Human-driven environmental changes threaten the region's dominant trees. China's fengshui forests harbor ancient trees with cultural and ecological significance, yet their climate resilience remains uncertain. By integrating genome and resequencing data, we investigate the structural variants, demographic dynamics, and local adaptation of Q. gilva, a threatened East Asian oak vital to fengshui traditions. The genome structural variants are enriched in critical pathways such as stress response and genome maintenance. Divergence of Q. gilva populations into Chinese and Japanese lineages occurs during mid-Pliocene climatic shifts. The Chinese lineage carries a higher genetic load, including deleterious mutations in histone deacetylase-associated genes that may impair adaptability. We propose four populations (Changning, Kiyosumi, Tama, and Lianyuan) as preliminary conservation priorities due to their higher genetic diversity and lower genetic load. In contrast, the Jianou population, which contains at least 240 ancient trees, may be susceptible to inbreeding depression as a result of its low genetic diversity and high genetic load. However, enhancing population resilience to future climate change through genetic rescue will depend on further comprehensive genetic and ecological studies.

Mimicry is a manifestation of natural selection that provides a key system for exploring the evolution of complex adaptive traits. Epicopeiidae moths are strikingly diverse morphologically, having evolved resemblance to multiple butterfly and moth models despite their recent origin. To uncover the genomic basis of this rapid morphological diversification, we sequenced high-quality genomes for eight Epicopeiidae species (three at the chromosome level), and conducted comparative genomics, developmental transcriptomics, and chromatin accessibility analyses. We found that genomic structural variations and gene family expansions contributed little to morphological evolution, whereas genes under positive selection in the ancestral Epicopeiidae were enriched for neural and visual functions, likely linked to the shift from nocturnal to diurnal activity of the Epecopeiidae ancestor. In contrast, accelerated conserved noncoding elements (aCNEs) and Epicopeiidae-specific accessible chromatin regions (ACRs) were enriched near morphogenetic genes, suggesting that changes in regulatory elements played a key role in morphological innovation. Our analyses also found that Epicopeiidae experienced a pronounced burst of transposable element (TE) activity between 40-10 Mya, temporally coinciding with morphological diversification. Approximately two-thirds of ACRs overlapped with TEs, and TE-derived ACRs were enriched near morphogenetic genes. These findings suggest that TE-driven regulatory innovation rewired developmental gene networks of Epicopeiidae and facilitated the emergence of multiple mimetic forms. Epicopeiidae thus provide a compelling example for understanding how TE-mediated regulatory evolution might fuel phenotypic innovation.

Introduction. B-cell prolymphocytic leukemia (B-PLL) is an extremely rare condition, accounting for less than 1% of all lymphoid leukemias. The identification of more than 55% of lymphocytes in the blood or bone marrow with prolymphocytic morphology is the hallmark feature of B-PLL. Conventional cytogenetic and molecular testing can detect MYC and TP53 abnormalities and mutations, identifying 3 distinct B-PLL groups with different clinical outcomes. Methods. Optical genome mapping (OGM) is a new genome-wide technology that can detect structural genomic variations (SVs) including translocations, inversions, deletions, duplications etc., copy number variations (CNVs) and whole-chromosome aneuploidies with high resolution. In the present study, cryopreserved mononuclear cells obtained from 3 patients with B-PLL were processed to obtain Ultra-high molecular weight (UHMW) DNA samples useful to perform OGM analyses by Bionano Saphyr instrumentation.Results. OGM detected an extremely complex genome with extensive copy number alterations and chromosomal rearrangements in all patients (Figure 1). OGM analyses found in case#1 the deletion of TNFRSF10A/B/C/D (alias DR4, DR5, BcR1 and DcR2) cluster and IKBKB gene in 8p loss, deletion of FAS and PTEN in loss of chromosome 10 and deletion of TP53 gene in 17p loss, implying that both intrinsic and extrinsic apoptotic pathways may be affected in this patient. Of interest, in case #1, the 1.25Mb loss at 13q22.2q22.3 comprised FBXL3 and MYCBP2 genes involved in MYC regulation. In case#2, deletion of BCL2L11 (alias BIM) in 2q loss, deletion of TP53 in chromosome 17p loss, together with amplification of BCL2 gene in 18q gain and MDM2 in chromosome 12 gain were observed, implying multifactorial alterations that can affect the intrinsic apoptotic pathway in case#2. Additionally, OGM detected gains of CDK2, CDK4 on chromosome 12, and gain of BCL6 and KLHL6 genes on chromosome 3, implicated in cell cycle regulation and germinal center formation. Interestingly, in case#2 chromosomes 12,17, and 21 were involved in multiple chained translocations, a typical pattern of complex genomic rearrangements that fall under the category of chromoanagenesis (Figure 1). In case#3, 11p15p11 CNV gain comprised WT1 and CD44 gene, whereas TP53 and BCOR were present in CNV losses identified by OGM analyses. Conclusions. OGM revealed that, in addition to the frequent TP53 dysfunction (deletions and mutations) and MYC alterations, multiple concomitant genomic changes affect other genes and pathways involved in apoptosis and cell-cycle regulation. These findings highlight the intricate genomic landscape of B-PLL, indicating that further pathogenetic mechanisms may contribute to disease, and underscores the ability of OGM to comprehensively capture this genomic complexity, including catastrophic rearrangements and multiple structural variations.

