The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.

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Big data: Astronomical or genomical?

MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.pl, we included new features: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5′-end capping process, and a catalogue of ‘building blocks’ for chemical synthesis of a large variety of modified nucleosides. The MODOMICS collections of RNA modifications, RNA-modifying enzymes and modified RNAs have been also updated. A number of newly identified modified ribonucleosides and more than one hundred functionally and structurally characterized proteins from various organisms have been added. In the RNA sequences section, snRNAs and snoRNAs with experimentally mapped modified nucleosides have been added and the current collection of rRNA and tRNA sequences has been substantially enlarged. To facilitate literature searches, each record in MODOMICS has been cross-referenced to other databases and to selected key publications. New options for database searching and querying have been implemented, including a BLAST search of protein sequences and a PARALIGN search of the collected nucleic acid sequences.

MODOMICS: a database of RNA modification pathways—2013 update

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.

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OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems Arthropods compete with humans for food and transmit devastating diseases They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists, With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind

The i5K initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment

WHEN E. O. WILSON PROCLAIMED THAT INSECTS ARE THE “little creatures who run the world” (1), he was simply reaffi rming the long-recognized dominance of the largest class of animals on our planet. Insects constitute approximately 53% of all living species, with one group alone (the ants), accounting for almost a quarter of terrestrial animal biomass (2). These tiny creatures also exert outsized impacts on human affairs. By serving as pollinators to more than 75% of fl owering plant species (3), insects are essential to the maintenance and productivity of natural and agricultural ecosystems. But other insects consume or damage more than 25% of all agricultural, forestry, and livestock production in the United States, costing our economy more than $30 billion annually (4). These losses occur despite more than 150 years of concerted efforts to prevent them. Insects and other arthropods not only affect our food supply, they also carry disease. Parasites and pathogens carried by insects and their relatives have led to more loss of human life than all wars in recorded history; even today, insect-borne diseases are a leading cause of death of children under the age of 5 (5). The annual cost of vector-borne diseases worldwide is estimated at almost $50 billion (6). Clearly, our health and well-being depend on our ability to understand and manage arthropods of agricultural, medical, and veterinary importance. In the past decade, biomedical research has increasingly relied on information obtained from sequencing the human genome, and early genome-enabled successes have inspired a new vision of genomic medicine (7). We believe that genomics also can improve our lives by contributing to a better understanding of insect biology and transforming our ability to manage arthropods that threaten our health, food supply, and economic security. Because of the overwhelming diversity and abundance of insects, achieving these goals will require a project of grand scale. Therefore, we, the undersigned, are pleased to announce the launch of the “i5k” initiative to sequence the genomes of 5000 species of insects and other arthropods during the next 5 years (8). This project is aimed at sequencing and analyzing the genomes of all species known to be important to worldwide agriculture and food safety, medicine, and energy production; all species used as models in biology; the most abundant insects in world ecosystems; and, to achieve a deep understanding of arthropod evolution, representatives of insect relatives in every major branch of arthropod phylogeny. The i5k initiative will be broad and inclusive, seeking to involve scientists from around the world and obtain funding from academia, governments, industry, and private sources. We also aim to encourage new collaborative research by computer scientists, bioinformaticians, and biologists to overcome the challenges of handling this unprecedented volume of data and derive meaning from these genomes. GENE E. ROBINSON,* KEVIN J. HACKETT, MARY PURCELL-MIRAMONTES, SUSAN J. BROWN, JAY D. EVANS, MARIAN R. GOLDSMITH, DANIEL LAWSON, JACK OKAMURO, HUGH M. ROBERTSON, DAVID J. SCHNEIDER Department of Entomology, University of Illinois at UrbanaChampaign, Urbana, IL 61801, USA. USDA Agricultural Research Service, Beltsville, MD 20705, USA. USDA National Institute of Food and Agriculture, Washington, DC 20250, USA. Division of Biology, Kansas State University, Manhattan, KS 66506–4190, USA. Arthropod Genomics Consortium and European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA. USDA Agricultural Research Service, Ithaca, NY 14853, USA.

https://science.sciencemag.org/content/sci/331/6023/1386.full.pdf

Mary Purcell-Miramontes

Papers

The i5K initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment

Creating a buzz about insect genomes.