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Microbes have often been overlooked as indicators of how the ecological status is affected by human pressures. Recently, the biotic index microgAMBI was proposed to assess the status of marine sediments and waters, and it has been tested under different pressures and biogeographical areas. This index is based on the assignation of microbial taxa to one of two ecological groups: sensitive or tolerant to pollution or disturbance. The resulting taxa list has grown significantly since its first publication. Given the growing use of microgAMBI, it is crucial to make it more FAIR: Findable, Accessible, Interoperable and Reusable. Hence, this work provides the calculation template, the updated taxa list (1,974 taxa currently), and instructions on how to access and use them for assessing marine microbial ecological status.

Natural history collections contain a wealth of information on species diversity, distribution and ecology. However, due to historical and practical constraints, this valuable information is not always available to researchers. Our project aimed at unlocking data handwritten in notebooks owned by Johanna Bonne-Wepster, a Culicidae researcher. These handwritten notes refer to specimens labeled with a number only. The notebooks were scanned and entered into a Google spreadsheet. The specimens were provided with a unique identifier, labeled with the information from the notebooks and the data exported to the Global Biodiversity Information Facility. In addition, the type specimens were photographed. Besides Johanna Bonne-Wepster's collection, mosquitoes from the former Rijksmuseum van Natuurlijk Historie collection and the former Zoölogisch Museum Amsterdam Nederland collection were digitized. All specimens are now housed at the Naturalis Biodiversity Center museum in Leiden. This paper describes the efforts to mobilize this data and the problems we encountered.

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

Characterizing the entomological profile of malaria transmission at fine spatiotemporal scales is essential for developing and implementing effective vector control strategies. Here, we present a fine-grained dataset of Anopheles mosquitoes (Diptera: Culicidae) collected in 55 villages of the rural districts of Korhogo (Northern Côte d'Ivoire) and Diébougou (South-West Burkina Faso) between 2016 and 2018. In the framework of a randomized controlled trial, Anopheles mosquitoes were periodically collected by Human Landing Catches experts inside and outside households, and analyzed individually to identify the genus and, for a subsample, species, insecticide resistance genetic mutations, Plasmodium falciparum infection, and parity status. More than 3,000 collection sessions were carried out, achieving about 45,000 h of sampling efforts. Over 60,000 Anopheles were collected (mainly A. gambiae s.s., A. coluzzii, and A. funestus). The dataset is published as a Darwin Core archive in the Global Biodiversity Information Facility, comprising four files: events, occurrences, mosquito characterizations, and environmental data.

Snakes are a vital component of wildlife resources and are widely distributed across the globe. The many-banded krait Bungarus multicinctus is a highly venomous snake found across Southern Asia and central and southern China. Snakes are an ancient reptile group, and their genomes can provide important clues for understanding the evolutionary history of reptiles. Additionally, genomic resources play a crucial role in comprehending the evolution of all species. However, snake genomic resources are still scarce. Here, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides genomic information on the genes involved in venom gland functions.

Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species' unique biological and evolutionary features, helping promote its conservation.

Antibiotic resistance is increasing at an alarming rate, and three related mycobacteria are sources of widespread infections in humans. According to the World Health Organization, Mycobacterium leprae, which causes leprosy, is still endemic in tropical countries; Mycobacterium tuberculosis is the second leading infectious killer worldwide after COVID-19; and Mycobacteroides abscessus, a group of non-tuberculous mycobacteria, causes lung infections and other healthcare-associated infections in humans. Due to the rise in resistance to common antibacterial drugs, it is critical that we develop alternatives to traditional treatment procedures. Furthermore, an understanding of the biochemical mechanisms underlying pathogenic evolution is important for the treatment and management of these diseases. In this study, metabolic models have been developed for two bacterial pathogens, M. leprae and My. abscessus, and a new computational tool has been used to identify potential drug targets, which are referred to as bottleneck reactions. The genes, reactions, and pathways in each of these organisms have been highlighted; the potential drug targets can be further explored as broad-spectrum antibacterials and the unique drug targets for each pathogen are significant for precision medicine initiatives. The models and associated datasets described in this paper are available in GigaDB, Biomodels, and PatMeDB repositories.

Cosmocercoid nematodes are common parasites of the digestive tract of amphibians. Genomic resources are important for understanding the evolution of a species and the molecular mechanisms of parasite adaptation. So far, no genome resource of Cosmocercoid has been reported. In 2020, a massive Cosmocercoid infection was found in the small intestine of a toad, causing severe intestinal blockage. We morphologically identified this parasite as A. chamaeleonis. Here, we report the first A. chamaeleonis genome with a genome size of 1.04 Gb. The repeat content of this A. chamaeleonis genome is 72.45%, and the total length is 751 Mb. This resource is fundamental for understanding the evolution of Cosmocercoid and provides the molecular basis for Cosmocercoid infection and control.

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.

In silico models of biological systems are usually very complex and rely on a large number of parameters describing physical and biological properties that require validation. As such, parameter space exploration is an essential component of computational model development to fully characterize and validate simulation results. Experimental data may also be used to constrain parameter space (or enable model calibration) to enhance the biological relevance of model parameters. One widely used computational platform in the mathematical biology community is PhysiCell, which provides a standardized approach to agent-based models of biological phenomena at different time and spatial scales. Nonetheless, one limitation of PhysiCell is the lack of a generalized approach for parameter space exploration and calibration that can be run without high-performance computing access. Here, we present PhysiCOOL, an open-source Python library tailored to create standardized calibration and optimization routines for PhysiCell models.