Introduction. Approximately 10-30% of adults with acute myeloid leukemia (AML) experience persistent leukemia following intensive induction therapy. To date, management of these patients remains challenging due to low response rate to savage chemotherapy and poor overall survival (OS) rate. Methods. Diagnostic samples from bone marrow (BM) were analyzed by conventional cytogenetics and next-generation sequencing (NGS). Optical genome mapping (OGM) is a new genome-wide technology that can detect structural genomic variations (SVs), copy number variations and whole-chromosome aneuploidies with high resolution. In the present study, available cryopreserved mononuclear cells were processed to obtain Ultra-high molecular weight (UHMW) DNA samples useful to perform OGM analyses by Bionano Saphyr instrumentation.Results. We collected a retrospective cohort of 25 patients with AML who do not achieve remission after one to two cycles of induction therapy (primary refractory AML, PR-AML). Median age at diagnosis was 60 years (range, 25-82). The median OS was 14 months. Conventional karyotyping, FISH analyses, and NGS classified 14 patients into ICC categories, including 7 AML with myelodysplasia-related cytogenetic abnormalities, 5 AML with myelodysplasia-related mutations, 1 AML with MECOM rearrangement, 1 with NPM1 mutation. NGS analyses identified mutations comprising DTA (DNMT3A, ASXL1, TET2; 50% of cases), RUNX1 (38%), IDH1 and IDH2 (38%), splicing factors (25%), RAS pathway (25%), FLT3 (19%), CSF3R (19%), WT1 (6%) and NPM1 (6%). Twelve patients (60%) showed normal karyotype, and 1 patient showed the uncommon translocation t(3;6)(q26;q24) including MECOM gene. All patients were negative for TP53 alterations (mutations and/or deletions). OGM confirmed genomic abnormalities (trisomy 8, del5q, del7q and monosomy 7 with loss of EZH2 gene, and del20q comprising TOP1 gene) identified by karyotyping and FISH, but also found additional alterations including the classifying lesion t(5;11)(q35.3;p15.4) NDS1-NUP98 translocation in two cases (Figure 1), dup(11)(q23.3; q23.3) KMT2A duplication in one case, and SVs involving MECOM gene (2 insertions and 1 allelic imbalance) in 2 cases. One patient diagnosed as AML with NPM1 mutation and normal karyotype showed two insertions in inositol triphosphate 3 kinase (ITPKB) and leukemia inhibitor factor receptor (LIFR) genes, which are RUNX1-regulated tumor-suppressors involved in HSC homeostasis and myeloid differentiation. A 14q11.2 deletion was detected in one patient with AML with normal karyotype and any mutation identified by NGS. Conclusions. To our knowledge, the present study represents the first application of OGM technology to a selected cohort of patients with primary refractory AML, not harbouring TP53 alterations. Our data indicate that OGM can be used to identify additional structural variations relevant to improve AML classification and better define the pathogenetic alterations in this subset.

