Distinct Genomic Features Research Articles

Abstract 1251: Decoding tumour evolution and relapse drivers in EGFR mutant NSCLC in never smokers

Abstract Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related deaths worldwide. Unlike smoking-related NSCLC, the incidence of lung cancer among never-smokers in East Asia is rising, often driven by oncogenes such as EGFR. While Tyrosine Kinase Inhibitors (TKIs) have improved outcomes in EGFR-mutated NSCLC, resistance remains a significant challenge. Identifying the genomic and transcriptomic features that underpin tumour progression and relapse in early-stage EGFR-mutated NSCLC in non-smokers is crucial for developing novel therapeutic approaches to improve patient outcomes. Due to the diverse evolutionary trajectories of EGFR mutated NSCLC, our capacity to forecast disease trajectory is still limited. To address this, we performed 578 multi-region whole-exome and transcriptome sequencing from 180 treatment naïve early-stage EGFR-mutated resected NSCLC tumours. Among these, 56 (31%) patients eventually relapsed, while 124 (69%) did not, with a mean follow-up of 5.4 years. Our findings revealed that driver mutations in EGFR, TP53, and RBM10 were predominantly clonal, while a multitude of subclonal driver mutations contributed to increased tumour diversity. Interestingly, mutational signature SBS40a, of unknown origin, was prevalent as clonal alterations, suggesting early involvement in EGFR-mutated tumours. Notably, relapsed tumours exhibited distinct genomic features, including elevated subclonal APOBEC mutational signatures, higher rates of whole-genome doubling, and increased chromosomal aberrations, linking these features to greater mutational burden, intra-tumour heterogeneity and poorer outcomes. Overall, our results demonstrate the diversity of clonal and subclonal mutational processes that shape the clonal architecture of EGFR-mutated NSCLC in non-smokers and identify key features driving relapse. Ongoing efforts are focused on leveraging these features to identify potential prognostic markers for risk stratification and therapeutic targets for early-stage disease. Citation Format: Komal Gupta, Dawn Lau Pingxi, Ngak Leng Sim, Kenneth Chow, Lan Ying Wang, Mengyuan Pang, Stephanie Saw, Wanjin Hong, Anders Martin Jacobsen Skanderup, Regina Hoo, Daniel Shao Weng Tan. Decoding tumour evolution and relapse drivers in EGFR mutant NSCLC in never smokers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1251.

Development and characterization of the novel MYD88 mutated, 6q deleted BCWM.2 cell line for Waldenström macroglobulinaemia.

Cell lines have enabled a comprehensive understanding of disease biology and the advancement of new therapeutics in Waldenström macroglobulinaemia (WM). Herein, we report the development of BCWM.2, a novel WM cell line derived from an untreated symptomatic WM patient. Immunophenotypic and genomic analyses confirmed its origin from primary bone marrow WM cells. Flow cytometry revealed expression of CD19, CD20, CD23, CD38, CD45RA, CD52, immunoglobulin M (IgM) heavy chain and λ light chain on BCWM.2 cells. Whole genome sequencing demonstrated that, unlike BCWM.1, MWCL-1 and RPCI-WM1, which harbour MYD88L265P mutations, BCWM.2 carries MYD88S243N. BCWM.2 also exhibited hallmark WM genetic aberrations, including 6q deletion and 6p amplification, along with unique mutations in LYN, AKAP9, HDAC5, RUNX3 and SPI1. BCWM.2 cells exhibited optimal growth when co-cultured with HS-5 stromal cells and developed subcutaneous flank masses in all five NOD-SCID mice, along with measurable serum human IgM levels. BCWM.2 cells also showed remarkable sensitivity to the B-cell lymphoma 2 inhibitor venetoclax and the Janus kinase 2/Interleukin-1 receptor-associated kinase 1 inhibitor pacritinib, underscoring their utility for identification of pharmacologically active agents. BCWM.2 represents a novel myeloid differentiation primary response 88-mutated, 6q-deleted cell line with distinct genomic features for invivo and invitro studies for WM.

ELOC-Mutated Renal Cell Carcinoma is a Rare Indolent Tumor with Distinctive Genomic Characteristics.

ELOC-Mutated Renal Cell Carcinoma is a Rare Indolent Tumor with Distinctive Genomic Characteristics.

The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork.

