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1.
Nucleic Acids Res ; 52(D1): D891-D899, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37953337

RESUMEN

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.


Asunto(s)
Bases de Datos Genéticas , Genómica , Animales , Genoma , Anotación de Secuencia Molecular , Filogenia , Programas Informáticos , Humanos
2.
Nucleic Acids Res ; 52(D1): D808-D816, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37953350

RESUMEN

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.


Asunto(s)
Biología Computacional , Eucariontes , Animales , Biología Computacional/métodos , Invertebrados , Bases de Datos Factuales
3.
Nucleic Acids Res ; 50(D1): D898-D911, 2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34718728

RESUMEN

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.


Asunto(s)
Bases de Datos Factuales , Vectores de Enfermedades/clasificación , Interacciones Huésped-Patógeno/genética , Fenotipo , Interfaz Usuario-Computador , Animales , Apicomplexa/clasificación , Apicomplexa/genética , Apicomplexa/patogenicidad , Bacterias/clasificación , Bacterias/genética , Bacterias/patogenicidad , Enfermedades Transmisibles/microbiología , Enfermedades Transmisibles/parasitología , Enfermedades Transmisibles/patología , Enfermedades Transmisibles/transmisión , Biología Computacional/métodos , Minería de Datos/métodos , Diplomonadida/clasificación , Diplomonadida/genética , Diplomonadida/patogenicidad , Hongos/clasificación , Hongos/genética , Hongos/patogenicidad , Humanos , Insectos/clasificación , Insectos/genética , Insectos/patogenicidad , Internet , Nematodos/clasificación , Nematodos/genética , Nematodos/patogenicidad , Filogenia , Virulencia , Flujo de Trabajo
4.
Nucleic Acids Res ; 50(D1): D996-D1003, 2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34791415

RESUMEN

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.


Asunto(s)
Bases de Datos Genéticas , Genómica , Internet , Programas Informáticos , Animales , Biología Computacional , Genoma Bacteriano/genética , Genoma Fúngico/genética , Genoma de Planta/genética , Plantas/clasificación , Plantas/genética , Vertebrados/clasificación , Vertebrados/genética
5.
BMC Genomics ; 24(1): 408, 2023 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-37468834

RESUMEN

BACKGROUND: The group of > 40 cryptic whitefly species called Bemisia tabaci sensu lato are amongst the world's worst agricultural pests and plant-virus vectors. Outbreaks of B. tabaci s.l. and the associated plant-virus diseases continue to contribute to global food insecurity and social instability, particularly in sub-Saharan Africa and Asia. Published B. tabaci s.l. genomes have limited use for studying African cassava B. tabaci SSA1 species, due to the high genetic divergences between them. Genomic annotations presented here were performed using the 'Ensembl gene annotation system', to ensure that comparative analyses and conclusions reflect biological differences, as opposed to arising from different methodologies underpinning transcript model identification. RESULTS: We present here six new B. tabaci s.l. genomes from Africa and Asia, and two re-annotated previously published genomes, to provide evolutionary insights into these globally distributed pests. Genome sizes ranged between 616-658 Mb and exhibited some of the highest coverage of transposable elements reported within Arthropoda. Many fewer total protein coding genes (PCG) were recovered compared to the previously published B. tabaci s.l. genomes and structural annotations generated via the uniform methodology strongly supported a repertoire of between 12.8-13.2 × 103 PCG. An integrative systematics approach incorporating phylogenomic analysis of nuclear and mitochondrial markers supported a monophyletic Aleyrodidae and the basal positioning of B. tabaci Uganda-1 to the sub-Saharan group of species. Reciprocal cross-mating data and the co-cladogenesis pattern of the primary obligate endosymbiont 'Candidatus Portiera aleyrodidarum' from 11 Bemisia genomes further supported the phylogenetic reconstruction to show that African cassava B. tabaci populations consist of just three biological species. We include comparative analyses of gene families related to detoxification, sugar metabolism, vector competency and evaluate the presence and function of horizontally transferred genes, essential for understanding the evolution and unique biology of constituent B. tabaci. s.l species. CONCLUSIONS: These genomic resources have provided new and critical insights into the genetics underlying B. tabaci s.l. biology. They also provide a rich foundation for post-genomic research, including the selection of candidate gene-targets for innovative whitefly and virus-control strategies.


Asunto(s)
Hemípteros , Virus de Plantas , Animales , Filogenia , África , Asia
6.
Nucleic Acids Res ; 48(D1): D689-D695, 2020 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-31598706

RESUMEN

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.


