Journal of Genetics and Genomics

Polyploidization plays a fundamental role in plant evolution and crop domestication. However, due to the high similarity of genomic sequences between some homologous or homeologous chromosomes, the assembly of some polyploid genomes is extremely difficult, frequently resulting in erroneous assemblies, such as sequence chimeras and sequence collapse. The genus Brachypodium is an important model system for the study of polyploidy in grasses. However, high-quality reference genomes are still lacking for its complex polyploid perennial species. In this study, we developed a bioinformatic pipeline for the accurate assembly of high-quality reference genomes at the chromosomal level for two representative perennial Brachypodium species with conflicting collapsed segments, the allotetraploid B. phoenicoides (2n = 4x = 28) and the autohexaploid B. boissieri (2n = 6x = 48). We developed an innovative methodology (CollapsedChrom) that uses depth-of-read profiling and relies on prior karyotypic information to systematically detect and rescue collapsed regions. This depth-sensitive curation strategy successfully recovered 328.9 Mb and 195.8 Mb of previously collapsed sequences in the genomes of B. phoenicoides and B. boissieri, respectively. Comprehensive quality assessments demonstrated the high quality of our final assemblies. Our chromosomal-level assemblies fully capture the genomic architectures of these species. These robust genomic resources overcome long-standing challenges in polyploid assembly and provide an essential foundation for future research on the evolutionary dynamics, subgenomic interactions, and functional biology of complex polyploid plant genomes.

The fission yeast Schizosaccharomyces pombe is a prominent model organism widely used to investigate fundamental cellular mechanisms. In addition to S. pombe, the genus Schizosaccharomyces includes six other species--S. octosporus, S. japonicus, S. cryophilus, S. osmophilus, S. lindneri, and S. versatilis. These fission yeast species share a common ancestor from which the genus diversified over more than 200 million years. This extensive evolutionary divergence provides opportunities for comparative genomics. Here, we present the Schizosaccharomyces orthogroup (SOG) resource, a web platform developed from our high-quality genome assemblies, gene annotations, and orthology assignments. Most fission yeast genes are assigned to one of over 5,000 orthogroups. The platform enables users to visualize orthogroup sequence alignments and phylogenetic trees, retrieve coding and flanking sequences, and explore the conservation of local synteny. This resource will benefit researchers focusing on individual genes as well as those investigating gene evolution at broader scales. It is freely accessible at https://www.sogweb.org. TAKE AWAYO_LIThe SOG resource covers all known species of Schizosaccharomyces. C_LIO_LIThe platform is built on high-quality genome assemblies and annotations. C_LIO_LIMost genes are assigned to one of over 5,000 orthogroups. C_LIO_LIUsers can view and explore alignments, phylogenetic trees, and local synteny. C_LIO_LIThis free resource aids functional and evolutionary research. C_LI

Enhancer-regulating epigenetic modifiers play critical roles in normal physiological processes and human pathogenesis. The major enhancer regulator paralogs MLL3 and MLL4 (MLL3/4) belong to the lysine methyltransferase 2 (KMT2) family, which catalyzes the methylation of lysine 4 on histone H3 (H3K4me). MLL3/4 are required for enhancer activation and are essential for mammalian development and stem cell differentiation. Recent studies have linked MLL3/4 with different metabolic pathways in the context of stem cell self-renewal and cancer cell growth; however, the underlying mechanisms remain elusive. Here, we utilize Seahorse extracellular flux analysis, stable isotope tracing, stem cell biology techniques, and transcriptomic analysis to investigate the functional relationship of MLL3/4, cellular respiration, and stem cell differentiation. Our results indicate that the loss of MLL3/4 impairs glycolytic activity and mitochondrial respiration in murine embryonic stem cells by downregulating the rate-limiting glycolytic enzyme Hexokinase 2 (HK2) and impairing the function of the Alpha-ketoglutarate dehydrogenase (OGDH) complex. Furthermore, simultaneously overexpression of HK2 and OGDH rescues defects in both cellular respiration and differentiation caused by MLL3/4 loss. Taken together, our study reveals a novel mechanism by which epigenetic machineries such as MLL3/4 govern the differentiation of pluripotent stem cells and facilitates the understanding of disease pathogenesis driven by enhancer malfunction.

