya vulpina (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence has a total length of 554.00 megabases. Most of the assembly (98.85%) is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.72 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,599 protein-coding genes.

The genome sequence of the Black Medic, Medicago lupulina L

We present a genome assembly from a specimen of Black Medic, Medicago lupulina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 575.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 294.12 kilobases and 123.99 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,424 protein-coding genes.

The genome sequence of spotted medick, Medicago arabica (L.) Huds. (Fabaceae)

We present a genome assembly from an individual Medicago arabica (the spotted medick; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 515.5 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 324.47 kilobases and 125.07 kilobases in length, respectively. Gene annotation of this assembly on Ensembl identified 24,619 protein-coding genes.

The genome sequence of the alder spittlebug, Aphrophora alni (Fallén, 1805)

We present a genome assembly from an individual male Aphrophora alni (the alder spittlebug; Arthropoda; Insecta; Hemiptera; Aphrophoridae). The genome sequence has a total length of 1,781.50 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 27.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,940 protein-coding genes.

The genome sequence of the common awl robberfly, Neoitamus cyanurus (Loew, 1849)

We present a genome assembly from an individual female Neoitamus cyanurus (the common awl robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 365.5 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,046 protein-coding genes.

The genome sequence of the willow leaf beetle, Lochmaea capreae Linnaeus, 1758

We present a genome assembly from an individual female Lochmaea capreae (the willow leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 534.7 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.85 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,254 protein coding genes.

The genome sequence of fat-hen, Chenopodium album L

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2 n = 6 x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758)

We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.

The genome sequence of a leaf beetle, Galeruca laticollis Sahlberg, C.R., 1838

We present a genome assembly from an individual leaf beetle, Galeruca laticollis (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 2,154.60 megabases. Most of the assembly (99.92%) is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.98 kilobases in length. Gene annotation of this assembly on Ensembl identified 32,229 protein-coding genes.

The genome sequence of Langmaid's Yellow Underwing moth, Noctua janthina (Denis & Schiffermüller) 1775

We present a genome assembly from an individual male Noctua janthina (Langmaid's Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 539.70 megabases. Most of the assembly (99.99%) is scaffolded into 31 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 12,089 protein-coding genes.

The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759)

We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.

The genome sequence of the common green Tenthredo, Tenthredo mesomela Linnaeus, 1758

We present a genome assembly from an individual female Tenthredo mesomela (the common green Tenthredo; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 392.8 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,086 protein coding genes.

Discovery of prognostic lncRNAs in colorectal cancer using spatial transcriptomics

Colorectal cancer (CRC) exhibits significant genetic and epigenetic diversity, evolving into sub-clonal populations with varied metastatic potentials and treatment responses. Predicting metastatic disease in CRC patients remains challenging, underscoring the need for reliable biomarkers. While most research on therapeutic targets and biomarkers has focused on proteins, non-coding RNAs such as long non-coding RNAs (lncRNAs) comprise most of the transcriptome and demonstrate superior tissue- and cancer-specific expression. We utilised spatial transcriptomics to investigate lncRNAs in CRC tumours, offering more precise cell-type-specific expression data compared to bulk RNA sequencing. Our analysis identified 301 lncRNAs linked to malignant CRC regions, which we validated with public data. Further validation using RNA-FISH revealed three lncRNAs (LINC01978, PLAC4, and LINC01303) that are detectable in stage II tumours but not in normal epithelium and are upregulated in metastatic tissues. These lncRNAs hold potential as biomarkers for early risk assessment of metastatic disease.

The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758)

We present a genome assembly from an individual female Haliaeetus albicilla (the white-tailed eagle; Chordata; Aves; Accipitriformes; Accipitridae). The genome sequence has a total length of 1,320.30 megabases. Most of the assembly is scaffolded into 34 chromosomal pseudomolecules, including the Z and W sex chromosomes. Gene annotation of this assembly on Ensembl identified 17,501 protein-coding genes.

