SEARCH · Search bioRxiv

Results for “Genomics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,063 records · Page 59Linked to original sources

bioRxiv2026

Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

genomics↗

bioRxiv2017

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture

Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1-3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.

microbiology↗

bioRxiv2017

Unexpected Properties of Short Genomic Tandem Repeats

Length polymorphisms in genomic short tandem repeats have been implicated in a variety of diseases, most notably human neurodegenerative disorders. Expansions of tandem repeats are also associated with genomic instability in cancer. Our previous study of length-3 tandem repeats uncovered a surprising pattern in the length distribution of certain such repeats in the non-coding regions of the human reference genome: a bias towards repeats of length 3n - 1, (n > 3). That is, the observed frequency of repeats of this length in the human genome is higher than expected by chance based on the frequency of shorter repeats.\n\nWe have hypothesized that this pattern may be a general property of genomic DNA. If true, this could have implications with regard to the dynamics of repeat expansion generally. To test this hypothesis, we have analyzed the genomic sequences of a broad range of eukaryotic organisms as well as several complete human genomes and obtained a number of thought provoking results. We establish that this unexpected elevation in frequency of 3n - 1 long repeats is statistically significant. We also expanded this analysis to different classes of genomic regions and tandem repeats of length four and five. The specific pattern was found in 13 of the 20 organisms analyzed, including all chordate and insect genomes tested. The bias pattern, however, was not confined to a single branch of the evolutionary tree. For some genomes, such as Drosophila melanogaster, the repeat bias surprisingly was also identified in exons. The pattern is present in both small and large genomes. A similar pattern was also found in tetranucleotide and pentanucleotide repeats in the human genome. Another surprising property was identified for the flanking GC content for triplet repeats of length 3n. These findings indicate a puzzling new genomic phenomenon with possible evolutionary and disease-related implications.

bioinformatics↗

bioRxiv2020

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility

DNA topoisomerase II-{beta} (TOP2B) is fundamental to remove topological problems linked to DNA metabolism and 3D chromatin architecture, but its cut-and-reseal catalytic mechanism can accidentally cause DNA double-strand breaks (DSBs) that can seriously compromise genome integrity. Understanding the factors that determine the genome-wide distribution of TOP2B is therefore not only essential for a complete knowledge of genome dynamics and organization, but also for the implications of TOP2-induced DSBs in the origin of oncogenic translocations and other types of chromosomal rearrangements. Here, we conduct a machine-learning approach for the prediction of TOP2B binding sites using publicly available sequencing data. We achieve highly accurate predictions, with accessible chromatin and architectural factors being the most informative features. Strikingly, TOP2B is sufficiently explained by only three features: DNase I hypersensitivity, CTCF and cohesin binding, for which genome-wide data are widely available. Based on this, we develop a predictive model for TOP2B genome-wide binding that can be used across cell lines and species, and generate virtual probability tracks that accurately mirror experimental ChIP-seq data. Our results deepen our knowledge on how the accessibility and 3D organization of chromatin determine TOP2B function, and constitute a proof of principle regarding the in silico prediction of sequence-independent chromatin-binding factors. Author summaryType II DNA topoisomerases (TOP2) are a double-edged sword. They solve topological problems in the form of supercoiling, knots and tangles that inevitably accompany genome metabolism, but they do so at the cost of transiently cleaving DNA, with the risk that this entails for genome integrity, and the serious consequences for human health, such as neurodegeneration, developmental disorders or predisposition to cancer. A comprehensive analysis of TOP2 distribution throughout the genome is therefore essential for a deep understanding of its function and regulation, and how this can affect genome dynamics and stability. Here, we use machine learning to thoroughly explore genome-wide binding of TOP2B, a vertebrate TOP2 paralog that has been linked to genome organization and cancer-associated translocations. Our analysis shows that TOP2B-DNA binding can be accurately predicted exclusively using information on DNA accessibility and binding of genome-architecture factors. We show that such information is enough to generate virtual maps of TOP2B binding along the genome, which we validate with de novo experimental data. Our results highlight the importance of TOP2B for accessibility and 3D organization of chromatin, and show that computationally predicted TOP2 maps can be accurately obtained using minimal publicly available datasets, opening the door for their use in different organisms, cell types and conditions with experimental and/or clinical relevance.

