GigaByte (Hong Kong, China)最新文献

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids.

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":"https://doi.org/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.

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.

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.

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

PhysiMeSS - a new physiCell addon for extracellular matrix modelling. PhysiMeSS - 用于细胞外基质建模的全新 physiCell 附加组件。

GigaByte (Hong Kong, China) Pub Date : 2024-10-16 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.136

Vincent Noël, Marco Ruscone, Robyn Shuttleworth, Cicely K Macnamara

引用次数: 0

NucBalancer: streamlining barcode sequence selection for optimal sample pooling for sequencing. NucBalancer：简化条形码序列选择，优化测序样本池。

GigaByte (Hong Kong, China) Pub Date : 2024-10-11 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.138

Saurabh Gupta, Ankur Sharma

{"title":"NucBalancer: streamlining barcode sequence selection for optimal sample pooling for sequencing.","authors":"Saurabh Gupta, Ankur Sharma","doi":"10.46471/gigabyte.138","DOIUrl":"10.46471/gigabyte.138","url":null,"abstract":"Recent advancements in next-generation sequencing (NGS) technologies have brought to the forefront the necessity for versatile, cost-effective tools capable of adapting to a rapidly evolving landscape. The emergence of numerous new sequencing platforms, each with unique sample preparation and sequencing requirements, underscores the importance of efficient barcode balancing for successful pooling and accurate demultiplexing of samples. Recently launched new sequencing systems claiming better affordability comparable to more established platforms further exemplifies these challenges, especially when libraries originally prepared for one platform need conversion to another. In response to this dynamic environment, we introduce NucBalancer, a Shiny app developed for the optimal selection of barcode sequences. While initially tailored to meet the nucleotide, composition challenges specific to G400 and T7 series sequencers, NucBalancer's utility significantly broadens to accommodate the varied demands of these new sequencing technologies. Its application is particularly crucial in single-cell genomics, enabling the adaptation of libraries, such as those prepared for 10x technology, to various sequencers including G400 and T7 series sequencers. NucBalancer efficiently balances nucleotide composition and sample concentrations, reducing biases and enhancing the reliability of NGS data across platforms. Its adaptability makes it invaluable for addressing sequencing challenges, ensuring effective barcode balancing for sample pooling on any platform.Availability and implementation: NucBalancer is implemented in R and is available at https://github.com/ersgupta/NucBalancer. Additionally, a shiny interface is available at https://ersgupta.shinyapps.io/NucBalancer/.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte138"},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482350","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