The genome sequence of the common alder, Alnus glutinosa (L.) Gaertn. (Betulaceae)

We present a genome assembly of a diploid specimen of Alnus glutinosa (the common alder; Streptophyta; Magnoliopsida; Fagales; Betulaceae). The genome sequence has a total length of 456.80 megabases. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome assemblies have lengths of 505.23 and 155.85 kilobases and the plastid genome is 160.82 kilobases long. Gene annotation of this assembly on Ensembl identified 23,728 protein-coding genes.

The genome sequence of the giant tachinid fly, Tachina grossa (Linnaeus, 1758)

We present a genome assembly from an individual female Tachina grossa (the giant tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence spans 936.90 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.82 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,428 protein-coding genes.

CapsNet-TIS: Predicting translation initiation site based on multi-feature fusion and improved capsule network

Genes are the basic units of protein synthesis in organisms, and accurately identifying the translation initiation site (TIS) of genes is crucial for understanding the regulation, transcription, and translation processes of genes. However, the existing models cannot adequately extract the feature information in TIS sequences, and they also inadequately capture the complex hierarchical relationships among features. Therefore, a novel predictor named CapsNet-TIS is proposed in this paper. CapsNet-TIS first fully extracts the TIS sequence information using four encoding methods, including One-hot encoding, physical structure property (PSP) encoding, nucleotide chemical property (NCP) encoding, and nucleotide density (ND) encoding. Next, multi-scale convolutional neural networks are used to perform feature fusion of the encoded features to enhance the comprehensiveness of the feature representation. Finally, the fused features are classified using capsule network as the main network of the classification model to capture the complex hierarchical relationships among the features. Moreover, we improve the capsule network by introducing residual block, channel attention, and BiLSTM to enhance the model's feature extraction and sequence data modeling capabilities. In this paper, the performance of CapsNet-TIS is evaluated using TIS datasets from four species: human, mouse, bovine, and fruit fly, and the effectiveness of each part is demonstrated by performing ablation experiments. By comparing the experimental results with models proposed by other researchers, the results demonstrate the superior performance of CapsNet-TIS.

An early Transcriptomic Investigation in Adult Patients with Spinal Muscular Atrophy Under Treatment with Nusinersen

Spinal muscular atrophy (SMA) is a rare degenerative disorder with loss of motor neurons caused by mutations in the SMN1 gene. Nusinersen, an antisense oligonucleotide, was approved for SMA treatment to compensate the deficit of the encoded protein SMN by modulating the pre-mRNA splicing of SMN2, the centromeric homologous of SMN1, thus inducing the production of a greater amount of biologically active protein. Here, we reported a 10-month transcriptomics investigation in 10 adult SMA who received nusinersen to search for early genetic markers for clinical monitoring. By comparing their profiles with age-matched healthy controls (HC), we also analyzed the changes in miRNA/mRNAs expression and miRNA-target gene interactions possibly associated with SMA. A multidisciplinary approach of HT-NGS followed by bioinformatics/biostatistics analysis was applied. Within the study interval, those SMA patients who showed some clinical improvements were characterized by having the SMN2/SMN1 ratio slightly increased over the time, while in the stable ones the ratio decreased, suggesting that the estimation of SMN2/SMN1 expression may be an early indicator of nusinersen efficacy. On the other hand, the expression of 38/147 genes/genetic regions DE at T0 between SMA and HC like TRADD and JUND resulted "restored" at T10. We also confirmed the dysregulation of miR-146a(-5p), miR-324-5p and miR-423-5p in SMA subjects. Of interest, miR-146a-5p targeted SMN1, in line with experimental evidence showing the key role of astrocyte-produced miR-146a in SMA motor neuron loss. Molecular pathways such as NOTCH, NF-kappa B, and Toll-like receptor signalings seem to be involved in the SMA pathogenesis.

The genome sequence of the Broom moth, Ceramica pisi Linnaeus, 1758

We present a genome assembly from an individual male Ceramica pisi (the Broom moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 732.70 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 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein-coding genes.

Genome-Wide Association Study for Milk Somatic Cell Score in Holstein Friesian Cows in Slovenia

Mastitis is a serious challenge for the dairy industry, leading to economic losses and affecting milk quality. The aim of this study is to identify genetic factors associated with mastitis resistance by conducting a genome-wide association study (GWAS) for the somatic cell score (SCS). Phenotypic records of 350 Holstein Friesian cows were obtained from the Slovenian Cattle Recording Scheme Database and consisted of around 1500 lactation data from 2012 to 2023 collected on a single farm in Slovenia. Corresponding genotypic data were also retrieved from the same database and genotyped using the Illumina BovineSNP50 BeadChip (Illumina, Inc., San Diego, CA, USA). For the association study, three SCS parameters were considered, including lactation mean somatic cell score (LM_SCS), maximum SCS value (SCSMAX), and top three mean value of SCS (TOP3). After performing a GWAS using FarmCPU and BLINK models, five significant SNPs associated with the TOP3 trait were found on BTA 14, 15, 22, and 29. The identified SNP markers were closely linked to six known candidate genes (DNASE1L3, SLC36A4, ARMC1, PDE7A, MMP13, CD44). These results indicate potential genetic markers associated with SCS in the Slovenian Holstein Friesian population.

The genome sequence of the ruby bryozoan, Bugula neritina (Linnaeus, 1758)

We present a genome assembly from a specimen of Bugula neritina (the ruby bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence has total length of 216.00 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,264 protein-coding genes.

The genome sequence of the lesser worm flesh fly, Sarcophaga ( Sarcophaga) subvicina Rohdendorf, 1937

We present a genome assembly from an individual male Sarcophaga subvicina (the lesser worm flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 71 megabases in span. Most of the assembly (95.91%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,793 protein coding genes.

The genome sequence of the Dogs-Mercury Flea Beetle, Hermaeophaga mercurialis (Fabricius, 1792)

We present a genome assembly from an individual Dogs-Mercury Flea Beetle, Hermaeophaga mercurialis (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a length of 479.40 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,633 protein-coding genes.

The genome sequence of the Scarce Cardinal Beetle, Schizotus pectinicornis (Linnaeus, 1758)

We present a genome assembly from an individual female Schizotus pectinicornis (the Scarce Cardinal Beetle; Arthropoda; Insecta; Coleoptera; Pyrochroidae). The genome sequence spans 181.10 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.59 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,605 protein-coding genes.

The genome sequence of a robberfly Leptogaster cylindrica (De Geer, 1776)

We present a genome assembly from an individual female Leptogaster cylindrica (robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence spans 196.60 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,816 protein-coding genes.

The genome sequence of the blonde ray, Raja brachyura Lafont, 1871

We present a genome assembly from an individual female Raja brachyura (Blonde Ray; Chordata; Chondrichthyes; Rajiformes; Rajidae). The genome sequence spans 2,700.50 megabases. Most of the assembly is scaffolded into 49 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,252 protein-coding genes.

Identification of key genes and long non‑coding RNA expression profiles in osteoporosis with rheumatoid arthritis based on bioinformatics analysis

BACKGROUND

Although rheumatoid arthritis (RA) is a chronic systemic tissue disease often accompanied by osteoporosis (OP), the molecular mechanisms underlying this association remain unclear. This study aimed to elucidate the pathogenesis of RA and OP by identifying differentially expressed mRNAs (DEmRNAs) and long non-coding RNAs (lncRNAs) using a bioinformatics approach.

METHODS

Expression profiles of individuals diagnosed with OP and RA were retrieved from the Gene Expression Omnibus database. Differential expression analysis was conducted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) pathway enrichment analyses were performed to gain insights into the functional categories and molecular/biochemical pathways associated with DEmRNAs. We identified the intersection of common DEmRNAs and lncRNAs and constructed a protein-protein interaction (PPI) network. Correlation analysis between the common DEmRNAs and lncRNAs facilitated the construction of a coding-non-coding network. Lastly, serum peripheral blood mononuclear cells (PBMCs) from patients with RA and OP, as well as healthy controls, were obtained for TRAP staining and qRT-PCR to validate the findings obtained from the online dataset assessments.

RESULTS

A total of 28 DEmRNAs and 2 DElncRNAs were identified in individuals with both RA and OP. Chromosomal distribution analysis of the consensus DEmRNAs revealed that chromosome 1 had the highest number of differential expression genes. GO and KEGG analyses indicated that these DEmRNAs were primarily associated with " platelets (PLTs) degranulation", "platelet alpha granules", "platelet activation", "tight junctions" and "leukocyte transendothelial migration", with many genes functionally related to PLTs. In the PPI network, MT-ATP6 and PTGS1 emerged as potential hub genes, with MT-ATP6 originating from mitochondrial DNA. Co-expression analysis identified two key lncRNA-mRNA pairs: RP11 - 815J21.2 with MT - ATP6 and RP11 - 815J21.2 with PTGS1. Experimental validation confirmed significant differential expression of RP11-815J21.2, MT-ATP6 and PTGS1 between the healthy controls and the RA + OP groups. Notably, knockdown of RP11-815J21.2 attenuated TNF + IL-6-induced osteoclastogenesis.

CONCLUSIONS

This study successfully identified shared dysregulated genes and potential therapeutic targets in individuals with RA and OP, highlighting their molecular similarities. These findings provide new insights into the pathogenesis of RA and OP and suggest potential avenues for further research and targeted therapies.

The genome sequence of a leaf beetle, Chrysolina haemoptera (Linnaeus, 1758)

We present a genome assembly from a female leaf beetle, Chrysolina haemoptera (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The total length of the genome sequence is 718.30 megabases. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.87 kilobases long. Gene annotation of this assembly on Ensembl identified 12,298 protein-coding genes.

The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis & Schiffermüller), 1775

We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 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 12,087 protein-coding genes.

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.

Exome-wide association study identifies KDELR3 mutations in extreme myopia

Extreme myopia (EM), defined as a spherical equivalent (SE) ≤ -10.00 diopters (D), is one of the leading causes of sight impairment. Known EM-associated variants only explain limited risk and are inadequate for clinical decision-making. To discover risk genes, we performed a whole-exome sequencing (WES) on 449 EM individuals and 9606 controls. We find a significant excess of rare protein-truncating variants (PTVs) in EM cases, enriched in the retrograde vesicle-mediated transport pathway. Employing single-cell RNA-sequencing (scRNA-seq) and a single-cell polygenic burden score (scPBS), we pinpointed PI16 + /SFRP4+ fibroblasts as the most relevant cell type. We observed that KDELR3 is highly expressed in scleral fibroblast and involved in scleral extracellular matrix (ECM) organization. The zebrafish model revealed that kdelr3 downregulation leads to elongated ocular axial length and increased lens diameter. Together, our study provides insight into the genetics of EM in humans and highlights KDELR3's role in EM pathogenesis.

The genome sequence of a braconid wasp, Aleiodes testaceus (Telenga, 1941)

We present a genome assembly from an individual female Aleiodes testaceus (braconid wasp; Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence spans 110.70 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,520 protein-coding genes.

The genome sequence of the Dark Crimson Underwing moth, Catocala sponsa Linnaeus, 1767

We present a genome assembly from an individual female Catocala sponsa (the Dark Crimson Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence spans 803.70 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 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,493 protein-coding genes.

The genome sequence of the moss carder bee, Bombus muscorum (Linnaeus, 1758)

We present a genome assembly from an individual female Bombus muscorum (the moss carder bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence spans 317.70 megabases. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,668 protein-coding genes.

The genome sequence of wood avens, Geum urbanum L., 1753

We present a genome assembly from an individual Geum urbanum the (wood avens; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 1,304.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 335.5 and 156.1 kilobases in length respectively. Gene annotation of this assembly on Ensembl identified 50,336 protein-coding genes.

The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798

We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.

The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869)

We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.