The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

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

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Dalla amatlanensis Warren, Gott & Legal, sp. nov., is described and illustrated from seven male specimens from the State of Morelos, Mexico. Its apparent larval foodplant is Chusquea circinata Soderstrom & Calderon, based on the observation of an ovipositing female. Based on wing phenotype and male genital morphology, this new species appears to be closely related to Dalla steinhauseri Freeman, 1991, D. bubobon (Dyar, 1921), D. freemani Warren, 1997, and D. austini Warren & De la Maza, 2011, species endemic to Mexico and Guatemala.

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A new species of Dalla Mabille, 1904, from Morelos, Mexico (Lepidoptera: Hesperiidae: Heteropterinae)

Stinga Evans, 1955, has been considered monotypic since its description despite geographical variation that has not been elucidated. The variation of Stinga morrisoni (W. H. Edwards, 1878) described and figured here includes a range of superficial phenotypes segregated by a combination of geography and elevation, but united by a common genital morphology of both sexes. In addition, a second species of the genus occurring in southern Mexico (Tlaxcala, Puebla and Oaxaca), with different genitalia and superficial traits outside the range of variation seen in S. morrisoni, is described and named as a new species.

Variation of Stinga Evans, 1955, with description of a new species from Mexico (Lepidoptera: Hesperiidae: Hesperiinae: Hesperiini)

Comments on the proposed designation of a neotype for the nominal species Chionobas chryxus Doubleday, 1849 (currently Oeneis chryxus; Insecta, Lepidoptera, NYMPHALIDAE) 2

The Neotropical skipper genus Sodalia Evans, 1955 and its respective species are revised. Sodalia includes five species: S. sodalis (Butler, 1877) (type species), S. argyrospila (Mabille, 1876), S. coler (Schaus, 1902), S. petiti Gaviria-Ortiz, Dolibaina & A. Warren sp. nov. (described from low to mid elevations of the western Andes of Ecuador and from the Cordillera de la Costa in Venezuela), and Sodalia spangla (Evans, 1955) comb. nov. hitherto combined with Mnasitheus Godman, 1900. Lectotypes for Pamphila sodalis Butler, 1877 and Achlyodes argyrospila Mabille, 1876 are designated. The genus and species are redescribed and illustrations of relevant morphological characters necessary for identification are provided, as well as updated distributional maps.

A review of the Neotropical skipper genus Sodalia Evans, 1955 (Lepidoptera: Hesperiidae: Hesperiinae) with the description of a new species

The Florida Museum of Natural History's McGuire Center for Lepidoptera and Biodiversity, on the University of Florida campus in Gainesville, Florida, has become one of the world's largest institutions for research on butterflies and moths, and an important research facility for insect science. The facility was constructed by combining the staff and merging the Lepidoptera holdings from the Allyn Museum of Entomology, the Florida State Collection of Arthropods and other University of Florida collections, and now includes over ten million specimens from all over the world, rivaling some of the largest Lepidoptera research collections globally. The facility includes a team of domestic and international researchers studying many areas of lepidopterology, including behavior, biodiversity, biogeography, ecology, genomics, physiology, systematics and taxonomy. In this paper, we introduce the McGuire Center, its staff, and the many research activities for researchers across entomological disciplines.

Andrew D. Warren

Papers

A new species of Dalla Mabille, 1904, from Morelos, Mexico (Lepidoptera: Hesperiidae: Heteropterinae)

Variation of Stinga Evans, 1955, with description of a new species from Mexico (Lepidoptera: Hesperiidae: Hesperiinae: Hesperiini)

Comments on the proposed designation of a neotype for the nominal species Chionobas chryxus Doubleday, 1849 (currently Oeneis chryxus; Insecta, Lepidoptera, NYMPHALIDAE) 2

A review of the Neotropical skipper genus Sodalia Evans, 1955 (Lepidoptera: Hesperiidae: Hesperiinae) with the description of a new species

A new institution devoted to insect science: The Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity