Genomic Organization Research Articles

Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope

AbstractSpatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.

Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania

BackgroundThe Leishmania genome harbors formerly active short interspersed degenerated retroposons (SIDERs) representing the largest family of repetitive elements among trypanosomatids. Their substantial expansion in Leishmania is a strong predictor of important biological functions. In this study, we combined multilevel bioinformatic predictions with high-throughput genomic and transcriptomic analyses to gain novel insights into the diversified roles retroposons of the SIDER2 subfamily play in Leishmania genome evolution and expression.ResultsWe show that SIDER2 retroposons form various evolutionary divergent clusters, each harboring homologous SIDER2 sequences usually located nearby in the linear sequence of chromosomes. This intriguing genomic organization underscores the importance of SIDER2 proximity in shaping chromosome dynamics and co-regulation. Accordingly, we show that transcripts belonging to the same SIDER2 cluster can display similar levels of expression. SIDER2 retroposons are mostly transcribed as part of 3'UTRs and account for 13% of the Leishmania transcriptome. Genome-wide expression profiling studies underscore SIDER2 association generally with low mRNA expression. The remarkable link of SIDER2 retroposons with downregulation of gene expression supports their co-option as major regulators of mRNA abundance. SIDER2 sequences also add to the diversification of the Leishmania gene expression repertoire since ~ 35% of SIDER2-containing transcripts can be differentially regulated throughout the parasite development, with a few encoding key virulence factors. In addition, we provide evidence for a functional bias of SIDER2-containing transcripts with protein kinase and transmembrane transporter activities being most represented.ConclusionsAltogether, these findings provide important conceptual advances into evolutionary innovations of transcribed extinct retroposons acting as major RNA cis-regulators.

Canker and dieback of Alnus rubra is caused by Lonsdalea quercina.

Understanding the ecology of pathogens is important for disease management. Recently a devastating canker disease was found on red alder (Alnus rubra) planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 kilometer apart and one strain from each group was used to complete Koch's postulates. Results showed that these bacteria can not only cause disease on red alder but also on two other alder species. Unexpectedly, analyses of genome sequences of bacterial strains identified them as Lonsdalea quercina, a pathogenic species previously known to cause dieback of oak species, but not alder. Additionally, a core genome phylogeny clustered bacterial strains isolated from red alder within a subclade of L. quercina strains isolated from symptomatic oak trees. Consistent with the close phylogenetic relationship, there was no obvious evidence for divergence in genome composition of strains isolated from red alder and oak. Altogether, findings indicate that L. quercina is a potential threat to Alnus species.

Comparative and Phylogenetic Analysis of Anthurium andraeanum Hybridization Based on Molecular and Morphological Traits

Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear genomic, and chloroplast genomic data of five A. andraeanum cultivars and explored the correlations between different traits and nuclear and chloroplast genome characteristics. A. andraeanum hybrid 1 is an A. andraeanum ‘Baron’ (♀) × A. andraeanum ‘Spice’ (♂) cross, and A. andraeanum hybrid 2 is an A. andraeanum ‘Cheers’ (♀) × A. andraeanum hybrid 1 (♂) cross. The A. andraeanum hybrids reflected their parents’ heterozygous features in their morphologies, nuclear genomes, and chloroplast genomes. The morphological traits in the F1 generation were widely separated, showing continuous variation. Based on cluster analysis, the five A. andraeanum cultivars could be divided into two groups. The ISSR analysis results were highly correlated with the spathe color. Among the five A. andraeanum cultivars, the composition and structure features of chloroplast genomes were completely the same or highly similar, respectively. Phylogenetic analysis based on complete chloroplast genome data showed that the genetic stability of the chloroplast is high in A. andraeanum, manifested as uniparental maternal inheritance, where the chloroplast genome composition and structural features of hybrids are highly similar to those of the maternal parent.

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis.

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

A new framework for SubtiWiki, the database for the model organism Bacillus subtilis.

Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism.

Loopy virus or controlled contortionist? 3D regulation of HCMV gene expression by CTCF-driven chromatin interactions.

Three-dimensional chromatin control of eukaryotic transcription is pivotal for regulating gene expression. This additional layer of epigenetic regulation is also utilized by DNA viruses, including herpesviruses. Dynamic, spatial genomic organization often involves looping of chromatin anchored by host-encoded CCCTC-binding factor (CTCF) and other factors, which control crosstalk between promoters and enhancers. Herein, we review the contribution of CTCF-mediated looping in regulating transcription during herpesvirus infection, with a specific focus on the betaherpesvirus, human cytomegalovirus (HCMV).

Haemoglobin Gene Repertoire in Teleost and Cichlid Fishes Shaped by Gene Duplications and Genome Rearrangements.

Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high-quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain a range of haemoglobin genes, from as few as five in fugu to as many as 43 in salmon, with the latter being the largest repertoire found in vertebrates. We find evidence that the teleost ancestor had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organisation of haemoglobin clusters in different teleost species. We further show that the evolution of paralogous rhbdf1 genes flanking both teleost clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environment plays role in species diversification. Our analysis of six cichlid genomes, including Pungu maclareni from the Barombi Mbo crater lake, for which we sequenced a representative genome, reveals 18-32 copies of the Hb genes, and elevated rates of non-synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how haemoglobin genes contribute to the adaptive potential of teleosts.

Chromosomal analysis of progenies between Lilium intersectional hybrids and wild species using ND-FISH and GISH

IntroductionIntersectional hybrids in lilies possess significant breeding value, but the lack of complete lily genomes and complex genotypes pose challenges for early identification of lily hybrids. This study aimed to use intersectional hybrid cultivars as female parents and wild lilies as male parents to facilitate early identification of hybrid offsprings and enhance the efficiency and convenience of the process.MethodsWe investigated the nature of cross combinations using Non-denaturing Fluorescence In Situ Hybridization (ND-FISH) and Genomic In Situ Hybridization (GISH) techniques. Three novel oligonucleotide probes—Oligo-pTa794, Oligo-pITS and Oligo-telo—were developed for lily chromosome research.ResultsOur results demonstrated successful hybridization between wild lilies and intersectional hybrid cultivars, producing a total of 130 hybrid progenies. The combination of ND-FISH and GISH analyses effectively revealed the genomic composition of the hybrid progeny and determined the parental origin of specific chromosomes.DiscussionThis research provides significant guidance for lily breeding practices and offers a valuable reference for the application of ND-FISH and GISH techniques in interspecific hybridization breeding and molecular cytogenetic research across various plant species. The methods developed enable more precise, efficient, and convenient identification of hybrid offsprings.

Draft genome sequence of Pseudomonas sp. ZS001 isolated from peanut plantation soil.

Pseudomonas sp. ZS001 is a bacterium potentially degrading soluble starch isolated from peanut plantation soil sprayed with starch-based material in Dasi Town, Tianjin. Reporting the genome sequence of strain ZS001 can help us understand the genome composition, potential functional characteristics, and application value of Pseudomonas members at the genetic level.

Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency.

Nuclear speckles are nuclear membraneless organelles in higher eukaryotic cells playing a vital role in gene expression. Using an in situ reverse transcription-based sequencing method, we study nuclear speckle-associated human transcripts. Our data indicate the existence of three gene groups whose transcripts demonstrate different speckle localization properties: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-messenger RNA stage, and not enriched. We find that stably enriched transcripts contain inefficiently excised introns and that disruption of nuclear speckles specifically affects splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, indicating a tight interplay between transcript speckle enrichment, genome organization, and splicing efficiency. Collectively, our data highlight a role of nuclear speckles in both co- and posttranscriptional splicing regulation. Last, we show that genes with stably enriched transcripts are over-represented among genes with heat shock-up-regulated intron retention, hinting at a connection between speckle localization and cellular stress response.

Comparative genomics of Fusarium species causing Fusarium ear rot of maize.

Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced.

Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase.

Determining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating the genetic underpinnings of convergent traits remain incompletely understood. Here, we use heterologous protein expression, biochemical assays, and phylogenetic analyses to confirm the origin of a luciferase gene from haloalkane dehalogenases in the brittle star Amphiura filiformis . Through database searches and gene tree analyses, we also show a complex pattern of presence and absence of haloalkane dehalogenases across organismal genomes. These results first confirm parallel evolution across a vast phylogenetic distance, because octocorals like Renilla also use luciferase derived from haloalkane dehalogenases. This parallel evolution is surprising, even though previously hypothesized, because many organisms that also use coelenterazine as the bioluminescence substrate evolved completely distinct luciferases. The inability to detect haloalkane dehalogenases in the genomes of several bioluminescent groups suggests that the distribution of this gene family influences its recruitment as a luciferase. Together, our findings highlight how biochemical function and genomic availability help determine whether distinct or shared genetic components are used during the convergent evolution of traits like bioluminescence.

L31 Transposons of Hexacorallia: Distribution, Diversity and Evolution

Transposable elements (TE) of eukaryotes – retrotransposons and DNA transposons – are nucleotide sequences that can move from locus to locus of the genome, as well as between the genomes of different organisms. L31 DNA transposons are an ancient and diverse group belonging to the large IS630/Tc1/mariner group. L31 transposons are not widespread and are present in a limited number of taxa. In addition to the sequence encoding the DDE/D transposase, L31 transposons carry another ORF (ORF2). Detailed analysis of L31 elements in the genomes of six-rayed corals has provided detailed information on the distribution, diversity and structure of the elements. Two large groups, L31-duo and L31-uno, were identified, differing in both catalytic domain pattern and structure. As a result of reconstruction of the evolution of L31 transposons, it was suggested that six-rayed corals received L31 transposons from bivalves. At the same time, the split-off group L31-uno may have been obtained by mollusks as a result of horizontal transfer from corals. Studies of the distribution and diversity of TE in marine invertebrates will contribute to a better understanding of the evolutionary processes of TE and their role in the evolutionary history of species.

