GigaByte (Hong Kong, China)最新文献

{"title":"A phased, chromosome-scale genome of 'Honeycrisp' apple (<i>Malus domestica</i>).","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":"<p><p>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.</p>","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}

{"title":"PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell","authors":"Daniel R. Bergman, Lauren Marazzi, Mukti Chowkwale, Deepa Maheshvare M, Supriya Bidanta, T. Mapder, Jialun Li","doi":"10.1101/2022.09.12.507681","DOIUrl":"https://doi.org/10.1101/2022.09.12.507681","url":null,"abstract":"Pharmacokinetics and pharmacodynamics are key considerations in any study of molecular therapies. It is thus imperative to factor their effects in to any in silico model of biological tissue involving such therapies. Furthermore, creation of a standardized and flexible framework will benefit the community by increasing access to such modules and enhancing their communicability. PhysiCell is an open source physics-based cell simulator, i.e. a platform for modeling biological tissue, that is quickly being adopted and utilized by the mathematical biology community. We present here PhysiPKPD, an open source PhysiCell-based package that allows users to include PKPD in PhysiCell models. Availability & Implementation The source code for PhysiPKPD is located here: https://github.com/drbergman/PhysiPKPD.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46267613","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}

{"title":"Sex-based <i>de novo</i> transcriptome assemblies of the parasitoid wasp <i>Encarsia suzannae</i>, a host of the manipulative heritable symbiont <i>Cardinium hertigii</i>.","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":"<p><p>Parasitoid wasps in the genus <i>Encarsia</i> 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 <i>Cardinium hertigii</i>, which can cause reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility (the last is mainly studied in <i>Encarsia suzannae</i>). Despite their biological and economic importance, there are no published <i>Encarsia</i> 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 <i>de novo</i> transcriptome assemblies for both female and male <i>E. suzannae</i> 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 <i>Encarsia</i> and their evolutionary relatives, particularly in studies involving insects of only one sex.</p>","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}

{"title":"The genome of a giant (trevally): <i>Caranx ignobilis</i>.","authors":"Brandon D Pickett, Jessica R Glass, Timothy P Johnson, Perry G Ridge, John S K Kauwe","doi":"10.46471/gigabyte.67","DOIUrl":"10.46471/gigabyte.67","url":null,"abstract":"<p><p><i>Caranx ignobilis</i>, commonly known as giant kingfish or giant trevally, is a large, reef-associated apex predator. It is a prized sportfish, targeted throughout its tropical and subtropical range in the Indian and Pacific Oceans. It also gained significant interest in aquaculture due to its unusual freshwater tolerance. Here, we present a draft assembly of the estimated 625.92 Mbp nuclear genome of a <i>C. ignobilis</i> individual from Hawaiian waters, which host a genetically distinct population. Our 97.4% BUSCO-complete assembly has a contig NG50 of 7.3 Mbp and a scaffold NG50 of 46.3 Mbp. Twenty-five of the 203 scaffolds contain 90% of the genome. We also present noisy, long-read DNA, Hi-C, and RNA-seq datasets, the latter containing eight distinct tissues and can help with annotations and studies of freshwater tolerance. Our genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of kingfishes and other carangoid fishes.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte67"},"PeriodicalIF":0.0,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10831316","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}

{"title":"First <i>De novo</i> whole genome sequencing and assembly of mutant <i>Dendrobium</i> 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":"<p><p>The <i>Dendrobium</i> 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 <i>de novo</i> 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 <i>Dendrobium huoshanense</i> 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 <i>Dendrobium</i> hybrid cultivars using mutation breeding.</p>","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}

{"title":"The genome of the mustard hill coral, <i>Porites astreoides</i>.","authors":"Kevin H Wong, Hollie M Putnam","doi":"10.46471/gigabyte.65","DOIUrl":"10.46471/gigabyte.65","url":null,"abstract":"<p><p>Anthropogenic effects have contributed to substantial declines in coral reefs worldwide. However, some corals are more resilient to environmental changes and have increased in relative abundance, thus these species may shape future reef communities. Here, we provide the first draft reference genome for the mustard hill coral, <i>Porites astreoides</i>, collected in Bermuda. DNA was sequenced via Pacific Biosciences (PacBio) HiFi long-read technology. PacBio read assembly with FALCON UnZip resulted in a 678-Mbp assembly with 3051 contigs with an N50 of 412,256 and the BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An <i>ab initio</i> transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% versus the metazoan gene set. Functional annotation was completed for 86.6% of proteins. These data are valuable resources for improving biological knowledge of <i>P. astreoides</i>, facilitating comparative genomics for corals, and supporting evidence-based restoration and human-assisted evolution of corals.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte65"},"PeriodicalIF":0.0,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10773250","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}

{"title":"Long-read HiFi sequencing correctly assembles repetitive <i>heavy fibroin</i> silk genes in new moth and caddisfly genomes.","authors":"Akito Y Kawahara, Caroline G Storer, Amanda Markee, Jacqueline Heckenhauer, Ashlyn Powell, David Plotkin, Scott Hotaling, Timothy P Cleland, Rebecca B Dikow, Torsten Dikow, Ryoichi B Kuranishi, Rebeccah Messcher, Steffen U Pauls, Russell J Stewart, Koji Tojo, Paul B Frandsen","doi":"10.46471/gigabyte.64","DOIUrl":"10.46471/gigabyte.64","url":null,"abstract":"<p><p>Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (<i>Plodia interpunctella</i>) and genomic sequences for the caddisfly <i>Eubasilissa regina</i>. Both genomes were highly contiguous (N50  = 9.7 Mbp/32.4 Mbp, L50  = 13/11) and complete (BUSCO complete  = 99.3%/95.2%), with complete and contiguous recovery of silk <i>heavy fibroin</i> gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte64"},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9693786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336291","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}

