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Nucleic Acids Research Advance Access published online on October 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp807
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

Hee Shin Kim1, Terence Murphy2, Jing Xia3, Doina Caragea1,3, Yoonseong Park4, Richard W. Beeman5, Marcé D. Lorenzen5, Stephen Butcher6, J. Robert Manak6,7 and Susan J. Brown1,*

1KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506, 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 3Department of Computer and Information Science, KSU, Manhattan, KS 66506, 4Department of Entomology, KSU, Manhattan, KS 66506, 5USDA-ARS Grain Marketing and Production Research Center, 1515 College Avenue, Manhattan KS 66502, 6Department of Biology, University of Iowa, Iowa City, IA 52242 and 7Roy J. Carver Center for Genomics, UI, Iowa City, IA 52242

*To whom correspondence should be addressed. Tel: +1 785 532 3935; Fax: +1 785 532 6653; Email: sjbrown{at}ksu.edu

Received August 14, 2009. Revised September 11, 2009. Accepted September 14, 2009.


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 DATA ACQUISITION
 IMPLEMENTATION
 FUNDING
 REFERENCES
 
BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relatational database using the Chado schema and visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
DATA ACQUISITION
 IMPLEMENTATION
 FUNDING
 REFERENCES
 
The red flour beetle, Tribolium castaneum, is a sophisticated genetic model organism for studies of insect development and pest biology as well as comparative genomics (1,2). A burgeoning wealth of genomic information, including a whole genome shotgun (WGS) assembly of the genome sequence, has become available in recent years (2).

BeetleBase was developed to provide a centralized database to serve the growing needs of the Tribolium research community. The first version of BeetleBase (3) was based on genome release Tcas_1.0. The database provided access to unmapped scaffolds, Fgenesh predicted genes, genetic markers, BAC-end sequences and ESTs. The database was implemented using an early version of the Chado schema, GBrowse, and CMAP developed by the Generic Model Organism Database (GMOD) project (http://www.gmod.org/).

Additional data has become available since the initial release of BeetleBase, including updates to the genome assembly and annotation, necessitating updates to the BeetleBase schema and data content. Here we present an updated version of BeetleBase (http://www.beetlebase.org), implemented using recent versions of Generic Model Organism Database (GMOD) tools, and integrated with BLAST (4) and BLAT (5) alignment tools. Data content has been expanded to include the latest version of the genome assembly (Tcas_3.0), a comprehensive collection of gene sets including the first unified release of the Tribolium Official Gene Set (OGS), EST alignments to the genome, and whole-genome transcriptional information from DNA tiling array experiments. These updates will provide a valuable resource for the Tribolium community, and serve as a foundation for integration of future datasets.


   DATA ACQUISITION
TOP
 ABSTRACT
 INTRODUCTION
 DATA ACQUISITION
IMPLEMENTATION
 FUNDING
 REFERENCES
 
Genome sequence
The initial assembly of the Tribolium genome (Tcas_1.0) was composed of 1107 unmapped genomic sequence scaffolds. For the second version of the assembly (Tcas_2.0), 70% of the genome sequence was mapped to 10 linkage groups corresponding to nine autosomes and the X chromosome (2,6). Subsequently, an additional forty-two of the largest unmapped scaffolds have been integrated into the genetic linkage map, and used by the Baylor College of Medicine to create the third version of the assembly (Tcas_3.0). The Tribolium genome sequence is assembled into 9686 contigs of 156 Mb in combined length. When these are assembled into scaffolds containing captured gaps of estimated length, the genome assembly is ~160 Mb. Scaffolds and contigs containing more than 90% of the sequenced genome have been assembled into 10 chromosome builds. The chromosome build statistics for Tcas_3.0 are summarized in Table 1. The GenBank accession numbers of the 9686 contigs that have been assembled into ten chromosome builds, 305 unmapped scaffolds and 1848 unmapped single contigs are AAJJ01000001–AAJJ01009708 (22 of which have been suppressed since their original submission), CM000276 [GenBank] –CM000285 [GenBank] and DS497665 [GenBank] –DS497969 [GenBank] and GG694051 [GenBank] –GG695897 [GenBank] , respectively. The genetic map has also been updated to include the additional 42 markers used to anchor scaffolds in the Tcas_3.0 assembly.


