GigaByte (Hong Kong, China)最新文献

The DNA molecule is a promising next-generation data storage medium. Recently, it has been theoretically proposed that non-natural or modified bases can serve as extra molecular letters to increase the information density. However, this strategy is challenging due to the difficulty in synthesizing non-natural DNA sequences and their complex structure. Here, we described a practical DNA data storage transcoding scheme named R+ based on an expanded molecular alphabet that introduces 5-methylcytosine (5mC). We demonstrated its experimental validation by encoding one representative file into several 1.3∼1.6 kbps in vitro DNA fragments for nanopore sequencing. Our results show an average data recovery rate of 98.97% and 86.91% with and without reference, respectively. Our work validates the practicability of 5mC in DNA storage systems, with a potentially wide range of applications.

Availability and implementation: R+ is implemented in Python and the code is available under a MIT license at https://github.com/Incpink-Liu/DNA-storage-R_plus.

We present the Biodepot Launcher, a desktop application that facilitates installation, management and deployment of bioinformatics workflows using the Biodepot-workflow-builder (Bwb). With the new app, Bwb can be started by double-clicking on an icon, eliminating the need for typing cryptic start up commands into the terminal. This creates an end-to-end graphical and easy-to-use interface to manage and launch containerized workflows on the local computer or cloud instances. Biodepot Launcher is written in React and Javascript, and uses the node.js framework Neutralinojs and web browser routines to allow the application to execute on Linux, Windows and Mac desktop environments.

The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with 94.5× coverage, the genome of the Sapphire Devil, Chrysiptera cyanea, was assembled and annotated. The final assembly comprises 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%, and 28,173 genes. Comparative analyses with chromosome-scale assemblies of related species identified contig-chromosome correspondences. This genome will be useful as a comparison to study specific adaptations linked to the symbiotic life of closely related anemonefish. Furthermore, C. cyanea is found in most tropical coastal areas of the Indo-West Pacific and could become a model for environmental monitoring. This work will expand coral reef research efforts, highlighting the power of long-read assemblies to retrieve high quality genomes.

Cardamine chenopodiifolia is an amphicarpic plant in the Brassicaceae family. Plants develop two fruit types, one above and another below ground. This rare trait is associated with octoploidy in C. chenopodiifolia. The absence of genomic data for C. chenopodiifolia currently limits our understanding of the development and evolution of amphicarpy. Here, we produced a chromosome-scale assembly of the C. chenopodiifolia genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mb and an N50 of 18.8 Mb. Genome completeness was estimated at 99.8%. We observed structural variation among homeologous chromosomes, suggesting that C. chenopodiifolia originated via allopolyploidy, and phased the octoploid genome into four sub-genomes using orthogroup trees. This fully phased, chromosome-level genome assembly is an important resource to help investigate amphicarpy in C. chenopodiifolia and the origin of trait novelties by allopolyploidy.

The expanding availability of large-scale genomic data and the growing interest in uncovering gene-disease associations call for efficient tools to visualize and evaluate gene expression and genetic variation data. Here, we developed a comprehensive pipeline that was implemented as an interactive Shiny application and a standalone desktop application. NeuroVar is a tool for visualizing genetic variation (single nucleotide polymorphisms and insertions/deletions) and gene expression profiles of biomarkers of neurological diseases. Data collection involved filtering biomarkers related to multiple neurological diseases from the ClinGen database. NeuroVar provides a user-friendly graphical user interface to visualize genomic data and is freely accessible on the project's GitHub repository (https://github.com/omicscodeathon/neurovar).

The Baikal seal (Pusa sibirica) is a freshwater seal endemic to Lake Baikal, where it became landlocked million years ago. It is an abundant species of least concern despite the limited habitat. Research on its genetic diversity had only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome was published. Here, we report the genome sequences of six Baikal seals, and one individual of the Caspian, ringed, and harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are similar to previously reported genomes. Also, the novel genome data of the other species contributed to a more complete phocid seal phylogeny based on whole-genome data. Despite the isolation of the land-locked Baikal seal, its genetic diversity is comparable to that of other seal species. Future targeted genome studies need to explore the genomic diversity throughout their distribution.

The vast majority of gecko species are capable of tail regeneration, but singular geckos of Correlophus, Uroplatus, and Nephrurus genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (Correlophus ciliatus) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make C. ciliatus particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of C. ciliatus with a total size of 1.65 Gb, 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Our assembly of the crested gecko genome provides a valuable resource for future comparative genomic studies between non-regenerative and regenerative geckos and other squamate reptiles.

Findings: We report genome sequencing, assembly, and annotation for the crested gecko, Correlophus ciliatus.

The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic-programming matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method is known to be highly time-consuming. The proposed TSTA algorithm leverages both vector-level and thread-level parallelism to accelerate pairwise and multiple sequence alignments.

Availability and implementation: Source codes are available at https://github.com/bxskdh/TSTA.

Underutilized sheep and goat breeds can adapt to challenging environments due to their genetics. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats. Here, we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata, mainly from SNP chip arrays on global small ruminant populations, with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via File Transfer Protocol and interact with the metadata through a web interface or using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database.

Availability and implementation: The code is available as open-source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database.

Global changes in cannabis legislation after decades of stringent regulation and heightened demand for its industrial and medicinal applications have spurred recent genetic and genomics research. An international research community emerged and identified the need for a web portal to host cannabis-specific datasets that seamlessly integrates multiple data sources and serves omics-type analyses, fostering information sharing. The Tripal platform was used to host public genome assemblies, gene annotations, quantitative trait loci and genetic maps, gene and protein expression data, metabolic profiles and their sample attributes. Single nucleotide polymorphisms were called using public resequencing datasets on three genomes. Additional applications, such as SNP-Seek and MapManJS, were embedded into Tripal. A multi-omics data integration web-service Application Programming Interface (API), developed on top of existing Tripal modules, returns generic tables of samples, properties and values. Use cases demonstrate the API's utility for various omics analyses, enabling researchers to perform multi-omics analyses efficiently.

Availability and implementation: The web portal can be accessed at www.icgrc.info.