Abstract The delayed flower bud opening of Lonicera japonica ‘Huajin 6’ extends its harvest window and enhances agricultural value, yet the underlying molecular basis remains unclear. Here, we assembled a chromosome-level genome of ‘Huajin 6’ using PacBio sequencing and high-throughput chromosome conformation capture (Hi-C) scaffolding (824.72 Mb, scaffold N50 = 91.2 Mb). Comparative genomic analyses revealed a subfamily-specific contraction of lipoxygenase (LOX) genes, particularly within the 9-LOX clade, which is associated with a reduced jasmonate biosynthetic capacity during floral development. Transcriptomic and hormone profiling showed coordinated suppression of jasmonic acid (JA) biosynthesis-related genes and a marked reduction of JA and its bioactive derivatives during the transition from the complete white stage to flower opening. A JA-responsive co-expression module enriched in cell wall modification genes exhibited attenuated activation in ‘Huajin 6’. Functional assays further demonstrated that exogenous JA restored timely flower bud opening in both ‘Huajin 6’ and L. macranthoides, while heterologous expression of Lonicera LOX genes enhanced jasmonate accumulation in Arabidopsis. Together, these findings are consistent with a jasmonate threshold model in which LOX gene contraction constrains JA accumulation during floral transition, contributing to delayed flower bud opening and highlighting how genome structural variation influences hormone-dependent flowering dynamics.

Pangenomes: new tools for ecological and evolutionary genomics.

Graph data science in fungal biotechnology: Opportunities and applications.

The increasing availability of reference genomes for non-traditional model species is enhancing research in ecology and evolution. Here, we present a high-quality chromosome-level genome assembly and annotation for the bank vole Clethrionomys glareolus, an emerging model mammal. The 2.24 Gb assembly is resolved into 28 chromosome-scale scaffolds, consistent with the known karyotype of the species. We predicted 40,393 gene loci, including 21,029 protein-coding genes supported by Swiss-Prot homology. Repetitive elements account for approximately 29% of the genome. The assembly achieves a 90.6% BUSCO score, underscoring its completeness. Compared to previously available fragmented assemblies, this genome enables investigation of genome architecture, selection and structural variation at unprecedented resolution. In particular, this chromosome-level resource supports research into ecological and evolutionary responses to climate variation across space and time. It also holds value for other fields, including developmental biology and studies of immunology and virology, where the bank vole is used as a model for host-pathogen interactions-expanding the relevance of this genomic resource across biological disciplines.

Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored. We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application. We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice. We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%). Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.

Identification of genomic rearrangements by microarrays or short-read sequencing frequently lacks information about the exact architecture and breakpoints of variants due to technical limitations. Independent verification of complex structural variants (SVs) is often performed using custom targeted assays, making confirmation of clinically relevant findings time consuming and laborious. In this study we evaluate Oxford Nanopore long-read adaptive sampling for flexible and rapid confirmation and characterization of complex genomic rearrangements and structural variants. Adaptive sampling is an in silico target enrichment, where continued sequencing or ejection of a fragment is based on whether it matches a defined reference sequence. Using adaptive sampling, we targeted 10 regions with different structural variant types, including deletions, translocations, and complex rearrangements. Each sample was analyzed on a MinION or PromethION flow-cell, and sequencing resulted in between 14.1-18.3 Gb of data per sample, with mean autosomal on-target coverage of 28.4x and off-target read depth coverage of 5.3x. We were able to verify all 10 rearrangements, with breakpoint spanning reads for nine of the ten regions, and fully resolved the architecture ofnine regions. We also show that background reads can be used to detect structural variants in non-targeted regions of the genome. Our results show that adaptive sampling represents a flexible and rapid strategy for confirmation and characterization of clinically relevant genomic rearrangements in clinical samples. By providing sequence information, read depth, and methylation data, nanopore adaptive sampling has advantages over other assays for variant confirmation used in diagnostic laboratories today.

The ability to distinguish between transcripts that differ by a single nucleotide positions our padlock assay as a highly accurate imaging tool for detecting disorders associated with structural variations in the human genome. In this study, we evaluated the effectiveness of the padlock assay in identifying TTR gene variants in a case of transthyretin amyloidosis (ATTR), a rare multisystemic disease. ATTR may result from autosomal dominant mutations in the TTR gene or occur in a wild-type form. We applied the padlock assay in combination with rolling circle amplification (RCA) and fluorescence microscopy, using peripheral blood mononuclear cells (PBMCs) as clinical samples. Using the padlock assay, 1) we detected intracellular TTR transcripts in 80% of PBMCs, including a benign variant caused by a single nucleotide substitution in intron 3, 2) we visualized the subcellular localization of both coding and non-coding regions of TTR transcripts, and 3) through dual staining, we simultaneously detected both wild-type and mutated TTR intron 3 in patient- derived cells. Additionally, we found that PBMCs and platelets are immunoreactive to TTR antibodies, suggesting that immunocompetent cells may contribute to the distribution of TTR protein across tissues and organs. We demonstrate that the padlock assay can serve as a non-invasive imaging test capable of spatially detecting genomic variants in ATTR. These findings suggest that the padlock assay has potential application in evaluating the efficacy of disease-modifying therapies in extra-hepatic cells. Moreover, this study is the first to highlight PBMCs as a valuable source for advancing our understanding of ATTR pathogenesis and for supporting the development of improved therapeutic approaches.

