Drosophila genome organization: conserved and dynamic aspects.
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Animals↗
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Endemic Circulation and Genetic Characterization of Foot-and-Mouth Disease Virus in Buffalo Populations of Bangladesh.
Foot-and-mouth disease (FMD) virus (FMDV) is endemic in Bangladesh, causing severe economic losses in the livestock sector. While it primarily affects cattle, buffaloes (Bubalus bubalis) remain highly susceptible. Therefore, this study aimed to determine the prevalence and molecular characteristics of FMDV in buffaloes across three districts (Sylhet, Rajshahi, and Noakhali) of Bangladesh from January to June 2024. In a cross-sectional study, a total of 622 nasal swabs from 67 herds were collected and tested for FMDV RNA using reverse transcription polymerase chain reaction (RT-PCR). Overall, 255 samples were positive, resulting in an individual-level prevalence of 41.0%(255/622), while 88.1% (59/67) of herds were FMDV-positive. Animal-level prevalence was highest in Sylhet (47.1%), followed by Noakhali (38.9%) and Rajshahi (37.1%). To further characterize circulating strains, eight representative RT-PCR-positive samples were sequenced, revealing the co-circulation of serotypes O (n = 5) and Asia-1 (n = 3). Phylogenetic analysis showed that the isolates belonged to the ME-SA/Ind2001e lineage of the serotype O and the Asia-1 Group V lineage, clustering with contemporary strains from Bangladesh and neighboring countries, suggesting possible intra- and transboundary transmission. Pairwise genetic distance evaluation revealed high regional similarity, while Mantel tests indicated significant associations between genetic, geographic, and temporal distances. Comparative genomic analysis revealed largely conserved genomic regions, whereas VP1 analysis indicated that purifying selection predominated across both serotypes, with serotype O exhibiting greater genetic diversity (π = 0.11642) than Asia-1 (π = 0.05258), suggesting localized antigenic variability and possible immune-mediated viral evolution. These findings highlight the need for strengthened surveillance, improved biosecurity, and integrated vaccination strategies to enhance FMD control and reduce economic losses in Bangladesh.
Animals↗
Reference genome of the Californian trapdoor spider Aptostichus stephencolberti Bond 2008 (Araneae: Mygalomorphae: Euctenizidae).
We present a reference genome assembly for the trapdoor spider Aptostichus stephencolberti. This species, described in 2008, is endemic to the highly fragmented coastal dune habitats of Northern California from Monterey to the San Francisco Bay Area. Trapdoor spiders are ideal taxa for landscape scale genomic studies owing to their extreme site fidelity and limited dispersal capabilities; these same characteristics make them prone to extinction. Genomic studies of species like A. stephencolberti can reveal novel areas of endemism and high conservation value that may not be evident in species with wider ranges and greater dispersal capabilities. As part of the California Conservation Genomics Project, we constructed the A. stephencolberti reference genome from high quality long-read sequences, scaffolded with proximity ligation Omni-C data. The primary assembly comprises 551 scaffolds spanning 3.63 Gbp, a scaffold N50 of 62.2 Mbp and BUSCO completeness of 95.6%. We estimate 52 chromosomes yet find no (TTAGG)n telomer repeats. Expanding the telomeric repeat search finds an ancestral loss of the repeat from all spiders. Automated annotation using the NCBI refseq pipeline and RNAseq data from whole adults finds 14,067 genes with a BUSCO annotation completeness of 95.56%. Repeat annotation identified 77% of the genome to be interspersed repeats. This resource, the first for family Euctenizidae will facilitate future study and resulting conservation actions of A. stephencolberti and other Aptostichus sp. populations associated with the rapidly changing California coastal dune ecosystem.
Aptostichus stephencolberti↗
GRS: a graphic tool for genome retrieval and segment analysis.