Endosymbiotic events in which an endosymbiont is retained within a cell that remains capable of phagocytosis, a situation known as mixotrophy, provide potentially important clues about the eukaryotic evolution. Here we describe the cell biology and genome of the giant mixotrophic ciliate Stentor pyriformis. We show that S. pyriformis contains Chlorella variabilis as an endosymbiont that retains the ability to live outside the host. Within the host, the Chlorella cells surrounded by microtubule "baskets" near the cell surface. Photosynthetic efficiency of the Chlorella is reduced inside the Stentor cell compared with outside the host, due to increased nonphotochemical quenching. S. pyriformis displays positive phototaxis via directed swimming that requires the presence of the Chlorella, implying a potential flow of information from the symbiont to direct the orientation and swimming of the host cell. We sequenced the S. pyriformis genome and found that it employs a standard genetic code, similar to other Stentor species but different from most other ciliates. We propose that S. pyriformis will serve as a useful model system for studying endosymbiosis, with unique advantages in terms of size and regenerative ability as well as distinct cellular and genomic features compared with other mixotrophic ciliate models.

Application of MALDI TOF and DART mass spectrometry as novel tools for classification of anaerobic gut fungi strains.

Anaerobic gut fungi (AGF) have emerged as promising candidates for optimized biogas and biofuel production due to their unique repertoire of potent lignocellulose-degrading enzymes. However, identifying AGF strains through standard fungal DNA barcodes still poses challenges due to their distinct genomic features. This study explored the applicability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI) and direct analysis in real-time (DART) mass spectrometry (MS) as alternative methods for AGF identification. Further, the capability of the methods to differentiate strains from different growth phases was investigated. The study found that both MALDI and DART were viable methods for AGF strain identification. MALDI proved to be a precise and robust technique for strain discrimination with prediction accuracies of 94% for unknown standard samples. Even at longer growth times (>3weeks) MALDI achieved good prediction accuracies with 84%; however, younger cultures (72h) were only predicted with 63% accuracy. The fast on-target lysis with minimal chemical demand yielded suitable spectra for strain differentiation. DART MS, while effective with prediction accuracies of samples with the same age of up to 93%, exhibited lower prediction accuracies for cultures of different ages, with 14% for young (72h) and 71% for old (>3weeks) samples. Further research could enhance the capabilities of these mass spectrometry methods for AGF identification and broaden their application to species-level discrimination and a wider range of AGF genera.

Genetic Diversity Estimation and Genome-Wide Selective Sweep Analysis of the Bazhou Yak.

The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai-Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (FST, Pi ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as MTOR, APOA1, and GPAT4. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks.

Revealing the distinct genomic features of Japanese soybeans.

Revealing the distinct genomic features of Japanese soybeans.

The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars

Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated ‘Asm2sv’, identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.

Global identification and functional characterization of Z-DNA in rice.

Z-DNA is a left-handed double helix form of DNA that is believed to be involved in various DNA transactions. However, comprehensive investigations aimed at global profiling of Z-DNA landscapes are still missing in both humans and plants. We here report the development of two techniques: anti-Z-DNA antibody-based immunoprecipitation followed by sequencing (ZIP-seq), and cleavage under targets and tagmentation (CUT&TAG) for characterizing Z-DNA in nipponbare rice (Oryza sativa L., Japonica). We found that Z-DNA-IP+ (Z-DNA recognized by the antibody) exhibits distinct genomic features as compared to Z-DNA-IP- (Z-DNA not recognized by the antibody). The concomitant presence of G-quadruplexes (G4s) and i-motifs (iMs) may promote Z-DNA formation. DNA modifications such as DNA-6mA/-4acC generally disfavours Z-DNA formation, while modifications like DNA-5mC (CHH) and 8-oxodG promote it, highlighting the distinct roles of DNA base modifications in modulating Z-DNA formation. Importantly, Z-DNA located at transcription start sites (TSSs) enhances gene expression, whereas Z-DNA in genic regions represses it, underscoring its dual roles in regulating the expression of genes involved in fundamental biological functions and responses to salt stress. Furthermore, Z-DNA may play a role in transcriptional initiation and termination rather than in transcriptional elongation. Finally, the presence of Z-DNA in promoters is correlated with the coevolution of overlapping genes, thereby regulating gene domestication. Consequently, our study represents as a pivotal point and a solid foundation for reliably launching genome-wide investigations of Z-DNA, thereby advancing the understanding of Z-DNA biology in both plants and non-plant systems.

Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina.