The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. We investigated the genetic basis of red/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to epidermal bladder cells (EBCs), with red EBCs accumulating betacyanin levels ~ 50-fold higher than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76ADα) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a ~ 4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a multicopy CYP76ADα-DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76ADα genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.

Crataegus spp. plants are valuable horticultural crops because of their extensive use in Chinese herbal medications, cosmetics, food production, and other industries. However, the wide variety of species, similar morphological characteristics, inherent hybridization, apomixis, and polyploidy have led to confusion in terms of their taxonomic status. Herein, a total of 18 complete chloroplast genomes including 17 Crataegus species and 1 Mespilus species were newly sequenced and comprehensively analyzed for comparative genomics and phylogenetic relationships. The 18 chloroplast genomes possessed typical quadripartite structures with lengths from 159,638 to 159,973 bp in size. These chloroplast genomes encode 119-131 genes, including 37 transfer RNA (rRNA) genes, 8 ribosomal RNA (tRNA) genes, and 74-85 protein-coding genes (PCGs). In addition, 23-54 long repeat sequences and 74-87 simple sequence repeats (SSRs) were detected. The examination of Ka/Ks ratios for 18 chloroplast genomes revealed that the rpoC2 gene was significantly positively selected. Additionally, we identified nine distinct hotspot regions (infA, ndhC, pasl, rps19, ndhC~trnV-UAC, psbZ~trnG-UCC, rpl33~rps18, trnH-GUG~psbA, and trnR-UCU~atpA), and verified that ndhC~trnV-UAC might be used as a foundation for subsequent molecular marker studies aimed at identifying Crataegus species. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed genetic relationships among Crataegus and Mespilus species, and confirmed the taxonomic status of Crataegus accessions (GSSZ, JRY, RR2H, RR3H, ZWSZ). The results of divergence time showed that the crown age of C. subg. Crataegus was about 33.487 Ma, and then started to diverge into the C. subg. Americanae and C. subg. Sanguineae around 27.059 Ma. Based on the results of molecular evidence, we speculate that genus Crataegus originated earliest from European-derived species within C. subg. Crataegus. Biogeographic and molecular dating analyses suggested that China represented a putative maternal origin of Crataegus species. The complete chloroplast genomes of Crataegus not only enable the resolution of phylogenetic relationships within the genus but also offer novel insights into chloroplast genome structure variation and evolution. Additionally, the identified divergent DNA regions hold significant utility for species identification and phylogenetic reconstruction in Crataegus.

Advances in transcriptomics have transformed our understanding of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, revealing disrupted gene expression profiles and highlighting the multi-system biology of ALS. Despite major advances, transcriptomic studies have only begun to capture the complexity and the molecular hierarchy of transcriptomic alterations in ALS. To resolve and characterize the transcriptome in ALS, we performed a comprehensive reanalysis of bulk RNA sequencing from the New York Genome Center ALS Consortium cohort across five post-mortem tissues including motor and frontal cortex, cervical and lumbar spinal cord, and cerebellum. By deploying dual analytical pipelines - one reference-based to model canonical events and one de novo to detect transcript structural novelties - we disentangled the quantitative and qualitative architectures of ALS. Our reference-based analysis revealed that ALS transcriptome is defined primarily by splicing failure rather than changes in gene expression. Aberrant splicing events, particularly intron retention, outnumbered differentially expressed genes by an order of magnitude. This widespread loss of fidelity disproportionately affected RNA-binding proteins, suggesting a collapse in their autoregulatory feedback loops. Deconvolution of these signals identified distinct cellular vulnerabilities: transcriptional disruptions were enriched in glial cells in sporadic cases but in neuronal cells in C9ORF72-positive cases. Furthermore, we observed sex-specific dysregulation, with male patients exhibiting greater disruption in guanosine triphosphatase signaling and ciliary organization pathways. In parallel, our de novo analysis uncovered a significant burden of disease-specific gene fusions that were absent in controls. Whole-genome sequencing of the same individuals, together with a larger reference population confirmed that disease-specific fusions do not arise from genomic structural variants, indicating a transcriptional rather than genomic origin. Investigation into the mechanism of these RNA-based fusions revealed a critical deviation in splice site definition: while canonical splice junctions exhibit a high density of binding motifs for polyA-binding or 3'-cleaveage proteins approximately 50 base pairs upstream of the splice donor site (left junction), ALS-specific fusion junctions displayed a dramatic depletion of these motifs in the same region. Functionally, the presence of these sparse disease-specific fusions was strongly correlated with severe splicing outliers in genes governing guanosine triphosphatase activity, converging with the tissue- and male-specific defects identified in our reference-based analysis. Altogether, our results delineated a transcriptome characterized by aberrant splicing with tissue-and sex-specific changes and identified structural-variant-independent RNA fusions as candidate disease modifiers that may amplify pathology. This integrated view provides a mechanistic scaffold for splicing-centered and RNA-structural therapeutic strategies for ALS.