GRS is a graphic tool for retrieval and visualization of genome segments from partially or completely sequenced genomes. To facilitate visual identification of conserved genomic motifs, genes are color-coded according to their presumed functional roles. Aligned genes can be rapidly screened for potential homology by automatic retrieval and alignment of the corresponding protein sequences. Furthermore, the map location of any genome segment can be visually compared to the position of the same segment in other genomes or to the position of other segments within the same genome. The gene string analysis option of GRS allows the identification of genes that are identically arranged in any pairwise set of genomes. Finally, the program allows the user to create new gene table format files to enable comparisons of gene order structures in recently determined sequence data to the patterns of genes in already existing microbial and organellar databases. With the help of GRS, the genomic contexts of genes for which no identifiable homologues exist can be analyzed to provide an additional source of information for sequence annotations. We illustrate the use of GRS by analyzing the structure and distribution of phylogenetically conserved motifs in closely as well as more distantly related microbial genomes.
Computer Graphics↗
Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana.
Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous positions in the Arabidopsis genome on the basis of sequence similarity. Blocks of genetically linked loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This comparative analysis allowed the identification of a minimum of 21 conserved genomic units within the Arabidopsis genome, which can be duplicated and rearranged to generate the present-day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B. napus genetic map, equivalent to approximately 9 Mb of contiguous sequence in the Arabidopsis genome. There was also evidence for conservation of chromosome landmarks, particularly centromeric regions, between the two species. The observed segmental structure of the Brassica genome strongly suggests that the extant Brassica diploid species evolved from a hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids.
Arabidopsis↗
Larger rearranged mitochondrial genomes in Dekkera/Brettanomyces yeasts are more closely related than smaller genomes with a conserved gene order.
Mitochondrial genomes from yeasts in the Dekkera/Brettanomyces/Eeniella group vary in size from 28 to 101 kb. Mapping of genes has shown that the three smallest genomes, of 28-42 kb, have the same gene order, whereas the three larger mitochondrial DNAs of 57-101 kb are rearranged relative to the smaller molecules and between themselves. To examine the relationships between these genomes, a phylogenetic tree has been constructed by sequence comparison of the mitochondrial-encoded cytochrome oxidase subunit gene (COX2) from the six species. Contrary to expectation, the tree shows that the larger rearranged genomes are more closely related than the smaller mtDNAs. This result indicates that the gene order of the smaller mtDNAs (28-42 kb) is ancestral and that larger mtDNA molecules (57-101 kb) are more prone to rearrangement than smaller forms.
Base Sequence↗
Comparative genomics of foot-and-mouth disease virus.
Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L(pro), 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.
3' Untranslated Regions↗
Past genomes guide future conservation: insights from extinct populations of the endangered Pacific pocket mouse.
Efforts to recover endangered species often rely on restoring populations to their historical range, yet reestablishing lost genetic variation is challenging when the ancestral genetic landscape is poorly understood. The Pacific pocket mouse (Perognathus longimembris pacificus), a federally endangered heteromyid rodent, has been extirpated from most of its range in coastal southern California. Recovery efforts call for establishing new populations in their historic range through translocation, but the extent to which historical patterns of genetic variation can be recapitulated is unknown. To inform conservation planning, we sequenced whole genomes of historical samples, including individuals from populations that went extinct in the mid-1900s. Phylogenetic analyses revealed that mice from the southernmost extirpated population form a clade with a different subspecies, while populations to the north form a sister clade. These findings support morphological evidence calling for a taxonomic revision, which would modify the definition of the historic range and complicate the interpretation of suitable reintroduction sites. Despite this divergence, D-statistics and demographic models indicate historical gene flow among coastal populations, suggesting that alleles reintroduced to the southern coast may echo ancestral connectivity. Thus, management efforts should consider potential receiver sites that contain suitable habitat within this range as viable for population creation. These results highlight the value of historical genomics in guiding conservation decisions, particularly when taxonomic uncertainty, extirpation, and limited genetic diversity constrain modern management. Although historical baselines often cannot be restored, conservation strategies can leverage genomic insights to enhance future adaptive potential and long-term resilience of threatened species.