bioinformatics↗

bioRxiv2020

Tumor-specific changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma

Intra-host evolved tumor virus variants have provided insights into the risk, pathogenesis and treatment responses of associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has not been explored at the whole viral genome level. An accurate and detailed description of KSHV intra-host diversity in whole KSHV genomes from matching tumors and oral swabs from Ugandan adults with HIV-associated KS was obtained by deep, short read sequencing, using duplex unique molecular identifiers (dUMI) - random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors down to [~]10-9/base. KSHV genomes were assembled de novo, and identified rearrangements were confirmed by PCR. 131-kb KSHV genome sequences, excluding major repeat regions and averaging 2.3 x 104 reads/base, were successfully obtained from 23 specimens from 9 individuals, including 7 tumor-oral pairs. Sampling more than 100 viral genomes in at least one specimen per individual showed that KSHV genomes were virtually homogeneous within samples and within individuals at the point mutational level. Heterogeneity, if present, was due to point mutations and genomic rearrangements in tumors. In 2 individuals, the same mutations were found in distinct KS tumors. The K8.1 gene was inactivated in tumors from 3 individuals, and all KSHV genomic aberrations retained the region surrounding the first major internal repeat (IR1). These findings suggest that lytic gene alterations may contribute to KS tumorigenesis or persistence. Author summaryKaposi sarcoma (KS) is a leading cancer in sub-Saharan Africa and in those with HIV co-infection. Infection by Kaposi sarcoma-associated herpesvirus (KSHV) is necessary for KS, yet why only few KSHV infections develop into KS is largely unknown. While strain differences or mutations in other tumor viruses are known to affect the risk and progression of their associated cancers, whether KSHV genetic variation is important to the natural history of KS is unclear. Most studies of KSHV diversity have characterized only [~]4% of its 165-kb genome and may have been impacted by PCR or cloning artifacts. Here, we performed highly sensitive, single-molecule sequencing of whole KSHV genomes in paired KS tumors and oral swabs from 9 individuals with KS. We found that KSHV genomes were virtually identical within individuals, with no evidence of quasispecies formation nor multistrain infection. However, KSHV genome aberrations and inactivating mutations appeared to be a common, tumor-associated phenomenon, with some mutations shared by distinct tumors within an individual. Certain regions of the KSHV genome featured prominently among tumor-associated mutations, suggesting that they are important contributors to the pathogenesis or persistence of KS.

microbiology↗

bioRxiv2020

Genomic selection strategies for clonally propagated crops

For genomic selection in clonal breeding programs to be effective, crossing parents should be selected based on genomic predicted cross performance unless dominance is negligible. Genomic prediction of cross performance enables a balanced exploitation of the additive and dominance value simultaneously. Here, we compared different strategies for the implementation of genomic selection in clonal plant breeding programs. We used stochastic simulations to evaluate six combinations of three breeding programs and two parent selection methods. The three breeding programs included i) a breeding program that introduced genomic selection in the first clonal testing stage, and ii) two variations of a two-part breeding program with one and three crossing cycles per year, respectively. The two parent selection methods were i) selection of parents based on genomic estimated breeding values, and ii) selection of parents based on genomic predicted cross performance. Selection of parents based on genomic predicted cross performance produced faster genetic gain than selection of parents based on genomic estimated breeding values because it substantially reduced inbreeding when the dominance degree increased. The two-part breeding programs with one and three crossing cycles per year using genomic prediction of cross performance always produced the most genetic gain unless dominance was negligible. We conclude that i) in clonal breeding programs with genomic selection, parents should be selected based on genomic predicted cross performance, and ii) a two-part breeding program with parent selection based on genomic predicted cross performance to rapidly drive population improvement has great potential to improve breeding clonally propagated crops.