Individual phenotypes often depend on the genotypes of other individuals within a group. These phenomena are termed indirect genetic effects (IGEs) and have been distinguished from direct genetic effects (DGEs) using quantitative genetic models. Recent studies have utilized high-resolution polymorphism data to enable genomic prediction (GP) and genome-wide association study (GWAS) of IGEs, but unified methods remain limited. Here we integrate polygenic and oligogenic IGEs using a multi-kernel mixed model incorporating two random effects with a single covariance parameter. Underlying this implementation, the Ising model of ferromagnetics enabled us to simplify locus-wise and background IGEs for GWAS and GP, respectively. Our simulations demonstrated that, while the previous and present models exhibited similar performance, the present model can infer a trade-off between DGEs and IGEs. By applying this method to three species of woody plants, we found evidence for intergenotypic competition in aspen and apple trees, but limited evidence in climbing grapevines. Based on GWAS, we also detected significant variants associated with the competitive IGEs on the apple trunk growth. Our study offers a flexible implementation for GWAS/GP of IGEs, thereby providing an effective tool to dissect the genetic architecture of group performance.

Whole-genome duplication (WGD) is a major evolutionary event that drives molecular and species diversification. However, few studies have traced how WGD has shaped the long-term functional evolution of individual genes. Here, we investigated the olfactory marker protein (omp) genes duplicated by the teleost-specific WGD ([~]300 million years ago) through phylogenetic, syntenic, expression, and promoter analyses. Our results suggest that the duplicated omp gene pair has retained redundancy over an extended evolutionary period, leading to both non- and sub-functionalization, thereby generating molecular diversity. Moreover, evolutionary analyses of the olfactory signal transduction cascade revealed prolonged redundancy across its components, likely constrained by gene dosage balance. These findings imply that WGD may have introduced unexpected diversity into the entire olfactory signaling machinery of teleosts through dosage-constrained functional divergence. HighlightsO_LITeleost-specific WGD generated duplicated omp genes that persisted for [~]300 million years. C_LIO_LIExtended redundancy in ompa/ompb led to both non- and sub-functionalization. C_LIO_LIOlfactory transduction genes also show long-term redundancy shaped by dosage constraints. C_LIO_LIWGD likely introduced diversification into teleost olfactory signaling via dosage constraints. C_LI

The central apparatus of motile cilia, consisting of central microtubules and various protein projections, is essential for dictating the ciliary movement. Although three proteins (FAP65, FAP147, and FAP70) have been localized to the C2a projection in Chlamydomonas reinhardtii, the full protein composition and functional roles of the vertebrate C2a remain inadequately defined. Here, we use three knockout mouse models corresponding to their respective homologs (Ccdc108, Mycbpap, and Cfap70) to systematically investigate their functions in vertebrates. Notably, all three knockout strains exhibit distinct phenotypes related to primary ciliary dyskinesia (PCD), including hydrocephalus and sinusitis. The ciliary incorporation of CCDC108, MYCBPAP, and CFAP70 is essential for one anothers stability, with the loss of any single component triggering C2a collapse, which destabilizes the central pair microtubules and ultimately alters the ciliary movement pattern. Furthermore, we significantly expand the vertebrate C2a proteome by identifying ARMC3 and MYCBP as additional C2a components. Collectively, our findings illuminate the proteomic composition and strict physiological requirements of the vertebrate C2a projection, providing new insights into the molecular pathogenesis of PCD.

Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700-900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to [~]6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of [~]2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred [~]1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

Astrocytes play a key role in neuronal homeostasis and in various neural disorders. The generation of astrocytes from neural progenitor cells (NPCs) and its functions are under a complex control of several signaling networks and transcription factors. In this study, we demonstrate that the transcription factor, GLIS similar 3 (GLIS3), which has been implicated in several neurodegenerative diseases, is highly expressed in astrocytes, and is required for the efficient differentiation of human NPCs into astrocytes. Loss of GLIS3 function greatly impairs astrocytes differentiation, resulting in reduced expression of astrocyte markers, whereas expression of exogenous GLIS3 restores the induction of astrocyte specific genes indicating a critical role for GLIS3 in astrocyte differentiation. Integrated transcriptomic and cistromic analyses revealed that GLIS3 directly regulates the transcription of several astrocyte-associated genes, including GFAP, SLC1A2, NFIA, and ATF3, in coordination with lineage-determining factors, such as STAT3, NFIA, and SOX9. We hypothesize that GLIS3 dysfunction disrupts this transcriptional network thereby contributing to astrocyte-associated neurological disorders. Identification of GLIS3 as a key regulator of astrocyte differentiation and gene expression will advance our understanding of its role in neurodegenerative diseases and may provide a new therapeutic target.