Endangered Species↗
The First Highly Contiguous Genome Assembly for the Western Bluebird (Sialia mexicana).
The western bluebird (Sialia mexicana) is a secondary cavity-nesting thrush that has experienced historical population declines, local extirpations, and more recent recoveries associated with nest box programs. Despite these regional successes, recent eBird estimates suggest continued range-wide declines and substantial geographic variation in population trajectories, making this species a useful system for future studies of demographic change, connectivity, and conservation genomics. However, genomic resources for western bluebirds remain limited, and no reference genome currently exists for any species in the genus Sialia. Here, we present the first high-quality de novo reference genome for S. mexicana. Using PacBio HiFi long-read sequencing from an adult female, we generated a highly contiguous, phased 1.3 Gb nuclear assembly with a contig N50 of 24.8 Mb and high BUSCO completeness of 98.3%. We annotated the nuclear genome using transcriptomic and protein evidence, identifying 16,656 protein-coding genes and 26,060 transcripts/protein isoforms. We also assembled a complete ∼16 kb mitochondrial genome from Illumina short-read data. This reference genome provides a foundational resource for future studies of population structure, genetic diversity, connectivity, demographic history, and adaptation in western bluebirds and related taxa.
Animals↗
Longitudinal whole-genome analysis of bluetongue virus identifies conserved serotype-specific genomes and distinct genomic constellations within a Colorado sheep flock (2021-2023).
Bluetongue virus (BTV) is a segmented double-stranded RNA virus of ruminants transmitted by Culicoides spp. biting midges. Although the genome consists of ten segments, classification into serotypes is primarily based on genome segment 2. However, reassortment among genomic segments is a major driver of BTV evolution and diversity. This study used longitudinal whole-genome sequencing to characterize BTV genomes collected from 2021 to 2023 within a single sheep flock in Colorado, where multiple serotypes co-circulate. Whole-genome sequences were generated from fourteen blood samples representing four serotypes: BTV-6, -11, -13, and -17. Longitudinal sampling identified multiple BTV serotypes within individual sheep across consecutive years. Tanglegram analysis comparing segment phylogenies to the segment 2 tree demonstrated incongruent topologies across all genomic segments, suggestive of reassortment or the circulation of distinct genomic constellations. Nucleotide-level comparisons revealed high sequence homology among same-serotype samples from the same year, while the greatest genetic divergence was observed among BTV-17 genomes collected in different years. Additionally, all BTV-13 genomes contained a previously undescribed nonsynonymous substitution in segment 10 predicted to extend the encoded protein by three amino acids. Together, these findings demonstrate that highly conserved BTV genomes and distinct genomic constellations can be detected at the flock level across multiple years. This longitudinal whole-genome approach reveals the genetic complexity of endemic BTV populations, including novel variants and genomic patterns consistent with reassortment that are lost with conventional serotyped-based approaches, highlighting the need to integrate whole-genome characterization into endemic BTV monitoring programs.
Animals↗
Genome trees from conservation profiles.
The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component "presence-absence" protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings.
Animals↗
Use of pulsed-field gel electrophoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations.
