GigaByte (Hong Kong, China)最新文献_第9页

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

A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica). 蜜脆 "苹果（Malus domestica）的分阶段染色体级基因组。

GigaByte (Hong Kong, China) Pub Date : 2022-09-19 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.69

Awais Khan, Sarah B Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas

{"title":"A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica).","authors":"Awais Khan, Sarah B Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas","doi":"10.46471/gigabyte.69","DOIUrl":"10.46471/gigabyte.69","url":null,"abstract":"The apple cultivar 'Honeycrisp' has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of 'Honeycrisp' apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most 'Honeycrisp' genes are assigned into orthogroups shared with other genomes, with 121 'Honeycrisp'-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte69"},"PeriodicalIF":0.0,"publicationDate":"2022-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336295","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:PhysicCell的药代动力学和药效学模块

GigaByte (Hong Kong, China) Pub Date : 2022-09-15 DOI: 10.1101/2022.09.12.507681

Daniel R. Bergman, Lauren Marazzi, Mukti Chowkwale, Deepa Maheshvare M, Supriya Bidanta, T. Mapder, Jialun Li

引用次数: 3

Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii. 寄生蜂 Encarsia suzannae（一种可操纵遗传共生体 Cardinium hertigii 的宿主）基于性别的全新转录组组装。

GigaByte (Hong Kong, China) Pub Date : 2022-09-02 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.68

Dylan L Schultz, Evelyne Selberherr, Corinne M Stouthamer, Matthew R Doremus, Suzanne E Kelly, Martha S Hunter, Stephan Schmitz-Esser

{"title":"Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii.","authors":"Dylan L Schultz, Evelyne Selberherr, Corinne M Stouthamer, Matthew R Doremus, Suzanne E Kelly, Martha S Hunter, Stephan Schmitz-Esser","doi":"10.46471/gigabyte.68","DOIUrl":"10.46471/gigabyte.68","url":null,"abstract":"Parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or the field. They are also hosts of the bacterial endosymbiont Cardinium hertigii, which can cause reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility (the last is mainly studied in Encarsia suzannae). Despite their biological and economic importance, there are no published Encarsia genomes and only one public transcriptome. Here, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. Our male and female transcriptomes will be valuable tools to better understand the biology of Encarsia and their evolutionary relatives, particularly in studies involving insects of only one sex.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte68"},"PeriodicalIF":0.0,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10772806","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

The genome of a giant (trevally): Caranx ignobilis. 巨鲹的基因组：Caranx ignobilis.

GigaByte (Hong Kong, China) Pub Date : 2022-08-30 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.67

Brandon D Pickett, Jessica R Glass, Timothy P Johnson, Perry G Ridge, John S K Kauwe

引用次数: 0

First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar 'Emma White'. 首次对突变的铁皮石斛杂交栽培品种'Emma White'进行全新全基因组测序和组装。

GigaByte (Hong Kong, China) Pub Date : 2022-08-09 eCollection Date: 2022-01-01 DOI: 10.46471/gigabyte.66

Rubina Sherpa, Ramgopal Devadas, Penna Suprasanna, Sadashiv Narayan Bolbhat, Tukaram Dayaram Nikam

{"title":"First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar 'Emma White'.","authors":"Rubina Sherpa, Ramgopal Devadas, Penna Suprasanna, Sadashiv Narayan Bolbhat, Tukaram Dayaram Nikam","doi":"10.46471/gigabyte.66","DOIUrl":"10.46471/gigabyte.66","url":null,"abstract":"The Dendrobium hybrid cultivar 'Emma White' is an ornamental, successfully commercialised orchid. We used a gamma ray-induced early flowering mutant and the Illumina HiSeqX10 sequencing platform to generate the first draft de novo whole genome sequence and assembly. The draft sequence was 678,650,699 bp in length, comprising 447,500 contigs with an N50 of 1423 and 33.48% GC content. Comparing 95,529 predicted genes against the Uniprot database revealed 60,741 potential genes governing molecular functions, biological processes and cellular components. We identified 216,232 simple sequence repeats and 138,856 microsatellite markers. Chromosome-level genome assembly of Dendrobium huoshanense was used to RagTag-scaffold available contigs of the mutant, revealing a total length of 687,254,899 bp with an N50 of 2096. The longest final contiguous length was 18,000,059 bp from 30,571 bp. BUSCO genome completeness was 93.6%. This study is valuable for investigating the mechanisms of mutation, and developing Dendrobium hybrid cultivars using mutation breeding.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte66"},"PeriodicalIF":0.0,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336293","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