Cnidarians are important models for the studying the evolution of animal development, regeneration, cell type differentiation, and allorecognition. The marine hydrozoan Podocoryna americana is related to the well-established model species Hydractinia symbiolongicarpus. Although both species possess a sessile polyp stage, P. americana differs in that it also has a free-swimming medusa (jellyfish) stage in its life cycle. We used a combination of PacBio CLR long-read and Illumina Hi-C short-read genome sequencing to produce a chromosome-level genome assembly for P. americana. The final assembly is 327 Mbp in total length with 17 chromosome-scale scaffolds representing 98% of the assembly. Comprehensive functional annotation with BRAKER3 generated a total of 19,085 predicted protein-coding genes in this assembly, covering 91.2% of the metazoan BUCSO gene set. Comparison of the P. americana genome to other chromosome-level cnidarian genome assemblies revealed a high degree of macrosynteny conservation, and ortholog identification and gene family evolution analysis identified 522 expanded and 1,026 contracted gene families in P. americana. This high-quality, chromosome-level genome assembly of P. americana will be an invaluable resource for researchers studying the evolution of development, regeneration, and allorecognition in cnidarians and other metazoans.

The N-degron pathways of ubiquitin mediated proteolysis target proteins for degradation dependent on the amino terminal residue, often produced after endopeptidase activity. Very few substrates have been identified in plants even though enzymes of these pathways are highly conserved in eukaryotes. Here we identify ELONGATED HYPOCOTYL5 (HY5), a master transcriptional regulator involved in many aspects of plant development, as a target for the endopeptidase METACASPASE (MC)9, producing the carboxy-terminal protein fragment (proteoform) E59-HY5. E59-HY5 is shown to be a substrate of the arginyl transferase (ATE) N-degron pathway, and influences physiological processes known to be controlled by HY5, including photomorphogenesis and the unfolded protein response. Conditional stability of E59-HY5 was shown to result from environmentally controlled ATE function, which may highlight a general mechanism for N-degron pathway regulation of proteoform and proteome function during growth and development.

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

Osteoporosis affects millions of women globally. In this study, we applied bioinformatics methods to screen for novel diagnostic biomarkers of osteoporosis in women using the GSE62402 and GSE56814 datasets. PCSK5, ZNF225, and H1FX were used to construct a diagnostic model. ROC, calibration, and decision curve analyses were performed to assess the diagnostic performance on the training (GSE56814) and external (GSE56815) datasets. The expression level of model genes was validated in GEO datasets. Furthermore, five transcription factors (ETS1, NOTCH1, MAZ, ERG, and FLI1) were identified as common upstream regulators of model genes. PCSK5, ZNF225, and H1FX serve as novel diagnostic biomarkers, providing new insights into the pathogenesis of and treatment strategies for osteoporosis in women.

Complex genomic regions harbor different structural arrangements that can mutate quite rapidly, which makes determining their functional effects very difficult. Characterization of inversions originated by homologous mechanisms is especially challenging due to the presence of inverted repeats at the breakpoints and the fact that most of them are recurrent. Imputation can infer missing genotypes, but it has been mainly limited to simple variants and little is known about how well it works for human inversions. Here, we tested five common imputation programs to impute a set of 52 inversions experimentally genotyped in multiple samples that lacked SNPs in perfect linkage disequilibrium. Using whole genome sequencing data and simulated microarrays with variable SNP density, we found that 40.4-75.5% of inversions could be accurately imputed in three human populations by at least one program, with results depending mainly on the number of SNPs available, the genotyped samples and the recurrence of inversions. Also, genotype probability filtering was a key factor for inversion imputation accuracy. In particular, Minimac4 and IMPUTE5 showed more accurately imputed inversions and less poorly imputed individuals with respect to the other methods. This work therefore contributes to optimize inversion imputation, making possible the study of their functional impact.

The {gamma}- to {beta}-globin switch is intricately regulated during human ontogeny, and this process is manipulated for therapeutic approaches to treat {beta}-hemoglobinopathies by activating {gamma}-globin expression. Several genetic strategies to reactivate HbF have partially reversed the {gamma}- to {beta}-globin switch and ameliorated the clinical symptoms of {beta}-hemoglobinopathies. However, whether the {gamma}- to {beta}-globin switch can be completely reversed remains unknown. Completely reversing the {gamma}- to {beta}-globin switch requires a thorough redirection of the locus control region (LCR) from interacting with the {beta}-globin gene (HBB) to interacting with the {gamma}-globin gene (HBG). Here, we found that disrupting the KLF1-mediated HBB-LCR interaction by mutating the CACCC motif in HBB leads to the release of the LCR and its retargeting to other {beta}-like globin genes. Moreover, simultaneously disrupting the KLF1-mediated HBB-LCR interaction and the epigenetic repression of HBG by combined editing of the CACCC motif in HBB and the TGACCA motif in HBG reinforces the HBG-LCR interaction, resulting in almost exclusive {gamma}-globin expression while nearly absent {beta}-globin expression, achieving near complete reversal of the {gamma}- to {beta}-globin switch. This finding demonstrates the comprehensive regulation of the {gamma}- to {beta}-globin switch by gene competition and gene silencing mechanisms. This finding also suggests that silenced genes can be fully activated through the redirection of enhancer-promoter contacts and that the specificity of enhancer-promoter contact within chromosomal domains is achieved through the transcription factor clusters binding to enhancers and promoters. Combined editing of the CACCC&TGACCA motifs also offer a more optimal therapeutic strategy for {beta}-hemoglobinopathies.

Mainland China experienced multiple waves of COVID19 pandemic during 2020 2022, driven by emerging variants and changes in public health and social measures (PHSMs). We developed a hypergraph-based Susceptible Vaccinated Exposed Infectious Recovered Susceptible (SVEIRS) model to reconstruct epidemic dynamics across 31 provinces, capturing transmission heterogeneity associated with clustered contacts. We assessed key characteristics of transmission at national and provincial levels during four outbreak periods: initial, localized predelta, Delta, and widespread Omicron, which accounted for 96.7% of all infections. We found significant diversity in transmission contributions across cluster sizes, with a small fraction of larger clusters responsible for a disproportionate share of infections. Counterfactual analyses showed that reducing clustersize heterogeneity, while holding overall exposure constant, could have lowered national infections by 11.70 to 30.79%, with the largest effects during Omicron period. Ascertainment rates increased over time but remained spatially heterogeneous with a range: (14.40, 71.93)%. Population susceptibility declined following mass vaccination (to 42.49% in Aug 2021, nationally) and rebounded (to 89.89% in Nov 2022) due to waning immunity with variations across the provinces. Effective reproduction numbers displayed marked temporal and spatial variability, with higher estimates during Omicron. Overall, these results highlight critical role of group contact heterogeneity in shaping epidemic dynamics.

Though whole-genome duplication (WGD) contributes to cancer progression, the mechanism of post-WGD cell proliferation remains unclear. Here, using 6-day live-imaging, we analyzed the proliferation dynamics of more than 150 post-WGD HCT116 cell lineages. A quantitative comparison of mitotic patterns and cell fates between proliferative and non-proliferative lineages revealed that multipolar chromosome segregation in early mitosis is a key factor limiting the proliferative capacity of post-WGD progenies. Multipolar chromosome segregation suppressed post-WGD cell viability, particularly when accompanied by drastic chromosome loss or when it repeatedly occurred. Tracing proliferative lineages elucidated that they proliferated mainly by imposing the risk of multipolar chromosome segregation on one of two sub-lineages that formed after the first bipolar division. Meanwhile, a considerable proportion of proliferative lineages consisted entirely of progeny of early multipolar chromosome segregation events. Our results highlight key cellular events that determine the proliferation dynamics and diversity of post-WGD progenies, providing a fundamental reference for understanding WGD-associated bioprocesses. Summary statementLive image tracing of >150 cell lineages reveals the cross-generation dynamics of multipolar chromosome segregation that determine the fates of post-whole-genome duplication progeny cells.

Eusociality in bees represents a major evolutionary transition and understanding its molecular basis is fundamental for sociogenomic studies. Comparative genomics has revealed correlations between transcription factor binding site (TFBS) abundance and social complexity; however, when and where these TFBSs function in a eusocial context remains largely unclear. In this study, we performed cap analysis of gene expression (CAGE) during worker metamorphosis in the honeybee Apis mellifera to identify TFBSs within active enhancers and decipher the regulatory relationships between these enhancers and their target genes. We identified 17,349 transcription start sites (TSSs) and 842 candidate enhancers. Using CAGE, we identified five clusters based on expression patterns. Notably, genes associated with the canonical metamorphic regulators, Broad complex (Br-c) and E93, were found within specific clusters. By integrating the correlations between enhancer and TSS activities with motif enrichment analysis, we identified 15 transcription factor-enhancer-TSS regulatory relationships. Among these, tramtrack (ttk)-binding sites were identified in five enhancers associated with four target genes, including Br-c. The number of target genes regulated by ttk was the highest in our dataset. To examine whether this regulatory relationship is conserved across bee species with varying levels of sociality, we analyzed the sequence conservation of ttk-binding sites in Br-c enhancers and found that perfect sequence conservation of ttk-binding site was restricted to the Apis genus. The ttk-binding sites of other target genes exhibited the same Apis-specific conservation pattern. Our findings suggest that gene regulatory relationships during worker metamorphosis occur in a lineage-specific manner in the Apis genus. SignificanceHoneybees produce distinct castes--queens and workers--from genetically identical larvae via differences in gene regulation. Although enhancers have been computationally predicted, their actual activity during bee development has rarely been measured directly, and the CAGE technology has never been applied for this purpose. We identified active enhancers during worker metamorphosis and discovered that the transcription factor ttk may regulate Br-c, a key developmental gene. This study provides the first direct evidence of active enhancers and their regulatory roles in honeybee worker metamorphosis.