genetics↗

bioRxiv2020

Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Haustoriidae: Amphipoda)

Genome sizes vary by orders of magnitude across the Tree of Life and lack any correlation with organismal complexity. Some crustacean orders, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that natural selection may constrain genome sizes due to physiological pressures. In this study, we examine the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncover a 6-fold genome size variation within a clade that is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. Finally, we find evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays. Significance StatementThe evolution of genome size has been a long-standing puzzle in biology. In this work, we find that genome sizes may be driven by different selection regimes following shifts to a new habitat. Dramatic genome size changes can occur rapidly, in only a few million years. Data Availability StatementRaw data sheets have been deposited on Dryad: SUBMITTED. Raw sequence reads are available at from NCBI under Bioproject SUBMITTED.

evolutionary biology↗

bioRxiv2020

Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus genome as a potential successor of the current Reference genome and assessed its effect on the accuracy of RNA-seq read alignment. In order to find the best haploid genome representation, we constructed consensus genomes at the Pan-human, Super-population and Population levels, utilizing variant information from the 1000 Genomes project. Using personal haploid genomes as the ground truth, we compared mapping errors for real RNA-seq reads aligned to the consensus genomes versus the Reference genome. For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of ~2-3 when the Reference was replaced with the Pan-human consensus genome. Interestingly, we also found that using more population-specific consensuses resulted in little to no increase over using the Pan-human consensus, suggesting a limit in the utility of incorporating more specific genomic variation. To assess the functional impact, we compared splice junction expression in the different genomes and found that the Pan-human consensus increases accuracy of splice junction quantification for hundreds of splice junctions.

bioinformatics↗

bioRxiv2021

Constructing phylogenetic relationship based on the independent selection law of genome sequences

Exploring the composition and evolution regularity of genome sequences and constructing phylogenetic relationship by alignment-free method in genome level are high-profile topics. Our previous researches discovered the CG and TA independent selection law s existed in genome sequences by analysis on the spectral features of 8-mer subsets of 920 eukaryote and prokaryote genomes. We found that the evolution state of genomes is determined by the intensity of the two independent selections and the degree of the mutual inhibition between them. In this study, the two independent selection patterns of 22 primate and 28 insect genome sequences were analyzed further. The two complete 8-mer motif sets containing CG or TA dinucleotide and their feature of relative frequency are proposed. We found that the two 8-mer sets and their feature are related directly to sequence evolution of genomes. According to the relative frequency of two 8-mer sets, phylogenetic trees were constructed respectively for the given primate and insect genomes. Through analysis and comparison, we found that our phylogenetic trees are more consistent with the known conclusions. The two kinds of phylogenetic relationships constructed by CG 8-mer set and TA 8-mer set are similar in insect genomes, but the phylogenetic relationship constructed by CG 8-mer set reflect the evolution state of genomes in current age and phylogenetic relationship constructed by TA 8-mer set reflect the evolution state of genomes in a slight earlier period. We thought it is the result that the TA independent selection is repressed by the CG independent selection in the process of genome evolution. Our study provides a theoretical approach to construct more objective evolution relationships in genome level.