A guide to studying 3D genome structure and dynamics in the kidney.

The human genome is tightly packed into the 3D environment of the cell nucleus. Rapidly evolving and sophisticated methods of mapping 3D genome architecture have shed light on fundamental principles of genome organization and gene regulation. The genome is physically organized on different scales, from individual genes to entire chromosomes. Nuclear landmarks such as the nuclear envelope and nucleoli have important roles in compartmentalizing the genome within the nucleus. Genome activity (for example, gene transcription) is also functionally partitioned within this 3D organization. Rather than being static, the 3D organization of the genome is tightly regulated over various time scales. These dynamic changes in genome structure over time represent the fourth dimension of the genome. Innovative methods have been used to map the dynamic regulation of genome structure during important cellular processes including organism development, responses to stimuli, cell division and senescence. Furthermore, disruptions to the 4D genome have been linked to various diseases, including of the kidney. As tools and approaches to studying the 4D genome become more readily available, future studies that apply these methods to study kidney biology will provide insights into kidney function in health and disease.

Sporosarcina hypophthalmichthys sp. nov. Isolated From Gastrointestinal Tract of Fish Hypophthalmichthys molitrix (Valenciennes, 1844).

A rod-shaped, motile, Gram-stain-positive bacterial strain RKN2T, was isolated from gut of silver carp (Hypophthalmichthys molitrix) residing in Gobindsagar reservoir, Himachal Pradesh, India. Having the greatest sequence similarity to Sporosarcina koreensis F73T (98.51%), Sporosarcina luteola Y1T (98.4%) and Sporosarcina aquimarina SW28T (98.36%), the 16S rRNA gene phylogeny confirmed the belonging of strain RKN2T to genus Sporosarcina. Digital DNA-DNA hybridization values were 21.7%, 20.6%, and 19.2%, and average nucleotide identity values were 76.42%, 80.16%, 76.51%, of strain RKN2T with Sporosarcina koreensis F73T, Sporosarcina luteola Y1T, and Sporosarcina aquimarina SW28T, respectively. The genomic analysis of strain RKN2T showed various biological properties including nitrate reduction, genes responsible for carbohydrate-active enzymes production, antimicrobial compounds, as well as potential metabolism of aromatic compounds and heavy metals. G+C composition of RKN2T genome was 52.7%. This strain can grow in temperatures between 10°C and 40°C (optimum, 28°C-30°C), NaCl concentrations up to 6.0% (w/v), and 6.0-8.0 (optimum, 6.5-7.5) pH range. MK-7 was the dominant respiratory quinone, A-4 type cell wall peptidoglycan was present with anteiso-C15:0, iso-C15: 0, and anteiso-C17:0 being the major fatty acids and Lys-Glu being main amino acids. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the strain RKN2T's three main polar lipids. The strain is a novel species under genus Sporosarcina based on polyphasic approach and the name Sporosarcina hypophthalmichthys sp. nov. is given for strain RKN2T. RKN2T is a type strain (= MCC 4365T = JCM34522T = CCM9112T).

Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.

Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.

DeepIndel: An Interpretable Deep Learning Approach for Predicting CRISPR/Cas9-Mediated Editing Outcomes.

CRISPR/Cas9 has been applied to edit the genome of various organisms, but our understanding of editing outcomes at specific sites after Cas9-mediated DNA cleavage is still limited. Several deep learning-based methods have been proposed for repair outcome prediction; however, there is still room for improvement in terms of performance regarding frameshifts and model interpretability. Here, we present DeepIndel, an end-to-end multi-label regression model for predicting repair outcomes based on the BERT-base module. We demonstrate that our model outperforms existing methods in terms of accuracy and generalizability across various metrics. Furthermore, we utilized Deep SHAP to visualize the importance of nucleotides at various positions for DNA sequence and found that mononucleotides and trinucleotides in DNA sequences surrounding the cut site play a significant role in repair outcome prediction.

Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose.

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida 'Samantha' ('JACmantha') and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of 'Samantha' exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis 'Old Blush'. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.

Sequencing of historic samples provides complete coding sequences of chicken calicivirus from the United States.

Here, we report the coding-complete genomic sequences of two chicken caliciviruses from US poultry flocks in 2003 and 2004. They show the same genomic organization as that of other members of the Bavovirus genus and have the highest nucleotide identity (~88%) with strains from clinically normal chickens from Germany in 2004 and Netherlands in 2019.