GigaByte (Hong Kong, China)最新文献

The basic analysis steps of spatial transcriptomics require obtaining gene expression information from both space and cells. The existing tools for these analyses incur performance issues when dealing with large datasets. These issues involve computationally intensive spatial localization, RNA genome alignment, and excessive memory usage in large chip scenarios. These problems affect the applicability and efficiency of the analysis. Here, a high-performance and accurate spatial transcriptomics data analysis workflow, called Stereo-seq Analysis Workflow (SAW), was developed for the Stereo-seq technology developed at BGI. SAW includes mRNA spatial position reconstruction, genome alignment, gene expression matrix generation, and clustering. The workflow outputs files in a universal format for subsequent personalized analysis. The execution time for the entire analysis is ∼148 min with 1 GB reads 1 × 1 cm chip test data, 1.8 times faster than with an unoptimized workflow.

Trimeresurus albolabris, also known as the white-lipped pit viper or white-lipped tree viper, is a highly venomous snake distributed across Southeast Asia and the cause of many snakebite cases. In this study, we report the first whole genome assembly of T. albolabris obtained with next-generation sequencing from a specimen collected in Mengzi, Yunnan, China. After genome sequencing and assembly, the genome of this male T. albolabris individual was 1.51 Gb in length and included 38.42% repeat-element content. Using this genome, 21,695 genes were identified, and 99.17% of genes could be annotated using gene functional databases. Our genome assembly and annotation process was validated using a phylogenetic tree, which included six species and focused on single-copy genes of nuclear genomes. This research will contribute to future studies on Trimeresurus biology and the genetic basis of snake venom.

The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a northern Atlantic fish inhabiting open seagrass environments that recently expanded its distribution range. Here, we present a highly contiguous, near chromosome-scale genome of E. aequoreus. The final assembly spans 1.6 Gbp in 7,391 scaffolds, with a scaffold N50 of 62.3 Mbp and L50 of 12. The 28 largest scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions identified in vertebrates. Our demographic modeling identified a peak in population size during the last interglacial period, suggesting the species might benefit from warmer water conditions. Our updated snake pipefish assembly is essential for future analyses of the morphological and molecular changes unique to the Syngnathidae.

Understanding the distribution of Anopheles species is essential for planning and implementing malaria control programmes. This study assessed the composition and distribution of cryptic species of the main malaria vector, the Anopheles gambiae complex, in different districts of Kinshasa. Anopheles were sampled using CDC light traps in the four Kinshasa districts between July 2021 and June 2022, and then morphologically identified. Equal proportions of Anopheles gambiae s.l. per site were subjected to polymerase chain reaction to identify the cryptic species of the Anopheles gambiae complex. Anopheles gambiae complex specimens were identified throughout Kinshasa. The average density significantly differed inside and outside households. Two species of this complex circulate in Kinshasa: Anopheles gambiae and Anopheles coluzzii. In all the study sites, Anopheles gambiae was the most widespread species. Our results provide an important basis for future studies on the ecology and dynamics of cryptic species of the Anopheles gambiae complex in Kinshasa.

Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insights into how these reservoirs change and impact public health. Enriching for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and Flongle flow cells. Using adaptive sampling, we observed consistent enrichment by composition. On average, adaptive sampling resulted in a target composition 4× higher than without adaptive sampling. Despite a decrease in total sequencing output, adaptive sampling increased target yield in most replicates. We also demonstrate enrichment in a diverse community using an environmental sample. This method enables rapid and flexible genomic surveillance.

The king ratsnake (Elaphe carinata) of the genus Elaphe is a common large, non-venomous snake widely distributed in Southeast and East Asia. It is an economically important farmed species. As a non-venomous snake, the king ratsnake predates venomous snakes, such as cobras and pit vipers. However, the immune and digestive mechanisms of the king ratsnake remain unclear. Despite their economic and research importance, we lack genomic resources that would benefit toxicology, phylogeography, and immunogenetics studies. Here, we used single-tube long fragment read sequencing to generate the first contiguous genome of a king ratsnake from Huangshan City, Anhui province, China. The genome size is 1.56 GB with a scaffold N50 of 6.53M. The total length of the genome is approximately 621 Mb, while the repeat content is 42.26%. Additionally, we predicted 22,339 protein-coding genes, including 22,065 with functional annotations. Our genome is a potentially useful addition to those available for snakes.

Planorbidae comprises approximately 40 genera of freshwater gastropods, including roughly 250 species. Among the Planorbidae subfamilies, the significance of Planorbinae is due to its genus Biomphalaria, whose species are intermediate hosts of the trematode Schistosoma mansoni Sambon, 1907, which causes schistosomiasis in humans and animals. Here, we present the analysis of the dataset of Planorbidae housed in the Collection of Mollusks of the Oswaldo Cruz Institute, with a special focus on Biomphalaria species. This dataset includes 7,267 lots originating from 55 countries, representing 20 genera and 75 species collected from 1948 to 2023. Collections were performed in all regions of Brazil, comprising specimens from 26 states and the Federal District, particularly from the Southeast and Northeast. Within the dataset, Biomphalaria includes 3,926 lots of 31 species from 42 countries. These records will help improve our comprehension of schistosomiasis transmission dynamics and the geographic distributions of these medically important species.

Rodents, a globally distributed and ecologically important mammalian order, serve as hosts for various zoonotic pathogens. However, sampling of rodents and their pathogens suffers from taxonomic and spatial biases. This affects consolidated databases, such as IUCN and GBIF, limiting inference regarding the spillover hazard of zoonotic pathogens into human populations. Here, we synthesised data from 127 rodent trapping studies conducted in 14 West African countries between 1964 and 2022. We combined occurrence data with pathogen screening results to produce a dataset containing detection/non-detection data for 65,628 individual small mammals identified to the species level from at least 1,611 trapping sites. We also included 32 microorganisms, identified to the species or genus levels, that are known or potential pathogens. The dataset is formatted to Darwin Core Standard with associated metadata. This dataset can mitigate spatial and taxonomic biases of current databases, improving understanding of rodent-associated zoonotic pathogen spillover across West Africa.

In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species.