evolutionary biology↗

bioRxiv2021

Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale

The structural organization of the genome plays an important role in multiple aspects of genome function. Understanding how genomic sequence influences 3D organization can help elucidate their roles in various processes in healthy and disease states. However, the sequence determinants of genome structure across multiple spatial scales are still not well understood. To learn the complex sequence dependencies of multiscale genome architecture, here we developed a sequence-based deep learning approach, Orca, that predicts genome 3D architecture from kilobase to whole-chromosome scale, covering structures including chromatin compartments and topologically associating domains. Orca also makes both intrachromosomal and interchromosomal predictions and captures the sequence dependencies of diverse types of interactions, from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions. Orca enables the interpretation of the effects of any structural variant at any size on multiscale genome organization and provides an in silico model to help study the sequence-dependent mechanistic basis of genome architecture. We show that the models accurately recapitulate effects of experimentally studied structural variants at varying sizes (300bp-80Mb) using only sequence. Furthermore, these sequence models enable in silico virtual screen assays to probe the sequence-basis of genome 3D organization at different scales. At the submegabase scale, the models predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, based on virtual screens of sequence activities, we propose a new model for the sequence basis of chromatin compartments: sequences at active transcription start sites are primarily responsible for establishing the expression-active compartment A, while the inactive compartment B typically requires extended stretches of AT-rich sequences (at least 6-12kb) and can form passively without depending on any particular sequence pattern. Orca thus effectively provides an "in silico genome observatory" to predict variant effects on genome structure and probe the sequence-based mechanisms of genome organization.

bioinformatics↗

bioRxiv2021

Sustained replication of synthetic canine distemper virus defective genomes in vitro and in vivo

Defective interfering (DI) genomes restrict viral replication and induce type-I interferon. Since DI genomes have been proposed as vaccine adjuvants or therapeutic antiviral agents, it is important to understand their generation, delineate their mechanism of action, develop robust production capacities, assess their safety and in vivo longevity and determine their long-term effects. To address this, we generated a recombinant (r) canine distemper virus (CDV) from an entirely synthetic molecular clone designed using the genomic sequence from a clinical isolate obtained from a free-ranging raccoon with distemper. rCDV was serially passaged in vitro to identify DI genomes that naturally arise during rCDV replication. Defective genomes were identified by Sanger and next-generation sequencing techniques and predominant genomes were synthetically generated and cloned into T7-driven plasmids. Fully encapsidated DI particles (DIPs) were then generated using a rationally attenuated rCDV as a producer virus to drive DI genome replication. We demonstrate these DIPs interfere with rCDV replication in a dose-dependent manner in vitro. Finally, we show sustained replication of a fluorescent DIP in experimentally infected ferrets over a period of 14 days. Most importantly, DIPs were isolated from the lymphoid tissues which are a major site of CDV replication. Our established pipeline for detection, generation and assaying DIPs is transferable to highly pathogenic paramyxoviruses and will allow qualitative and quantitative assessment of the therapeutic effects of DIP administration on disease outcome. ImportanceDefective interfering (DI) genomes have long been considered inconvenient artifacts that suppressed viral replication in vitro. However, advances in sequencing technologies have led to DI genomes being identified in clinical samples, implicating them in disease progression and outcome. It has been suggested that DI genomes could be harnessed therapeutically. Negative strand RNA virus research has provided a rich pool of natural DI genomes over many years and they are probably the best understood in vitro. Here, we demonstrate identification, synthesis, production and experimental inoculation of novel CDV DI genomes in highly susceptible ferrets. These results provide important evidence that rationally designed and packaged DI genomes can survive the course of a wild-type virus infection.

