GigaByte (Hong Kong, China)最新文献

A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine.

GigaByte (Hong Kong, China) Pub Date : 2025-01-24 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.147

Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang, Zhi Ping

{"title":"A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine.","authors":"Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang, Zhi Ping","doi":"10.46471/gigabyte.147","DOIUrl":"10.46471/gigabyte.147","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte147"},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11791762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biodepot Launcher: an app to install, manage and launch bioinformatics workflows.

GigaByte (Hong Kong, China) Pub Date : 2025-01-14 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.146

Ling-Hong Hung, Thomas J Dahlstrom, Johnalbert Garnica, Emmanuel Munoz, Robert Schmitz, Ka Yee Yeung

引用次数: 0

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids. 蓝宝石雀鲷Chrysiptera cyanea的基因组：支持进一步研究Pomacentrids进化的新资源。

GigaByte (Hong Kong, China) Pub Date : 2024-12-31 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.144

Emma Gairin, Saori Miura, Hiroki Takamiyagi, Marcela Herrera, Vincent Laudet

{"title":"The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids.","authors":"Emma Gairin, Saori Miura, Hiroki Takamiyagi, Marcela Herrera, Vincent Laudet","doi":"10.46471/gigabyte.144","DOIUrl":"10.46471/gigabyte.144","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte144"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11711634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polyploid genome assembly of Cardamine chenopodiifolia. 小豆蔻的多倍体基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-12-23 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.145

Aurélia Emonet, Mohamed Awad, Nikita Tikhomirov, Maria Vasilarou, Miguel Pérez-Antón, Xiangchao Gan, Polina Yu Novikova, Angela Hay

{"title":"Polyploid genome assembly of Cardamine chenopodiifolia.","authors":"Aurélia Emonet, Mohamed Awad, Nikita Tikhomirov, Maria Vasilarou, Miguel Pérez-Antón, Xiangchao Gan, Polina Yu Novikova, Angela Hay","doi":"10.46471/gigabyte.145","DOIUrl":"10.46471/gigabyte.145","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte145"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NeuroVar: an open-source tool for the visualization of gene expression and variation data for biomarkers of neurological diseases. NeuroVar：一个用于神经系统疾病生物标志物的基因表达和变异数据可视化的开源工具。

GigaByte (Hong Kong, China) Pub Date : 2024-11-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.143

Hiba Ben Aribi, Najla Abassi, Olaitan I Awe

引用次数: 0

Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny. 对贝加尔湖海豹和其他海豹进行全基因组重测序，以了解它们的遗传多样性、人口统计学历史和系统发育。

GigaByte (Hong Kong, China) Pub Date : 2024-11-20 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.142

Marcel Nebenführ, Ulfur Arnason, Axel Janke

引用次数: 0

Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration. 冠壁虎（Correlophus ciliatus）染色体水平的基因组组装和注释，冠壁虎是一种无法进行尾部再生的蜥蜴。

GigaByte (Hong Kong, China) Pub Date : 2024-11-06 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.140

Marc A Gumangan, Zheyu Pan, Thomas P Lozito

{"title":"Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration.","authors":"Marc A Gumangan, Zheyu Pan, Thomas P Lozito","doi":"10.46471/gigabyte.140","DOIUrl":"10.46471/gigabyte.140","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte140"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142634020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method. TSTA：基于线程和 SIMD 的梯形配对/多序列比对方法。

GigaByte (Hong Kong, China) Pub Date : 2024-11-05 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.141

Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan

引用次数: 0

SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. SMARTER 数据库：整合绵羊和山羊品种 SNP 阵列数据集的工具。

GigaByte (Hong Kong, China) Pub Date : 2024-10-21 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.139

Paolo Cozzi, Arianna Manunza, Johanna Ramirez-Diaz, Valentina Tsartsianidou, Konstantinos Gkagkavouzis, Pablo Peraza, Anna Maria Johansson, Juan José Arranz, Fernando Freire, Szilvia Kusza, Filippo Biscarini, Lucy Peters, Gwenola Tosser-Klopp, Gabriel Ciappesoni, Alexandros Triantafyllidis, Rachel Rupp, Bertrand Servin, Alessandra Stella

{"title":"SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds.","authors":"Paolo Cozzi, Arianna Manunza, Johanna Ramirez-Diaz, Valentina Tsartsianidou, Konstantinos Gkagkavouzis, Pablo Peraza, Anna Maria Johansson, Juan José Arranz, Fernando Freire, Szilvia Kusza, Filippo Biscarini, Lucy Peters, Gwenola Tosser-Klopp, Gabriel Ciappesoni, Alexandros Triantafyllidis, Rachel Rupp, Bertrand Servin, Alessandra Stella","doi":"10.46471/gigabyte.139","DOIUrl":"https://doi.org/10.46471/gigabyte.139","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte139"},"PeriodicalIF":0.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research. 建立社区驱动的生物信息学平台，促进大麻多组学研究。

GigaByte (Hong Kong, China) Pub Date : 2024-10-18 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.137

Locedie Mansueto, Tobias Kretzschmar, Ramil Mauleon, Graham J King

{"title":"Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research.","authors":"Locedie Mansueto, Tobias Kretzschmar, Ramil Mauleon, Graham J King","doi":"10.46471/gigabyte.137","DOIUrl":"10.46471/gigabyte.137","url":null,"abstract":"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.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte137"},"PeriodicalIF":0.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0