In 1992 a helical microorganism associated with chronic active hepatitis and a high incidence of hepatocellular tumors was identified in the hepatic parenchyma of A/JCr mice. By using biochemical tests, phenotypic characterization, and 16S rRNA gene sequence analysis, the organism was classified as a novel Helicobacter species and named Helicobacter hepaticus. Recent surveys completed in our laboratory indicate that H. hepaticus is widespread in academic and commercial mouse colonies. The aim of this study was to examine the H. hepaticus genome by pulsed-field gel electrophoresis (PFGE) to determine the degree of genomic variation and genomic size. This technique has been used to identify significant genomic diversity among strains of Helicobacter pylori and to demonstrate only slight genomic diversity among strains of Helicobacter mustelae. Genomic DNAs from 11 isolates of H. hepaticus from the United States, Germany, France, and The Netherlands were subjected to PFGE after digestion with SmaI. Isolates from three independent sources within the United States had very similar PFGE patterns, suggesting that the genomic DNAs of these isolates are conserved. Genomic DNA isolated from a fourth source within the United States had a PFGE pattern different from those of the other U.S. isolates. Isolates obtained from Germany, France, and The Netherlands had PFGE patterns that differed markedly from those of the U.S. isolates and from one another. The use of DNA fingerprinting may be useful in subsequent epidemiological studies of H. hepaticus when the source and method of spread of this murine pathogen need to be ascertained. By PFGE, the genomic size of H. hepaticus is estimated to be roughly 1.3 Mb, which compares to 1.67 Mb for H. pylori and 1.7 Mb for H. mustelae.
Animals↗
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.
BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.
Alleles↗
Comparative genomic analysis reveals distinct population structure in Legionella anisa.
Legionella anisa has been frequently isolated from engineered water systems; however, its population structure remains understudied compared to Legionella pneumophila. Here, we generated complete genome sequences for four L. anisa isolates recovered from a healthcare facility in Rimouski, Canada. Further the population structure of this species was investigated by performing comparative genomic analyses of the genomes generated in this study together with publicly available L. anisa genomes. Genome-wide phylogenetic analysis revealed the presence of three distinct clades separated by substantial genetic divergence (∼500 SNP), with the Rimouski isolates forming a tightly clustered group, suggesting a clonal lineage. Comparative pangenome analysis indicated moderate core genome conservation accompanied by a highly variable accessory genome (∼50%). The isolates characterized in this study harbored multiple plasmids encoding genes associated with conjugation, heavy metal resistance, and other stress-related functions, suggesting potential roles in environmental persistence. Previous studies have shown that L. anisa can proliferate within protozoan host cells, although outcomes vary depending on the host species. Our isolates showed efficient proliferation within Acanthamoeba castellanii, but not within Vermamoeba vermiformis, under the conditions tested. Together, these findings underscore the genomic diversity of this understudied Legionella species and provide a framework for future investigations regarding environmental persistence and potential pathogenicity.
Legionella anisa, Whole genome sequencing↗
Geminivirus vectors for transient gene silencing in plants.
Both RNA and DNA viruses have been engineered to serve as vectors for transient silencing in intact plants. Host gene sequences carried by the virus are seen by the plant as "foreign," and homologous gene-silencing machinery acts on both the viral vector RNA and the endogenous host gene mRNA. DNA viruses, such as geminiviruses, are advantageous for silencing because only their mRNAs are silenced and their DNA genomes continue to replicate and move. The conserved genome organization of geminiviruses and the fact that they can be cloned into Escherichia coli plasmids, propagated, and then inoculated into plants for infection simplifies the procedure for silencing specific chromosomal genes in intact plants. This chapter describes the development of a silencing vector from cabbage leaf curl virus for use in Arabidopsis and procedures for silencing two genes simultaneously.
Cloning, Molecular↗
Search for Coxsackievirus B3 RNA in idiopathic dilated cardiomyopathy using gene amplification by polymerase chain reaction.