Local adaptation to aridity is often expected to promote genomic divergence by favoring the integration of drought-tolerance traits. Under this framework, functional trait variation should align with genetic structure; however, empirical evidence for such coupling remains limited, particularly when experimental validation is lacking. We tested this prediction in Aristotelia chilensis, a phenotypically variable tree spanning a 1,500-km precipitation gradient (<100 to >1,000 mm year-1). We combined nextRAD population genomics, trait-environment modeling, and a common garden drought experiment to assess how climatic and edaphic factors shape genomic structure, drought-related functional traits, reproductive traits, and antioxidant profiles. We identified four genetically distinct clusters that correspond to major biomes across the species' range-from the Atacama Desert to northern Patagonia-reflecting strong spatial genetic structuring. In contrast, functional traits were largely decoupled from genomic structure and responded independently to environmental variables. Critical photo-inactivation water content (SWC-PhI) showed no credible environmental associations but exhibited significant hierarchical variation among populations and clusters. Specific leaf area (SLA) was strongly influenced by edaphic conditions, decreasing with soil sand content and increasing with soil water-retention capacity, with most variation attributable to population-level differences. Root-shoot biomass ratio also varied hierarchically but was unrelated to climatic or soil predictors. Survival under experimental drought was uniformly low (1.7%) and did not differ among populations or clusters, indicating conserved physiological tolerance across the range. Together, these findings reveal that adaptation to aridity in A. chilensis arises from trait-specific, uncoupled responses rather than from an integrated drought-resistance syndrome. The pronounced genomic structure appears more consistent with historical biogeographic processes than with contemporary drought adaptation. These insights underscore the importance of selecting genotypes based on empirical trait performance under water stress-rather than geographic origin-to support climate-resilient fruit production and guide restoration strategies involving A. chilensis.

Spermatogenesis is a highly orchestrated germ cell differentiation process involving the dynamic regulation of cell fate transitions. Dissecting the molecular landscapes of spermatogenic cell types is crucial for identifying fertility-related problems and improving the reproductive performance of farm animals. Here, we conducted transcriptomic and chromosome spreading across meiotic stages of testicular cells from taurine cattle (Bos taurus), yak (Bos grunniens), and their hybrid progenies to describe the transcriptional landscape of normal spermatogenesis and identify potential regulators that are involved in hybrid sterility. The results revealed seven types of spermatogonia, ten spermatocytes and ten types of spermatids in the cattle or yak testes. In sharp contrast, the testes of the cattle-yak hybrids contained only seven spermatogonial subtypes and six types of spermatocytes. Notably, the arrest of spermatocytes at the diplotene-to-diakinesis transition was accompanied by defects in double-strand break repair. In the testes of backcrossed offspring, spermatogenic arrest was partially rescued, and round spermatozoa were produced. By performing joint analysis, we identified 115 genes that exhibited differential protein abundance in spermatocytes of cattle-yak. Among them, 24 genes carrying genomic structural variations were differentially expressed in spermatocytes of cattle-yak but recovered in those of backcrossed offspring. This work provides important insights into spermatogenesis in large animals and serves as a valuable resource for identifying the factors determining reproductive isolation.

