GigaByte (Hong Kong, China)最新文献_第8页

Improvements to the Gulf pipefish Syngnathus scovelli genome. 对墨西哥湾河豚Syngnathus scovelli基因组的改进。

GigaByte (Hong Kong, China) Pub Date : 2023-02-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.76

Balan Ramesh, Clay M Small, Hope Healey, Bernadette Johnson, Elyse Barker, Mark Currey, Susan Bassham, Megean Myers, William A Cresko, Adam Gregory Jones

{"title":"Improvements to the Gulf pipefish Syngnathus scovelli genome.","authors":"Balan Ramesh, Clay M Small, Hope Healey, Bernadette Johnson, Elyse Barker, Mark Currey, Susan Bassham, Megean Myers, William A Cresko, Adam Gregory Jones","doi":"10.46471/gigabyte.76","DOIUrl":"10.46471/gigabyte.76","url":null,"abstract":"The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli..","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte76"},"PeriodicalIF":0.0,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9561070","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

PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects PhysiCOOL:modeLing项目模型校准和优化的通用框架

GigaByte (Hong Kong, China) Pub Date : 2023-02-13 DOI: 10.1101/2022.11.17.516671

Inês G. Gonçalves, D. Hormuth, Sandhya Prabhakaran, C. Phillips, J. García-Aznar

引用次数: 1

Nanopore-based enrichment of antimicrobial resistance genes - a case-based study. 基于纳米孔的抗菌药耐药性基因富集--一项基于案例的研究。

GigaByte (Hong Kong, China) Pub Date : 2023-01-25 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.75

Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias W Pletz, Christian Brandt

{"title":"Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.","authors":"Adrian Viehweger, Mike Marquet, Martin Hölzer, Nadine Dietze, Mathias W Pletz, Christian Brandt","doi":"10.46471/gigabyte.75","DOIUrl":"10.46471/gigabyte.75","url":null,"abstract":"Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment (\"adaptive\") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compared its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then modelled the influence of several variables on the enrichment results and predicted the large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we showed how all relevant resistance genes are detected using adaptive sequencing on a miniature (\"Flongle\") flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte75"},"PeriodicalIF":0.0,"publicationDate":"2023-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9534172","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

Improvements to the Gulf pipefish Syngnathus scovelli genome 海湾管鱼(Syngnathus scovelli)基因组的改良

GigaByte (Hong Kong, China) Pub Date : 2023-01-20 DOI: 10.1101/2023.01.23.525209

B. Ramesh, CM Small, H. Healey, B. Johnson, E. Barker, M. Currey, S. Bassham, M. Myers, WA Cresko, Ag Jones

{"title":"Improvements to the Gulf pipefish Syngnathus scovelli genome","authors":"B. Ramesh, CM Small, H. Healey, B. Johnson, E. Barker, M. Currey, S. Bassham, M. Myers, WA Cresko, Ag Jones","doi":"10.1101/2023.01.23.525209","DOIUrl":"https://doi.org/10.1101/2023.01.23.525209","url":null,"abstract":"The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of the S. scovelli genome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set for S. scovelli. By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBI’s eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involving S. scovelli.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42096485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Distribution of mosquitoes (Diptera: Culicidae) in Thailand: a dataset. 泰国蚊类分布(双翅目:库蚊科):a dataset。

GigaByte (Hong Kong, China) Pub Date : 2023-01-01 DOI: 10.46471/gigabyte.90

Chutipong Sukkanon, Wannapa Suwonkerd, Kanutcharee Thanispong, Manop Saeung, Pairpailin Jhaiaun, Suntorn Pimnon, Kanaphot Thongkhao, Sylvie Manguin, Theeraphap Chareonviriyaphap

{"title":"Distribution of mosquitoes (Diptera: Culicidae) in Thailand: a dataset.","authors":"Chutipong Sukkanon, Wannapa Suwonkerd, Kanutcharee Thanispong, Manop Saeung, Pairpailin Jhaiaun, Suntorn Pimnon, Kanaphot Thongkhao, Sylvie Manguin, Theeraphap Chareonviriyaphap","doi":"10.46471/gigabyte.90","DOIUrl":"https://doi.org/10.46471/gigabyte.90","url":null,"abstract":"Mosquitoes play a crucial role as primary vectors for various infectious diseases in Thailand. Therefore, accurate distribution information is vital for effectively combating and better controlling mosquito-borne diseases. Here, we present a curated dataset of the mosquito distribution in Thailand comprising 12,278 records of at least 117 mosquito species (Diptera: Culicidae). The main genera included in the dataset are Aedes, Anopheles, Armigeres, Culex, and Mansonia. From 2007 to 2023, data were collected through routine mosquito surveillance and research projects from 1,725 locations across 66 (out of 77) Thai provinces. The majority of the data were extracted from a Thai database of the Thailand Malaria Elimination Program. To facilitate broader access to mosquito-related data and support further exploration of the Thai mosquito fauna, the data were translated into English. Our dataset has been published in the Global Biodiversity Information Facility, making it available for researchers worldwide.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte90"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10270936","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

HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols. HTGQC 和 shinyHTGQC：用于 HTG EDGE-seq 协议质量控制的 R 软件包和 shinyR 应用程序。

GigaByte (Hong Kong, China) Pub Date : 2022-12-02 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.74

Lodovico Terzi di Bergamo, Francesca Guidetti, Davide Rossi, Francesco Bertoni, Luciano Cascione

{"title":"HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols.","authors":"Lodovico Terzi di Bergamo, Francesca Guidetti, Davide Rossi, Francesco Bertoni, Luciano Cascione","doi":"10.46471/gigabyte.74","DOIUrl":"10.46471/gigabyte.74","url":null,"abstract":"Extraction-free HTG EdgeSeq protocols are used to profile sets of genes and measure their expression. Thus, these protocols are frequently used to characterise tumours and their microenvironments. However, although positive and control genes are provided, little indication is given concerning the assessment of the technical success of each sample within the sequencing run. We developed HTGQC, an R package for the quality control of HTG EdgeSeq protocols. Additionally, shinyHTGQC is a shiny application for users without computing knowledge, providing an easy-to-use interface for data quality control and visualisation. Quality checks can be performed on the raw sequencing outputs, and samples are flagged as FAIL or ALERT based on the expression levels of the positive and negative control genes.Availability & implementation: The code is freely available at https://github.com/LodovicoTerzi/HTGQC (R package) and https://lodovico.shinyapps.io/shinyHTGQC/ (shiny application), including test datasets.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte74"},"PeriodicalIF":0.0,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9166564","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

PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell. PhysiPKPD：PhysiCell 的药代动力学和药效学模块。

GigaByte (Hong Kong, China) Pub Date : 2022-11-30 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.72

Daniel Bergman, Lauren Marazzi, Mukti Chowkwale, Deepa Maheshvare M, Supriya Bidanta, Tarunendu Mapder, Jialun Li

引用次数: 0

The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae). Diadematoida, Diadematidae）的首个完整线粒体基因组。

GigaByte (Hong Kong, China) Pub Date : 2022-11-22 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.73

Audrey J Majeske, Alejandro J Mercado Capote, Aleksey Komissarov, Anna Bogdanova, Nikolaos V Schizas, Stephanie O Castro Márquez, Kenneth Hilkert, Walter Wolfsberger, Tarás K Oleksyk

引用次数: 0

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. 发热树（Cinchona pubescens Vahl）高度连续的支架级核基因组组装，是茜草科研究的新资源。

GigaByte (Hong Kong, China) Pub Date : 2022-10-06 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.71

Nataly Allasi Canales, Oscar A Pérez-Escobar, Robyn F Powell, Mats Töpel, Catherine Kidner, Mark Nesbitt, Carla Maldonado, Christopher J Barnes, Nina Rønsted, Natalia A S Przelomska, Ilia J Leitch, Alexandre Antonelli

{"title":"A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research.","authors":"Nataly Allasi Canales, Oscar A Pérez-Escobar, Robyn F Powell, Mats Töpel, Catherine Kidner, Mark Nesbitt, Carla Maldonado, Christopher J Barnes, Nina Rønsted, Natalia A S Przelomska, Ilia J Leitch, Alexandre Antonelli","doi":"10.46471/gigabyte.71","DOIUrl":"10.46471/gigabyte.71","url":null,"abstract":"The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82% of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte71"},"PeriodicalIF":0.0,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9164443","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

svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data. svaRetro 和 svaNUMT：用于注释基因组测序数据中线粒体 DNA 的逆转录转录本和核整合的模块化软件包。

GigaByte (Hong Kong, China) Pub Date : 2022-10-05 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.70

Ruining Dong, Daniel Cameron, Justin Bedo, Anthony T Papenfuss

{"title":"svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data.","authors":"Ruining Dong, Daniel Cameron, Justin Bedo, Anthony T Papenfuss","doi":"10.46471/gigabyte.70","DOIUrl":"10.46471/gigabyte.70","url":null,"abstract":"Nuclear integration of mitochondrial genomes and retrocopied transcript insertion are biologically important but often-overlooked aspects of structural variant (SV) annotation. While tools for their detection exist, these typically rely on reanalysis of primary data using specialised detectors rather than leveraging calls from general purpose structural variant callers. Such reanalysis potentially leads to additional computational expense and does not take advantage of advances in general purpose structural variant calling. Here, we present svaRetro and svaNUMT; R packages that provide functions for annotating novel genomic events, such as nonreference retrocopied transcripts and nuclear integration of mitochondrial DNA. The packages were developed to work within the Bioconductor framework. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets, and annotate processed transcripts in a public structural variant database. svaRetro and svaNUMT provide modular, SV-caller agnostic tools for downstream annotation of structural variant calls.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte70"},"PeriodicalIF":0.0,"publicationDate":"2022-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10831320","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