Asunto(s)
Biología Computacional/métodos , Bases de Datos Genéticas , Variación Genética , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Algoritmos , Animales , Caenorhabditis elegans/genética , Genómica , Internet , Anotación de Secuencia Molecular , Fenotipo , Plantas/genética , Valores de Referencia , Programas Informáticos , Interfaz Usuario-Computador
7.
BMC Biol ; 19(1): 41, 2021 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-33750380

RESUMEN

BACKGROUND: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. RESULTS: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. CONCLUSIONS: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.


Asunto(s)
Genoma de los Insectos , Interacciones Huésped-Parásitos/genética , Control de Insectos , Muscidae/genética , Animales , Reproducción/genética
8.
BMC Biol ; 18(1): 1, 2020 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-31898513

RESUMEN

BACKGROUND: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. RESULTS: We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. CONCLUSIONS: Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.


Asunto(s)
Anopheles/genética , Evolución Biológica , Cromosomas , Técnicas Genéticas/instrumentación , Genómica/métodos , Sintenía , Animales , Mapeo Cromosómico
9.
Nucleic Acids Res ; 46(D1): D802-D808, 2018 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-29092050

RESUMEN

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.


Asunto(s)
Archaea/genética , Bacterias/genética , Bases de Datos Genéticas , Bases de Datos de Proteínas , Eucariontes/genética , Genómica , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Minería de Datos , Predicción , Genoma , Anotación de Secuencia Molecular , ARN/genética , Interfaz Usuario-Computador
10.
Nature ; 487(7407): 375-9, 2012 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-22722859

RESUMEN

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.


Asunto(s)
Biodiversidad , Secuenciación de Nucleótidos de Alto Rendimiento , Malaria Falciparum/parasitología , Plasmodium falciparum/genética , Alelos , Genoma de Protozoos , Genotipo , Humanos , Filogenia , Plasmodium falciparum/clasificación , Polimorfismo de Nucleótido Simple , Análisis de Componente Principal
11.
Nucleic Acids Res ; 44(D1): D574-80, 2016 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-26578574

RESUMEN

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.


Asunto(s)
Bases de Datos Genéticas , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Invertebrados/genética , Animales , Diploidia , Eucariontes/genética , Variación Genética , Genoma , Poliploidía , Alineación de Secuencia
12.
Nucleic Acids Res ; 43(Database issue): D707-13, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-25510499

RESUMEN

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.


Asunto(s)
Bases de Datos Genéticas , Vectores de Enfermedades , Genómica , Animales , Ontologías Biológicas , Perfilación de la Expresión Génica , Variación Genética , Genoma , Humanos , Resistencia a los Insecticidas , Internet , Invertebrados/genética , Redes y Vías Metabólicas/genética
14.
Nucleic Acids Res ; 42(Database issue): D546-52, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24163254

RESUMEN

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.


Asunto(s)
Bases de Datos Genéticas , Genoma , Animales , Grano Comestible/genética , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Genómica , Internet , Anotación de Secuencia Molecular , Programas Informáticos
15.
BMC Genomics ; 16: 779, 2015 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-26462916

RESUMEN

BACKGROUND: The genome-wide association study (GWAS) techniques that have been used for genetic mapping in other organisms have not been successfully applied to mosquitoes, which have genetic characteristics of high nucleotide diversity, low linkage disequilibrium, and complex population stratification that render population-based GWAS essentially unfeasible at realistic sample size and marker density. METHODS: We designed a novel mapping strategy for the mosquito system that combines the power of linkage mapping with the resolution afforded by genetic association. We established founder colonies from West Africa, controlled for diversity, linkage disequilibrium and population stratification. Colonies were challenged by feeding on the infectious stage of the human malaria parasite, Plasmodium falciparum, mosquitoes were phenotyped for parasite load, and DNA pools for phenotypically similar mosquitoes were Illumina sequenced. Phenotype-genotype mapping was carried out in two stages, coarse and fine. RESULTS: In the first mapping stage, pooled sequences were analysed genome-wide for intervals displaying relativereduction in diversity between phenotype pools, and candidate genomic loci were identified for influence upon parasite infection levels. In the second mapping stage, focused genotyping of SNPs from the first mapping stage was carried out in unpooled individual mosquitoes and replicates. The second stage confirmed significant SNPs in a locus encoding two Toll-family proteins. RNAi-mediated gene silencing and infection challenge revealed that TOLL 11 protects mosquitoes against P. falciparum infection. CONCLUSIONS: We present an efficient and cost-effective method for genetic mapping using natural variation segregating in defined recent Anopheles founder colonies, and demonstrate its applicability for mapping in a complex non-model genome. This approach is a practical and preferred alternative to population-based GWAS for first-pass mapping of phenotypes in Anopheles. This design should facilitate mapping of other traits involved in physiology, epidemiology, and behaviour.