A polymerase chain reaction (PCR) amplification assay was developed to detect Coxsackievirus B3 ribonucleic acid (RNA) in blood and myocardial tissue of explanted hearts from 40 patients who underwent cardiac transplantation and in 1 normal heart. Twenty-one patients were affected by idiopathic dilated cardiomyopathy of different duration and 19 by coronary artery disease. Coxsackievirus B3 in vitro infected Vero cells and cells infected by related human enteroviruses (Coxsackievirus B2, B4, and poliovirus 1) were used as reaction controls. PCR was performed using 4 pairs of primers homologous to Coxsackie-virus B3 sequences. Three sets were located in regions of the genome conserved at nucleotide level between several enterovirus species (replicase gene, 5' noncoding region), while one was located in a Coxsackievirus B3-specific region (VP1 gene). Total RNA was prepared by acid guanidinium isothiocyanate extraction from tissue stored frozen at -80 degrees C. One microgram of total RNA was retrotranscribed with either antisense primer or with random hexanucleotide primers and then subjected to 40 cycles of amplification. PCR products were separated by electrophoresis on a 10% polyacrylamide gel, electrotransferred to a nylon membrane and then hybridized to oligonucleotide probes specific for the coxsackievirus B3 genome radiolabeled with radioactive isotope of phosphorous. All pairs of primers yielded specific amplification products when tested on Coxsackievirus B3-infected Vero cells, with a sensitivity of 1 infected cell out of 10(5) to 10(6) cells starting from 1 microgram total RNA. Primer sets for regions of Coxsackievirus B3 genome highly conserved between related enteroviral species gave positive amplification also when challenged with RNA from cells infected by Coxsackievirus B2, B4 and poliovirus 1.
Adult↗
Comparison of Pax1/9 locus reveals 500-Myr-old syntenic block and evolutionary conserved noncoding regions.
Identification of conserved genomic regions within and between different genomes is crucial when studying genome evolution. Here, we described regions of strong synteny conservation between vertebrate deuterostomes (tetrapods and teleosts) and invertebrate deuterostomes (amphioxus and sea urchin). The shared gene contents across phylogenetically distant species demonstrate that the conservation of the regions stemmed from an ancestral segment instead of a series of independent convergent events. Comparison of the syntenic regions allows us to postulate the primitive gene organization in the last common ancestor of deuterostomes and the evolutionary events that occurred to the 3 distinct lineages of sea urchin, amphioxus, and vertebrates after their separation. In addition, alignment of the syntenic regions led to the identification of 8 noncoding evolutionarily conserved regions shared between amphioxus and vertebrates. To our knowledge, this is the first report of conserved noncoding sequences shared by vertebrates and nonvertebrates. These noncoding sequences have high possibility of being elements that regulate neighboring genes. They are likely to be a factor in the maintenance of conserved synteny over long phylogenetic distance in different deuterostome lineages.
Amino Acid Sequence↗
Emerging trends in genome editing of wild animals.
Globally, nearly one million species are currently threatened with extinction, highlighting the need for more efficient solutions to biological conservation. Genome editing, which allows for faster and more precise changes in genomes, is a promising technique for boosting populations through facilitated adaptation, management of invasive or pathogenic populations, and potentially even facilitating the revival of extinct species. These approaches belong to a new field of research termed conservation biotechnology, which places a great responsibility on researchers and decision makers to ensure sustainability. In this paper, we have mapped the emerging trends in genome editing of wild animals. Current projects primarily focus on population control and de-extinction, with fewer initiatives aimed at preserving threatened species. We then explore four critical dimensions of conservation biotechnology: the technology itself, new perspectives on conservation practices, research organization, and governance and policy. Despite its potential, key questions remain-particularly whether genome editing can increase genetic diversity without causing unintended non-target impacts. Genome editing also provokes new perspectives on conservation practices where ecosystem-wide impact assessment, case-by-case evaluations, and post-release monitoring needs to be prioritized. Furthermore, conservation biotechnology is heavily funded through private funding showing varying stakeholder interest, which can lead to untraditional and less transparent research processes. Stakeholders, including local and indigenous people, are only to a certain degree involved, which may weaken inclusion of local knowledge and monitoring efforts. Finally, concerning governance and policy, there is an urgent need to develop more adequate regulation of conservation biotechnology, as environmental release of genome-edited animals challenges definitions and guidelines in current nature protection laws and GMO regulations. Based on our analysis, we outline key points for further investigation toward a more sustainable approach to conservation biotechnology.
Animals↗