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We report an analysis of the genomic diversity of isolates of Burkholderia pseudomallei, the cause of melioidosis, recovered in Colombia from routine surveillance during 2016-2017. B. pseudomallei appears genetically diverse, suggesting it is well established and has spread across the region.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

The taxon Elasmobranchii (sharks and rays) contains one of the most long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.

Background A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. Results To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants’ position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus ( qPH8-1 ) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). Conclusions Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.

Background A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of the seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate. Results To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome-wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combining quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences, and protein structure variation. Conclusions Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.

Background Long-term persistence of species with low genetic diversity is the focus of widespread attention in conservation biology. The snow leopard, Panthera uncia , is a big cat from high-alpine regions of Asia. However, its subspecies taxonomy, evolutionary history, evolutionary potential, and survival strategy remain unclear, which greatly hampers their conservation. Results We sequence a high-quality chromosome-level genome of the snow leopard and the genomes of 52 wild snow leopards. Population genomics reveal the existence of two large genetic lineages in global snow leopards, the northern and southern lineages, supported by the biogeography. The Last Glacial Maximum drove the divergence of two lineages. Microclimate differences and large rivers between the western and central Himalayas likely maintain the differentiation of two lineages. EPAS1 is positively selected in the southern lineage with almost fixed amino acid substitutions and shows an increased allele frequency with elevation. Compared to the southern lineage, the northern lineage exhibits a lower level of genomic diversity and higher levels of inbreeding and genetic load, consistent with its recent population decline. We find that snow leopards have extremely low genomic diversity and higher inbreeding than other Carnivora species; however, strong deleterious mutations have been effectively purged in snow leopards by historical population bottlenecks and inbreeding, which may be a vital genetic mechanism for their population survival and viability. Conclusions Our findings reveal the survival strategy of a species with low genetic diversity and highlight the importance of unveiling both genetic diversity and genetic burden for the conservation of threatened species.

Background Research into the genetic diversity of honey bee ( Apis mellifera L. ) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees ( Apis mellifera carnica ) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs. Results Our analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (F ST ), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee ( Apis mellifera ligustica ) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise F ST values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained. Conclusions This study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.

Runs of homozygosity (ROHs) arise due the transmission from parents to offspring of segments that are either identical by decent (IBD) or identical by state (IBS). The former is due to consanguineous matings whereas the latter is due to demographic processes. ROHs reduce individual nucleotide diversity (θ) as a function of homozygosity, and thus ROH distributions and θ are expected to vary among species because inbreeding levels, recombination rates, and demographic histories vary widely. To help interpret genetic diversity within and among species, we utilized genome sequence data from 78 mammalian species to compare θ and ROH burden (i.e., number and length of ROHs in the genome) among groups of mammals to assess genomic signatures of inbreeding. We compared θ and ROHs: (i) among threatened and non-threatened mammals to determine the significance of contemporary conservation status; (ii) among carnivorous and non-carnivorous mammals to determine the relevance of trophic effects; (iii) relative to body size because mutation rates generally vary with body mass; and (iv) across mammals from different latitudes to test for gradients in genomic diversity (e.g., due to effects of historic climatic regimes). Our results illustrate the considerable variance in genomic diversity across mammals, and that trophic level, body mass, and latitude have significant effects on θ and ROH burden. However, conservation status was not a reliable indicator of genomic diversity. We argue that genetic or genomic diversity should be an explicit component of conservation status, as such diversity is critical to the long-term sustainability of populations, and anticipate that ROHs will become more commonly used to estimate inbreeding in wild animals.

Genomic data are increasingly used in primatology to understand how landscape features, dispersal patterns, and historical processes shape population structure and conservation-relevant diversity. The gelada ( Theropithecus gelada ), an endemic primate of the Ethiopian highlands, is currently divided into three subspecies; yet little is known about the extent of genomic variation within these groups. This gap is most pronounced for the Central gelada ( T. gelada obscurus ), the most widespread subspecies, for which genomic data have until now been available from only three individuals from a single site. To broaden this representation, we generated whole-genome sequence data from ten Central gelada individuals sampled across four central Ethiopian sites and two Southern geladas ( T. gelada arsi ), doubling the number of available genomes for this recently Endangered subspecies. Combining these new data with previously published genomes, we assessed patterns of genomic diversity across the species and tested how major geophysical features of the Ethiopian highlands influence population connectivity. Models incorporating preferred altitudinal ranges for geladas provided a substantially better fit to observed genomic distances than models based only on straight-line geographic distance, indicating that elevational structure strongly constrains movement. Using this framework, we inferred the affinities of unsampled Northern populations, finding stronger support for an east-west than a north-south division between the Northern gelada ( T. gelada gelada ) and Central gelada. These results highlight the importance of highland topography in shaping gelada population structure and inform future research and conservation planning for Ethiopian primates.

Background Malaria remains a significant global health concern, with Plasmodium falciparum being the most dangerous of the malaria-causing parasites. Sierra Leone, with year-round transmission of malaria, continues to experience high infection rates, largely due to P. falciparum . Although genomic databases have provided valuable insights into malaria transmission patterns, drug resistance, and population structure, data from Sierra Leone has been limited. This study aims to build on our previous report by incorporating new samples and providing a more comprehensive genomic analysis of P. falciparum in Sierra Leone, with a particular focus on genetic diversity, population structure, and drug resistance. Methods We collected P. falciparum samples from Freetown, Sierra Leone, between December 2022 and March 2023. A total of 35 samples underwent sequencing using the MGISEQ and Illumina platforms, resulting in high-coverage genomic data. Population structure was assessed using PCA, NJ trees, and STRUCTURE analysis, alongside comparisons with a global dataset from the pf3k project. Genetic diversity was evaluated using metrics such as , ω , Tajima’s D, and iHS. XPEHH was used to examine selection pressures across different regions. Results Sequencing yielded over 376,450 high-quality SNPs across 35 Sierra Leone isolates, indicating substantial genetic variability. PCA, NJ trees, and STRUCTURE analysis revealed that the Sierra Leone isolates formed distinct clusters from both West African and Southeast Asian samples, with evidence of region-specific genetic adaptation. The low IBD we found suggested that infections were largely independent. Meanwhile the Tajima’s D and iHS analysis showed strong directional selection in genes associated with immune evasion and drug resistance genes, exhibiting ongoing evolutionary pressure due to therapeutic behavior. Conclusion This study provides us not only a genomic database but also a profile of P. falciparum in Sierra Leone, revealing high genetic diversity, strong selection pressure on drug resistance genes, and unique population structures. Our data emphasize the need for continued genomic surveillance to better manage malaria.