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  		Table 1. Genome sequence (Tcas_3.0) statistics

 
Gene models
Several gene prediction programs were previously used to annotate the Tcas_2.0 assembly, and were combined into a consensus GLEAN gene set (2,7). More than 2000 genes were manually curated by members of the Tribolium Genome Sequencing Consortium (2); however, new and updated gene models were not combined into a unified gene set. We generated the first Tribolium Official Gene Set (OGS) by merging the GLEAN gene set with the manually curated gene annotations. First, each manually curated gene was mapped to the Tcas_3.0 assembly, and the validity of the mRNA, CDS, and/or peptide sequence for each of the manually curated genes was checked to ensure that the peptide sequence represented the same exons/splice sites as the mRNA and CDS sequences. Incorrectly annotated exons were replaced with exon coordinates determined by Splign (8). In some cases, genes required manual curation to determine the correct or most likely gene structure. A non-redundant Official Gene Set was constructed by merging the GLEAN and manually curated gene sets, automatically replacing GLEAN models with overlapping, manually curated models. Finally, unique identifiers were assigned to each gene to facilitate communication of Tribolium genes in research publications. A total of 16 561 official genes were generated, assigned identifiers such as ‘TC######’, and submitted to NCBI (Table 2).


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  		Table 2. Gene model and EST statistics

 
Since some researchers may benefit from access to other gene sets, we migrated the AUGUSTUS, Ensembl, Fgenesh, NCBI supported and ab initio gene models, and the combined GLEAN genes from the Genboree database hosted at Baylor College of Medicine (http://www.genboree.org), and converted their coordinates into the genome coordinates of Tcas_3.0 (Table 2). Only a few of the predicted genes were lost when the scaffolds were reorganized. In addition, the latest RefSeq annotation from NCBI (build 2.1, based on the same Tcas_3.0 assembly), which includes 3613 protein accessions that are new or changed from the original annotation run used for the GLEAN set, was imported into BeetleBase. Each gene set is available for viewing in a separate track in GBrowse (Figure 1).


Figure 1
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  		Figure 1. Tribolium gene models. Various gene models are shown in different tracks for easy comparison. By clicking one of the gene models, detailed information can be retrieved. The RefSeq gene models are linked to NCBI Entrez Gene report pages. The Tribolium official gene models and manually-curated gene models link to the BeetleBase gene report pages. Other gene models link to detailed pages provided by GBrowse.

 
BeetleBase provides a detailed gene report page for each gene in the OGS, which can be accessed and managed through the web interface (Figure 2). The new BeetleBase database provides more comprehensive gene information than was previously available, including detailed information on the gene structure, nomenclature, and additional annotation data provided during the manual curation process. Links are also provided to overlapping RefSeq Gene and transcript records at NCBI (9,10) to facilitate use of data from both databases.


Figure 2
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  		Figure 2. Official gene report page. The report page provides detailed information for an official gene. The information can be modified by clicking ‘Edit’ after obtaining a password from the BeetleBase webmaster. The report page links to GBrowse by clicking ‘GBrowse’. The corresponding region will be highlighted in GBrowse.

 
EST and BAC-end sequences
EST and BAC-end sequences were downloaded from the dbEST and GSS databases, respectively, at NCBI. 55 616 ESTs from five different tissue- and stage-specific cDNA libraries (11) were cleaned and polyA sequences removed using in-house software tools (http://bioinformatics.ksu.edu/ArthropodEST) and aligned to the genome using the Exonerate algorithm (12). A total of 50 277 EST-genome alignments were generated. BAC-end sequences from the Tribolium BAC library (constructed by Exelixis, Inc, South San Francisco, CA and archived for distribution by the Clemson University Genomics Institute (https://www.genome.clemson.edu/) were mapped to the genome and added to the database. Out of 28 788 BAC-end sequences, 27 810 were aligned to the genome using BLAST.

Tiling arrays
Using Roche NimbleGen HD2 whole genome DNA tiling arrays, whole genome expression data have been collected for several developmental stages including three embryonic, the last larval, three pupal and two adult stages. Briefly, fluorescently labeled cDNAs were hybridized to the custom-designed microarrays; GFF files were constructed using the signal intensities from each feature on the array that were quantified directly from the scanned array images without any data management such as background subtraction. This was done to provide immediate access to the data to help verify computed gene models and assist manual annotation efforts while the data are processed and further analyzed. Figure 3 shows empirically derived transcriptome tiling array data generated from several developmental stages for a portion of the Tribolium genome.