microbiology↗

bioRxiv2021

Contribution of 3D genome topological domains to genetic risk of cancers

Genome-wide association studies have identified statistical associations between various diseases, including cancers, and a large number of single-nucleotide polymorphisms (SNPs). However, they provide no direct explanation of the mechanisms underlying the association. Based on the recent discovery that changes in 3-dimensional genome organization may have functional consequences on gene regulation favoring diseases, we investigated systematically the genome-wide distribution of disease-associated SNPs with respect to a specific feature of 3D genome organization: topologically-associating domains (TADs) and their borders. For each of 449 diseases, we tested whether the associated SNPs are present in TAD borders more often than observed by chance, where chance (i.e. the null model in statistical terms) corresponds to the same number of pointwise loci drawn at random either in the entire genome, or in the entire set of disease-associated SNPs listed in the GWAS catalog. Our analysis shows that a fraction of diseases display such a preferential location of their risk loci. Moreover, cancers are relatively more frequent among these diseases, and this predominance is generally enhanced when considering only intergenic SNPs. The structure of SNP-based diseasome networks confirms that TAD border enrichment in risk loci differ between cancers and non-cancer diseases. Different TAD border enrichments are observed in embryonic stem cells and differentiated cells, which agrees with an evolution along embryogenesis of the 3D genome organization into topological domains. Our results suggest that, for certain diseases, part of the genetic risk lies in a local genetic variation affecting the genome partitioning in topologically-insulated domains. Investigating this possible contribution to genetic risk is particularly relevant in cancers. This study thus opens a way of interpreting genome-wide association studies, by distinguishing two types of disease-associated SNPs: one with a direct effect on an individual gene, the other acting in interplay with 3D genome organization. Author summaryGenome-wide association studies comparing patients and healthy subjects have evidenced correlations between diseases and the presence of pointwise genetic variations known as single-nucleotide polymorphisms (SNPs). We exploit and extend this statistical analysis by investigating the location of risk loci, i.e. disease-associated SNPs, with respect to the 3D organization of the genome into spatially-insulated domains, the topologically-associating domains (TADs). We show that for certain diseases, mostly cancers, their associated risk loci are preferentially located in the borders of these topological domains. The predominance of cancers among these diseases is confirmed and even enhanced when considering only intergenic SNPs. A different enrichment behavior is observed in embryonic stem cells and derived cell lines at an early developmental stage, presumably due to the not fully mature TAD structure in these cells. Overall, our results show that genome variations in specific TAD borders may increase the risk of developing certain diseases, especially cancers. Our work underlines the importance of considering the genetic risk loci within their 3D genomic context, and suggests a role of 3D genome partitioning into topological domains in the genetic risk which differs between cancers and non-cancer diseases.

genetics↗

bioRxiv2021

Is the genomics cart before the restoration ecology horse? Insights from qualitative interviews and trends from the literature

Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation - a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives in harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasised the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems.

scientific communication and education↗

bioRxiv2021

Genome size distributions in bacteria and archaea are strongly linked to phylogeny

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses remain unclear. Moreover, statistical analyses on this topic have typically been limited to a narrow diversity of bacteria and archaea without considering the potential bias introduced by the shared recent ancestry of many lineages. In this study, we used a phylogenetic generalized least-squares (PGLS) analysis to evaluate the effect of different factors on the genome size of a broad diversity of bacteria and archaea. We used dN/dS to estimate the strength of purifying selection, and 16S copy number as a proxy for ecological strategy, which have both been postulated to play a role in shaping genome size. After model fit, Pagels lambda indicated a strong phylogenetic signal in genome size, suggesting that the diversification of this trait is strongly influenced by shared evolutionary histories. As a predictor variable, dN/dS showed a poor predictability and non-significance when phylogeny was considered, consistent with the view that genome reduction can occur under either weak or strong purifying selection depending on the ecological context. Copies of 16S rRNA showed poor predictability but maintained significance when accounting for non-independence in residuals, suggesting that ecological strategy as approximated from 16S rRNA copies might play a minor role in genome size variation. Altogether, our results indicate that genome size is a complex trait that is not driven by any singular underlying evolutionary force, but rather depends on lineage- and niche-specific factors that will vary widely across bacteria and archaea. Author SummaryThe evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, which complicates generalizations across the Tree of Life. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size is linked to evolutionary history in bacteria and archaea. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes. Our approach indicates that genome size in prokaryotes is strongly dependent on phylogenetic history, and that genome size is the result of the interaction of variables like past events, current selection regimes, and environmental complexity that are clade dependent.

evolutionary biology↗

bioRxiv2022

Conserved Untranslated Regions of Multipartite Viruses: Natural Markers of Novel Viral Genomic Components and Tags of Viral Evolution