Whole-genome analysis has provided insights into the evolution of Chlamydia trachomatis and, recently, into circulating strains that cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new ompA-genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), and then expanded globally. More recent work shows that this outbreak is diversifying into variants of described ompA-genotypes, with the same L2b genomic backbone. This study extends the investigation of LGV cases to Argentina and Finland. In 2017, an LGV outbreak was described in Argentina characterized by distinct genomic features shown by both ompA-genotyping and Multi-Locus Sequence Typing (MLST) analysis. We have obtained whole-genome sequences from cultured isolates and clinical samples via SureSelect (Agilent) target enrichment. Based on ompA and phylogenetic analyses, we describe further diversity within the ompA-genotype L2b clade, illustrating the transmission dynamics in Argentina and Finland. A key finding is that of a novel clade of Argentinian samples, characterized by a proposed new ompA-genotype L4. Additionally, we present the genome sequence of a non-LGV strain associated with anorectal proctitis. These findings contribute to the investigation of LGV evolution, particularly with the presence of the novel L4 lineage, and provide insights into genomic diversity and transmission dynamics of C. trachomatis.

Distinct genomic features of Transeurasian strains of Epstein-Barr virus in East Asia.

More than 95% of adult humans worldwide are latently infected with Epstein-Barr virus (EBV). Recent studies indicated that different EBV strains colonize different regions of Asia, where nasopharyngeal carcinoma (NPC) is endemic (southern China) or non-endemic (Japan/Korea). We searched for viral single nucleotide variant markers throughout the EBV genome by comparing the coding sequences of Japanese/Korean and NPC-endemic Chinese strains. We identified BamHI D fragment leftward reading frame 1 (BDLF1), BDLF2, and BDLF3 genes as viral geographical markers for distinguishing Japanese/Korean EBV strains from NPC-endemic Chinese EBV strains. Most significantly, BDLF-based EBV genotyping indicated that NPC-non-endemic Chinese and Mongolian EBV strains belong to the same group as Japanese/Korean EBV strains. We conclude that a particular type of EBV, designated as Transeurasian EBV, is prevalent among Transeurasian language speakers (Japanese, Korean, and Mongolian populations) and NPC-non-endemic Chinese populations.

Distinct genomic features and mutational signatures of nucleotide excision repair and mismatch repair in thymoma.

Thymoma is a rare malignancy with an unclear etiology of occurrence and development. We observed a higher incidence of thymoma in the Taiwanese population compared to other Western populations, suggesting the existence of different genomic features. Since most genomic studies are based on Western populations, we aimed to characterize the genomic profile of the Taiwanese population and compare it to the TCGA cohort in this study. We analyzed the genome of 47 thymoma patients using the Tumor Mutational Burden Panel to discover the genetic profile of the Taiwanese population. We also characterized the mutational signatures of these samples. Additionally, we leveraged RNA seq to estimate the gene expression profile and explored the featured pathways of thymoma in the Taiwanese population through gene set enrichment analysis.We identified several frequently mutated genes related to transcription, such as FAT1, KMT2D, and ZFHX3, as well as consensus mutational signatures associated with nucleotide excision repair (NER) and mismatch repair (MMR) deficiency. Our study also revealed increased activity of NER and MMR functions in our study cohort. Upon comparison with the TCGA cohort, we found dramatic differences in the most frequently mutated genes and mutational profiles between the Taiwanese and TCGA cohorts. Furthermore, we identified mismatch repair deficiency as a Taiwanese population-specific mutational signature with higher activity. These results highlight the distinct genomic background and molecular mechanisms of thymoma in the Taiwanese population, which may contribute to the development of new diagnostic and therapeutic strategies in the future.

Molecular Basis of Breast Tumor Heterogeneity.

Breast cancer (BC) is a profoundly heterogenous disease, with diverse molecular, histological, and clinical variations. The intricate molecular landscape of BC is evident even at early stages, illustrated by the complexity of the evolution from precursor lesions to invasive carcinoma. The key for therapeutic decision-making is the dynamic assessment of BC receptor status and clinical subtyping. Hereditary BC adds an additional layer of complexity to the disease, given that different cancer susceptibility genes contribute to distinct phenotypes and genomic features. Furthermore, the various BC subtypes display distinct metabolic demands and immune microenvironments. Finally, genotypic-phenotypic correlations in special histologic subtypes of BC inform diagnostic and therapeutic approaches, highlighting the significance of thoroughly comprehending BC heterogeneity.

Renal Juxtaglomerular Cell Tumors Exhibit Distinct Genomic and Epigenomic Features and Lack Recurrent Gene Fusions: Comprehensive Molecular Analysis of a Multi-institutional Series.

Juxtaglomerular cell tumor (JxGCT) is a rare type of renal neoplasm demonstrating morphologic overlap with some mesenchymal tumors such as glomus tumor (GT) and solitary fibrous tumor (SFT). Its oncogenic drivers remain elusive, and only a few cases have been analyzed with modern molecular techniques. In prior studies, loss of chromosomes 9 and 11 appeared to be recurrent. Recently, whole-genome analysis identified alterations involving genes of MAPK-RAS pathway in a subset, but no major pathogenic alterations have been discovered in prior whole transcriptome analyses. Considering the limited understanding of the molecular features of JxGCTs, we sought to assess a collaborative series with a multiomic approach to further define the molecular characteristics of this entity. Fifteen tumors morphologically compatible with JxGCTs were evaluated using immunohistochemistry for renin, single-nucleotide polymorphism array (SNP), low-pass whole-genome sequencing, and RNA sequencing (fusion assay). In addition, methylation analysis comparing JxGCT, GT, and SFT was performed. All cases tested with renin (n=11) showed positive staining. Multiple chromosomal abnormalities were identified in all cases analyzed (n=8), with gains of chromosomes 1p, 10, 17, and 19 and losses of chromosomes 9, 11, and 21 being recurrent. A pathogenic HRAS mutation was identified in one case as part of the SNP array analysis. Thirteen tumors were analyzed by RNA sequencing, with 2 revealing in-frame gene fusions: TFG::GPR128 (interpreted as stochastic) and NAB2::STAT6 . The latter, originally diagnosed as JxGCT, was reclassified as SFT and excluded from the series. No fusions were detected in the remaining 11 cases; of note, no case harbored NOTCH fusions previously described in GT. Genomic methylation analysis showed that JxGCT, GT, and SFT form separate clusters, confirming that JxGCT represents a distinct entity (ie, different from GT). The results of our study show that JxGCTs are a distinct tumor type with a recurrent pattern of chromosomal imbalances that may play a role in oncogenesis, with MAPK-RAS pathway activation being likely a driver in a relatively small subset.

Integrating genetic and morphological data to assess species delimitation of two Japanese large abalones: Haliotis discus discus and H. madaka

Two large abalone species prevalent in the Japanese archipelago, Haliotis discus discus and H. madaka, are considered to have different morphological characteristics, and previous population genomics analyses have suggested that they have distinct genomic features. However, integrated analyses comparing the genetic and morphological data from these species are lacking; thus, it remains unclear whether these two species are distinct biological species. In this study, we performed integrated genetic and morphological analyses on individuals of the two species captured in Tokushima Prefecture, Japan. Genetic analysis based on 118 species-diagnostic single-nucleotide polymorphism (SNP) loci showed that H. discus discus and H. madaka were clearly assigned to distinct genetic clusters corresponding to the two species, with the exception of one H. madaka individual showing evidence of genomic introgression from H. discus discus. Multiple statistical analyses based on quantitative characteristics of shell shape and foot muscle color suggested that this H. madaka individual with genomic introgression from H. discus discus had H. discus discus-like quantitative characteristics consistently. In summary, this study suggests that H. discus discus and H. madaka are distinct biological species reproductively isolated in natural environments, but genomic introgression possibly blurs the species boundary between H. discus discus and H. madaka.

Genomic Characterization of Bacillus sp. THPS1: A Hot Spring-Derived Species with Functional Features and Biotechnological Potential.

Bacillus sp. THPS1 is a novel strain isolated from a high-temperature hot spring in Thailand, exhibiting distinctive genomic features that enable adaptation to an extreme environment. This study aimed to characterize the genomic and functional attributes of Bacillus sp. THPS1 to understand its adaptation strategies and evaluate its potential for biotechnological applications. The draft genome is 5.38 Mbp with a GC content of 35.67%, encoding 5606 genes, including those linked to stress response and sporulation, which are essential for survival in high-temperature conditions. Phylogenetic analysis and average nucleotide identity (ANI) values confirmed its classification as a distinct species within the Bacillus genus. Pangenome analysis involving 19 others closely related thermophilic Bacillus species identified 1888 singleton genes associated with heat resistance, sporulation, and specialized metabolism, suggesting adaptation to nutrient-deficient, high-temperature environments. Genomic analysis revealed 12 biosynthetic gene clusters (BGCs), including those for polyketides and non-ribosomal peptides, highlighting its potential for synthesizing secondary metabolites that may facilitate its adaptation. Additionally, the presence of three Siphoviridae phage regions and 96 mobile genetic elements (MGEs) suggests significant genomic plasticity, whereas the existence of five CRISPR arrays implies an advanced defense mechanism against phage infections, contributing to genomic stability. The distinctive genomic features and functional capacities of Bacillus sp. THPS1 make it a promising candidate for biotechnological applications, particularly in the production of heat-stable enzymes and the development of resilient bioformulations.

Distinctive genomic features of human T-lymphotropic virus type 1-related adult T-cell leukemia-lymphoma in Western populations.

Adult T-cell leukemia-lymphoma (ATLL) is an aggressive malignancy driven by human T-cell leukemia virus type 1 (HTLV-1). Although patients from the Western hemisphere (Afro-Caribbean and South American) face worse prognoses, our understanding of ATLL molecular drivers derives mostly from Japanese studies. We performed multi-omic analyses to elucidate the genomic landscape of ATLL in Western cohorts. Recurrent deletions and/or damaging mutations involving FOXO3, ANKRD11, DGKZ, and PTPN6 implicate these genes as potential tumor suppressors. RNA-sequencing, published functional data and in vitro assays support the roles of ANKRD11 and FOXO3 as regulators of T-cell proliferation and apoptosis in ATLL, respectively. Survival data suggest that ANKRD11 mutation may confer a worse prognosis. Japanese and Western cohorts, in addition to acute and lymphomatous subtypes, demonstrated distinct molecular patterns. GATA3 deletion was associated with chronic cases with unfavorable outcomes. IRF4 and CARD11 mutations frequently emerged in relapses after interferon therapy. Our findings reveal novel putative ATLL driver genes and clinically relevant differences between Japanese and Western ATLL patients.

Role of CALCR expression in liver cancer: Implications for the immunotherapy response.

Liver hepatocellular carcinoma (LIHC) is a prevalent and lethal malignancy with a complex molecular landscape. Fibrosis and ferroptosis are implicated in LIHC progression, yet their roles remain to be elucidated. The present study investigated the expression and prognostic significance of calcitonin receptor (CALCR), a gene that intersects the pathways of fibrosis and ferroptosis, across LIHC and other types of cancer. Data were obtained from The Cancer Genome Atlas and the Molecular Signatures Database. LIHC patients were classified into two clusters based on fibrosis‑related gene expression using ConsensusClusterPlus. Single‑sample gene set enrichment analysis was employed to quantify fibrosis and ferroptosis levels. Correlation, survival and nomogram analyses were performed to assess the prognostic value of CALCR. Additionally, single‑cell RNA sequencing data from the Tumor Immune Single Cell Hub 2 (TISCH2) and pan‑cancer analyses of genomic heterogeneity features were incorporated. The present study also identified a putative regulatory role for CALCR in LIHC cell migration, proliferation and apoptosis. CALCR was identified as a significant prognostic marker for LIHC. Patients with high CALCR expression exhibited shortened overall survival (OS) and disease‑specific survival (DSS). Specifically, the hazard ratios (HRs) for OS and DSS were 1.76 [95% confidence interval (CI): 1.23=2.49) and 1.77 (95% CI: 1.13=2.78], respectively, with corresponding P‑values of 0.002 for OS and 0.013 for DSS. Analyses of immune cell infiltration revealed a more complex immune environment in patients with low CALCR expression, suggesting differential responses to immunotherapy. Furthermore, in HepG‑2 and HuH‑7 cells, small interfering (si)‑CALCR increased apoptosis while reducing proliferation and migration compared with si‑negative control. CALCR serves as a significant prognostic biomarker for LIHC, influencing both molecular pathways and the immune landscape. Its expression is associated with improved survival outcomes and distinct genomic features, positioning it as a potential therapeutic target and predictor of immunotherapy efficacy.

Recombination across distant coronavirid species and genera is a rare event with distinct genomic features.

Understanding the evolutionary events that led to SARS-CoV-2 emergence, spillover, and spread is crucial to prevent, or at least be prepared for, the same type of occurrence in the future. Given that SARS-CoV-2 has some characteristics not found in other closely related viruses, we aimed to systematically assess how likely these unique features may have been acquired through recombination. We found that, although recombination is a frequent phenomenon among betacoronaviruses, it is mostly limited to closely related members of the same species. Therefore, we conclude that the most likely scenario involved feature acquisition from recombination with a closely related virus that was circulating in a geographically overlapping area or through a different biological process, but not recombination from a virus of a different species, genus, or subgenus.

Genome sequence of Nitrosopumilus adriaticus CCS1 assembled from an ammonia-oxidizing enrichment culture.

We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related to Nitrosopumilus adriaticus NF5 but shows distinct genomic features compared to strain NF5.