Figure 3
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  		Figure 3. Tribolium genome tiling arrays. Tracks for 11 developmental time points are shown. Blue vertical bars of each track represent fluorescence intensity values for oligonucleotide probes tiled across a 54 kb region on the array. The official gene mRNA track (above time point tracks) contains purple gene structures. Note the different expression patterns of the annotated genes across development.

 
FTP site
Datasets that can be downloaded from BeetleBase (ftp://bioinformatics.ksu.edu/pub/BeetleBase/3.0/) include the contig sequences, GFF (.gff3) and assembly files (.agp) for Tcas_3.0. Sequences of GLEAN genes, GLEAN cDNAs and GLEAN peptides as well as the corresponding files for the OGS are also available.


   IMPLEMENTATION
TOP
 ABSTRACT
 INTRODUCTION
 DATA ACQUISITION
 IMPLEMENTATION
FUNDING
 REFERENCES
 
All the genomic information was compiled into Genetic Feature Format Version 3 (GFF3), which is the most common extension of GFF. The compiled information was implemented using GMOD tools (http://www.gmod.org) such as PostgreSQL-based Chado 1.0, GBrowse 1.68, and CMAP 1.0. To query sequences against the Tribolium genome, we also installed stand alone BLAST and BLAT servers. In this release of BeetleBase, we improved the usability by integrating these components.


   FUNDING
TOP
 ABSTRACT
 INTRODUCTION
 DATA ACQUISITION
 IMPLEMENTATION
 FUNDING
REFERENCES
 
Grant number P20 RR016475 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health. Work at NCBI was supported by the Intramural Research Program of the NIH, National Library of Medicine. Funding for open access charge: National Center for Research Resources National Institutes of Health (P20 RR016475).

Conflict of interest statement. None declared.


   Footnotes
 
Present address: Marcé D. Lorenzen, Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA


   REFERENCES
TOP
 ABSTRACT
 INTRODUCTION
 DATA ACQUISITION
 IMPLEMENTATION
 FUNDING
 REFERENCES
 

  1. Roth S, Hartenstein V. Development of Tribolium castaneum. Dev. genes Evol. (2008) 218:115–118.[CrossRef][Web of Science][Medline]

  2. Tribolium Genome Sequencing Consortium. The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 452:949–955.[CrossRef][Web of Science][Medline]

  3. Wang LJ, Wang S, Li Y, Paradesi MS, Brown SJ. Beetlebase: the model organism database for Tribolium castaneum. Nucleic Acid Res. (2007) 35:D476–D479.[Abstract/Free Full Text]

  4. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search. Nucleic Acids Res. (1997) 25:3389–3402.[Abstract/Free Full Text]

  5. Kent WJ. BLAT-The BLAST-like alignment tool. Genome Res. (2002) 12:656–664.[Abstract/Free Full Text]

  6. Lorenzen MD, Doyungan Z, Savard J, Snow K, Crumly LR, Shippy TD, Stuart JJ, Brown SJ, Beeman RW. Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags. Genetics (2005) 170:741–747.[Abstract/Free Full Text]

  7. Elsik CG, Worley KC, Zhang L, Milshina NV, Jiang H, Reese JT, Childs KL, Venkatraman A, Dickens CM, Weinstock GM, et al. Community annotation: Procedures, protocols, and supporting tools. Genome Res. (2007) 16:1329–1333.[CrossRef][Web of Science]

  8. Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct (2008) 3:20.[CrossRef][Medline]

  9. Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. (2007) 35:D61–D65.[Abstract/Free Full Text]

  10. Maglott DR, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. (2007) 35:D26–D31.[Abstract/Free Full Text]

  11. Park Y, Aikins J, Wang LJ, Beeman RW, Oppert B, Lord JC, Brown SJ, Lorenzen MD, Richards S, et al. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem. Mol. Biol. (2008) 38:380–386.[CrossRef][Web of Science][Medline]

  12. Slater GS, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 6:31.[CrossRef][Medline]


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