{"title":"A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340.","authors":"Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang","doi":"10.46471/gigabyte.63","DOIUrl":"10.46471/gigabyte.63","url":null,"abstract":"<p><strong>Background: </strong>Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red Cob Group with several desirable characteristics. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by using long HiFi reads, short reads, and Hi-C. The final assembly of the Dan340 genome was 2348.72 Mb, which was anchored to 10 chromosomes. Repeat sequences accounted for 73.40% of the genome and 39,733 protein-coding genes were annotated. Comparative genomic analysis between Dan340 and other maize lines identified that 1806 genes from 359 gene families were specific to Dan340.</p><p><strong>Conclusions: </strong>Our genome assembly and annotation provide a valuable resource for improving maize breeding and further understanding the intraspecific genome diversity in maize.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte63"},"PeriodicalIF":0.0,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9694154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9336292","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}

{"title":"Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes","authors":"A. Kawahara, Caroline G. Storer, A. Markee, J. Heckenhauer, A. Powell, David M. Plotkin, S. Hotaling, T. Cleland, Rebecca B. Dikow, Torsten Dikow, Ryoichi B. Kuranishi, Rebeccah L. Messcher, S. Pauls, R. Stewart, K. Tojo, P. Frandsen","doi":"10.1101/2022.06.01.494423","DOIUrl":"https://doi.org/10.1101/2022.06.01.494423","url":null,"abstract":"Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly, Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47676720","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}

{"title":"AIMSurv: First pan-European harmonized surveillance of <i>Aedes</i> invasive mosquito species of relevance for human vector-borne diseases.","authors":"Miguel Ángel Miranda, Carlos Barceló, Daniele Arnoldi, Xenia Augsten, Karin Bakran-Lebl, George Balatsos, Mikel Bengoa, Philippe Bindler, Kristina Boršová, Maria Bourquia, Daniel Bravo-Barriga, Viktória Čabanová, Beniamino Caputo, Maria Christou, Sarah Delacour, Roger Eritja, Ouafaa Fassi-Fihri, Martina Ferraguti, Eleonora Flacio, Eva Frontera, Hans-Peter Fuehrer, Ana L García-Pérez, Pantelis Georgiades, Sandra Gewehr, Fátima Goiri, Mikel Alexander González, Martin Gschwind, Rafael Gutiérrez-López, Cintia Horváth, Adolfo Ibáñez-Justicia, Viola Jani, Përparim Kadriaj, Katja Kalan, Mihaela Kavran, Ana Klobucar, Kornélia Kurucz, Javier Lucientes, Renke Lühken, Sergio Magallanes, Giovanni Marini, Angeliki F Martinou, Alice Michelutti, Andrei Daniel Mihalca, Tomás Montalvo, Fabrizio Montarsi, Spiros Mourelatos, Nesade Muja-Bajraktari, Pie Müller, Gregoris Notarides, Hugo Costa Osório, José A Oteo, Kerem Oter, Igor Pajović, John R B Palmer, Suncica Petrinic, Cristian Răileanu, Christian Ries, Elton Rogozi, Ignacio Ruiz-Arrondo, Isis Sanpera-Calbet, Nebojša Sekulić, Kivanc Sevim, Kurtesh Sherifi, Cornelia Silaghi, Manuel Silva, Nikolina Sokolovska, Zoltán Soltész, Tatiana Sulesco, Jana Šušnjar, Steffanie Teekema, Andrea Valsecchi, Marlen Ines Vasquez, Enkelejda Velo, Antonios Michaelakis, William Wint, Dušan Petrić, Francis Schaffner, Alessandra Della Torre","doi":"10.46471/gigabyte.57","DOIUrl":"10.46471/gigabyte.57","url":null,"abstract":"<p><p>Human and animal vector-borne diseases, particularly mosquito-borne diseases, are emerging or re-emerging worldwide. Six <i>Aedes</i> invasive mosquito (AIM) species were introduced to Europe since the 1970s: <i>Aedes aegypti</i>, <i>Ae. albopictus</i>, <i>Ae. japonicus</i>, <i>Ae. koreicus</i>, <i>Ae. atropalpus</i> and <i>Ae. triseriatus</i>. Here, we report the results of AIMSurv2020, the first pan-European surveillance effort for AIMs. Implemented by 42 volunteer teams from 24 countries. And presented in the form of a dataset named \"AIMSurv Aedes Invasive Mosquito species harmonized surveillance in Europe. AIM-COST Action. Project ID: CA17108\". AIMSurv2020 harmonizes field surveillance methodologies for sampling different AIMs life stages, frequency and minimum length of sampling period, and data reporting. Data include minimum requirements for sample types and recommended requirements for those teams with more resources. Data are published as a Darwin Core archive in the Global Biodiversity Information Facility- Spain, comprising a core file with 19,130 records (EventID) and an occurrences file with 19,743 records (OccurrenceID). AIM species recorded in AIMSurv2020 were <i>Ae. albopictus</i>, <i>Ae. japonicus</i> and <i>Ae. koreicus</i>, as well as native mosquito species.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2022 ","pages":"gigabyte57"},"PeriodicalIF":0.0,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9321529","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}