Long noncoding RNAs (LncRNAs) have emerged as a class of important regulatory ncRNAs and are known to fine-tune numerous cellular processes including proliferation, differentiation and development; however, their role in quiescence still remains largely unexplored. A miRNA host gene lncRNA, MIR503HG, has been reported to play important role in cancer development. Here, we demonstrate the role of MIR503HG lncRNA in regulating cellular quiescence. MIR503HG displays elevated levels in human diploid fibroblasts induced to undergo quiescence. Depletion of MIR503HG in HDFs affects the entry of cells into quiescence but has no effect on cell cycle progression, suggesting its role in quiescence attainment and/or maintenance. Additionally, MIR503HG depletion led to a drastic decrease in the levels of miR508 target, PTEN with a concomitant increase in pAkt levels, indicating its role in negative regulation of miR508. Further, we demonstrate that the lncRNA MIR503HG regulates PTEN levels by acting as a ceRNA for miR508 to maintain cellular quiescence. Our studies illustrate that MIR503HG can function synergistically with miR503 to maintain cells under quiescence and both the miRNA-HG and the miRNA encoded by its gene locus synergistically control the same biological process in different ways by regulating different downstream genes.

Text abstractsLipid homeostasis is essential for organismal physiology, and its disruption contributes to metabolic disorders. Using an unbiased genetic modifier screen in Drosophila, we identified GAR1, a core component of the box H/ACA small nucleolar ribonucleoprotein complex, as a pivotal regulator of systemic lipid storage. We show that the H/ACA snoRNP complex is essential for maintaining lipid droplet morphology in adipose tissue and preventing ectopic fat accumulation. Moreover, null mutants of Gar1 or Dkc1 exhibit severe developmental defects, including reduced body size and larval lethality. RNA-seq analysis revealed that Gar1 dysfunction triggered widespread alternative splicing defects, specifically targeting key transcripts within the insulin signaling cascade, including chico, Pi3K92E, sgg, and Lip4. Furthermore, knockdown of Gar1 impaired insulin signaling, as evidenced by the reduced membrane localization of the tGPH fluorescence. Genetic epistasis further positions GAR1 upstream of the lin-28/foxo axis, as knocking down lin-28 or foxo fully rescues the lipometabolic defects in GAR1-deficient animals. These findings reveal a previously unrecognized link between the snoRNP machinery and metabolic process, establishing the box H/ACA complex as an important coordinator that integrates RNA processing with insulin-mediated nutrient sensing to ensure developmental and lipid homeostasis. Article summaryLipid metabolism is tightly controlled by multiple factors. To find new regulators, the authors performed a genetic screen and identified a small nucleolar protein GAR1 participate in fat storage and larval development. They demonstrated a critical role of box H/ACA snoRNP complex in modulating alternative splicing and balancing insulin cascade. Blocking two insulin-related genes reversed the lipid defects caused by Gar1 loss. These findings revealed the box H/ACA complex integrates RNA processing with insulin-mediated nutrient sensing to ensure developmental and lipid homeostasis, offering a perspective for understanding the metabolic regulation network.

Lichens are composite organisms formed through the symbiotic association between fungi, algae and/or bacteria. Multiple independent origins of the lichenized lifestyle have been reported in both fungal and algal lineages, but the molecular mechanisms and evolution underpinning these symbiotic relationships remain largely unknown. In this study, we performed long-read metagenomic sequencing on 11 Peltigerales lichen species to characterize the genomic content of lichen symbionts via metagenome assembled genomes (MAGs). Peltigerales genomes generated in this work represent the largest Lecanoromycetes genome sequenced to date, driven by high transposable element content. Transposable elements (TEs) are known to drive genome evolution in other symbioses but have been underexplored in lichen symbionts due technological limitations. Transcriptomics revealed that many genes associated with adaptations to the lichenized lifestyle are associated with TEs suggesting that they may play a key role in the evolution of lichenization.