Viruses with split genomes are categorized as being either segmented or multipartite according to whether their genomic segments occur in single or different virions. Some complexity will exist, in that inherited "core" vital segments viruses may renew the others once host and environmental alterations keep driving viral evolution. Despite this uncertainty, empirical observations have been made across the split genomes in the untranslated regions (UTRs) on the short or long stretches of conserved or identical sequences. In this study, we describe a methodology that combines RNA and small RNA sequencing, conventional BLASTx, and iterative BLASTn of UTRs to detect viral genomic components even if they encode orphan genes (ORFans). Within the phylum Kitrinoviricota, novel putative multipartite viruses and viral genomic components were annotated using data obtained from our sampling or publicly available sources. The novel viruses, as extensions or intermediate nodes, enriched the information of the evolutionary networks. Furthermore, the diversity of novel genomic components emphasized the evolutionary roles of reassortment and recombination, as well as genetic deletion, strongly supporting the genomic complexity. These data also suggest insufficient knowledge of these genomic components for categorizing some extant viral taxa. The relative conservation of UTRs at the genome level may explain the relationships between monopartite and multipartite viruses and how the multipartite viruses can have a life strategy involving multiple host cells. Author summaryThe current workflows for virus identification are largely based on high-throughput sequencing and coupled protein sequence homology-dependent analysis methods and tools. However, for viruses with split genomes, the identification of genomic components whose deduced protein sequences are not homologous to known sequences is inadequate. Furthermore, many plant-infecting multipartite viruses contain conserved UTRs across their genomic components. Based on this, we propose a practical method of UTR-backed iterative BLASTn (UTR-iBLASTn) to explore the components with ORFans and study virus evolution using the UTRs as signals. These shed light on viral "dark matter"--unknown/omitted genomic components of segmented/multipartite viruses from different kingdoms and hosts, and the origins of these components.

microbiology↗

bioRxiv2022

Using nanopore sequencing to obtain complete genomes from saliva samples

Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e. multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (aka Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, 1 Lancefieldella parvula, and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing many additional draft genomes including many which are likely near-complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the specific taxa that have never been isolated or cultivated.

microbiology↗

bioRxiv2022

Genome size variation and evolution during invasive range expansion in an introduced plant

Plants demonstrate some of the greatest variation in genome size among eukaryotes, and their genome sizes can vary dramatically across individuals and populations within species. This genetic variation can have consequences for traits and fitness, but few studies have been able to attribute genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, USA. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for colonizer traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations.

evolutionary biology↗

bioRxiv2022

Functional annotation of the animal genomes: an integrated annotation resource for the horse

The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Currently, the horse genome is annotated using limited available RNA-seq data, as well as through comparative genomics by translating human and mouse genome annotation. While this approach has served the equine researchers well and led to various discoveries that would improve care and management of horses, many important questions remain unanswered. The limitation of the current annotation is two pronged. First, the heavy reliance on short-read sequencing-based RNA-seq data meant that alternate isoforms could not be accurately resolved. Second, epigenomic regulatory elements are crucial to detailed understanding of gene expression network but are yet to be systemically identified in the horse. Many of these regulatory elements, including enhancers, promoters, and insulators, are either not transcribed or transcribed at a very low level, necessitating alternate approaches to identify them. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, providing the equine research community an expanded set of genomics resources for studies of complex traits in the horse. Author SummaryFunctional annotation of a reference genome provides critical information that pertains the tissue-specific gene expression and regulation. Non-model organisms often rely on existing annotations of human and mouse genomes and the conservation between species for their genome annotation. This approach has limited power in annotating transcripts and regulatory elements that are less evolutionarily conserved. Such are the cases of alternatively spliced isoforms and enhancer elements. In a large-scale collaborated effort, Functional Annotation of Animal Genome (FAANG) aims to generate species-specific and tissue-aware functional annotation for farm animals. In this study, we present the overall annotation efforts and findings from the equine FAANG group. This integrated annotation for the horse genome provides, for the first time, a comprehensive overview of gene expression and regulation landscape in nine major equine tissues, as well as an analytical framework for further inclusion of other important tissues.

genetics↗