Background/Objectives: Segmental duplications (SDs) are major drivers of genome evolution and structural variation in primates, particularly within acrocentric chromosomes, where rDNA arrays and duplicated sequences are densely clustered. However, the evolutionary dynamics of rDNA-linked SDs across great ape lineages have remained poorly characterized due to longstanding technical limitations in genome assembly. Here, we investigate the organization, copy number variation, and evolutionary conservation of acrocentric SDs in great apes by integrating fluorescence in situ hybridization (FISH) with comparative analyses of telomere-to-telomere (T2T) genome assemblies. Methods: Using eight human-derived fosmid probes targeting SD-enriched regions flanking rDNA arrays, we analyzed multiple individuals from chimpanzee, bonobo, gorilla, and both Bornean and Sumatran orangutans. Results: Our FISH analyses revealed extensive lineage-specific variation in SD copy number and chromosomal distribution, with pronounced heteromorphism in African great apes, particularly gorillas, and more conserved patterns in orangutans. Several SDs showed fixed duplications across species, while others exhibited high levels of polymorphism and individual-specific organization. Conclusions: Comparison with T2T assemblies confirmed consistent genomic localization for a subset of probes, whereas others displayed partial discordance, highlighting the persistent challenges in resolving highly repetitive and structurally dynamic regions even with state-of-the-art assemblies. Genome-wide analyses further revealed species-specific enrichment of SDs on rDNA-bearing chromosomes, with chimpanzees and bonobos showing higher proportions than gorillas, and contrasting patterns between the two orangutan species. Overall, our results demonstrate that rDNA-linked SDs represent highly dynamic genomic compartments that have undergone differential expansion and remodeling during great ape evolution. These regions contribute substantially to inter- and intra-species structural variation and provide a mechanistic substrate for lineage-specific genome evolution, underscoring the importance of integrating cytogenetic and T2T-based approaches to fully capture the complexity of duplicated genomic landscapes.

Complete genome sequences and structural variants of pESI-like plasmids in multidrug-resistant Salmonella Infantis carrying blaCTX-M-65 from retail chicken meat in South Korea.

We present a large-scale study of structural variation (SV) in the Qatari population, based on short-read whole-genome sequencing (WGS) of 6,141 individuals, identifying 153,946 variants across 5 classes reflecting the region's diversity and evolutionary history. Leveraging consanguinity and biobank phenotypes, we identify >180 putative gene knockouts, and use proteomics to show functional consequences in homozygotes. Conversely, 52 genes show significant depletion of homozygous deletions, eight of which cause severe pediatric disease or murine embryonic lethality. Examining phenotypic extremes uncovers several non-exonic homozygous deletions with large effect, including in SPIRE2 (creatinine), MAGI2 (leanness) and a chr19 microRNA cluster (extreme obesity). Further, SV-GWAS reveals gene-trait associations independent of SNPs, including at ACY1 (acetylation), SLC2A9 (uric acid), UGT1A8 (bilirubin) and ZNF251 (alanine aminotransferase). Notably, 3.2% of Qataris carry findings in medically actionable genes, one-third attributable to SVs. Our findings offer a rich SV reference for a globally understudied population, and demonstrate the utility of consanguineous biobanks for studying SVs in health and disease. All common SVs and tag-SNPs are provided as imputation resource.

Genomic structural variants (SVs) are pervasive and can impose major phenotypic impacts. However, it is difficult to appreciate the individual significance of SVs when they are heterogeneously positioned across a genomic neighborhood. Further, ubiquitous variance in SV calling accuracy complicates SV counting and downstream analysis. Tools exist to simplify SV datasets, but they are not suited for all applications. Here, we present a new SV merger, SVCROWS: Structural Variation Consensus with Reciprocal Overlap and Weighted Sizes. This option-rich merger summarizes SV regions using a size-weighted reciprocal overlap framework, accounting for skewed impacts of variable-length SVs. User input directs stringency, enabling various levels of resolution in complex genome regions that harbor a spectrum of SV sizes. Further, by optimizing SVCROWS parameters, the user can tailor results to their study system. When compared to other SV merging programs, SVCROWS maintained accuracy and conserved rare genotypes from both simulated and real-world datasets. Visualization of merger output was critical for identifying how some algorithms derived erroneous conclusions while SVCROWS remained reliable, especially in complex regions. Overall, the novel SVCROWS algorithm presents an improved framework for SV interpretation; its intuitive nature and generalizability facilitate its application to virtually any workflow.