Asunto(s)
Anopheles/genética , Estudio de Asociación del Genoma Completo , Malaria Falciparum/genética , Plasmodium falciparum/genética , Receptores Toll-Like/genética , Animales , Anopheles/parasitología , Mapeo Cromosómico , Genoma de los Insectos , Genotipo , Interacciones Huésped-Parásitos/genética , Humanos , Insectos Vectores/genética , Malaria Falciparum/parasitología , Malaria Falciparum/transmisión , Fenotipo , Plasmodium falciparum/patogenicidad , Polimorfismo de Nucleótido Simple
16.
PeerJ ; 12: e16949, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38410806

RESUMEN

Whiteflies (Bemisia tabaci sensu lato) have a wide host range and are globally important agricultural pests. In Sub-Saharan Africa, they vector viruses that cause two ongoing disease epidemics: cassava brown streak disease and cassava mosaic virus disease. These two diseases threaten food security for more than 800 million people in Sub-Saharan Africa. Efforts are ongoing to identify target genes for the development of novel management options against the whitefly populations that vector these devastating viral diseases affecting cassava production in Sub-Saharan Africa. This study aimed to identify genes that mediate osmoregulation and symbiosis functions within cassava whitefly gut and bacteriocytes and evaluate their potential as key gene targets for novel whitefly control strategies. The gene expression profiles of dissected guts, bacteriocytes and whole bodies were compared by RNAseq analysis to identify genes with significantly enriched expression in the gut and bacteriocytes. Phylogenetic analyses identified three candidate osmoregulation gene targets: two α-glucosidases, SUC 1 and SUC 2 with predicted function in sugar transformations that reduce osmotic pressure in the gut; and a water-specific aquaporin (AQP1) mediating water cycling from the distal to the proximal end of the gut. Expression of the genes in the gut was enriched 23.67-, 26.54- and 22.30-fold, respectively. Genome-wide metabolic reconstruction coupled with constraint-based modeling revealed four genes (argH, lysA, BCAT & dapB) within the bacteriocytes as potential targets for the management of cassava whiteflies. These genes were selected based on their role and essentiality within the different essential amino acid biosynthesis pathways. A demonstration of candidate osmoregulation and symbiosis gene targets in other species of the Bemisia tabaci species complex that are orthologs of the empirically validated osmoregulation genes highlights the latter as promising gene targets for the control of cassava whitefly pests by in planta RNA interference.


Asunto(s)
Hemípteros , Manihot , Virus , Humanos , Animales , Filogenia , Manihot/genética , Hemípteros/genética , Verduras , Agua
17.
Sci Data ; 11(1): 918, 2024 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-39181902

RESUMEN

Phlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.


Asunto(s)
Genoma de los Insectos , Psychodidae , Animales , Psychodidae/genética , Phlebotomus/genética , Phlebotomus/clasificación , Insectos Vectores/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ADN
18.
Genetics ; 227(1)2024 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-38529759

RESUMEN

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.


Asunto(s)
Biología Computacional , Bases de Datos Genéticas , Hongos , Internet , Oomicetos , Oomicetos/genética , Hongos/genética , Biología Computacional/métodos , Genoma Fúngico , Genómica/métodos , Programas Informáticos
19.
BMC Genomics ; 13: 1, 2012 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-22214261

RESUMEN

BACKGROUND: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. RESULTS: We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. CONCLUSION: We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.


Asunto(s)
Biblioteca de Genes , Genoma de Protozoos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Composición de Base , ARN Polimerasas Dirigidas por ADN/metabolismo , Sitios Genéticos , Plasmodium falciparum/genética , Reacción en Cadena de la Polimerasa , Reproducibilidad de los Resultados , Proteínas Virales/metabolismo
20.
Bioinformatics ; 25(20): 2732-3, 2009 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-19687029

RESUMEN

UNLABELLED: Array-based comparative genomic hybridization (CGH) technology is used to discover and validate genomic structural variation, including copy number variants, insertions, deletions and other structural variants (SVs). The visualization and summarization of the array CGH data outputs, potentially across many samples, is an important process in the identification and analysis of SVs. We have developed a software tool for SV analysis using data from array CGH technologies, which is also amenable to short-read sequence data. AVAILABILITY AND IMPLEMENTATION: SnoopCGH is written in java and is available from http://snoopcgh.sourceforge.net/


Asunto(s)
Hibridación Genómica Comparativa/métodos , Biología Computacional/métodos , Genoma , Programas Informáticos , Hibridación Genómica Comparativa/instrumentación , Gráficos por Computador , Perfilación de la Expresión Génica/métodos , Genoma Bacteriano , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Plasmodium falciparum/genética
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