Donlin MJ (2007) Curr Protoc Bioinformatics "Using the Generic Genome Browser (GBrowse)."

Donlin MJ

[Curr Protoc Bioinformatics, 2007]

A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open-source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The software package can be downloaded from the web and run on a Windows, Mac OS X, or Unix-type system. Version 1.64, as described in this protocol, was released in November 2005, but the software is under active development and new versions are released about every six months.

Donlin MJ (2009) Curr Protoc Bioinformatics "Using the Generic Genome Browser (GBrowse)."

Donlin MJ

[Curr Protoc Bioinformatics, 2009]

A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open-source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The software package can be downloaded from the Web and run on a Windows, Mac OS X, or Unix-type system. Version 1.64, as described in the original protocol, was released in November 2005, but the software is under active development and new versions are released about every six months. This update includes instructions on updating existing data sources with new files from NCBI.

Memar N et al. (2018) Dev Biol "Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence."

Conradt B, Schiemann S, Memar N, Findeis D, Hennig C, Schnabel R

[Dev Biol, 2018]

The four Caenorhabditis species C. elegans, C. briggsae, C. remanei and C. brenneri show more divergence at the genomic level than humans compared to mice (Stein et al., 2003; Cutter et al., 2006; Cutter et al., 2008). However, the behavior and anatomy of these nematodes are very similar. We present a detailed analysis of the embryonic development of these species using 4D-microscopic analyses of embryos including lineage analysis, terminal differentiation patterns and bioinformatical quantifications of cell behavior. Further functional experiments support the notion that the early development of all four species depends on identical induction patterns. Based on our results, the embryonic development of all four Caenorhabditis species are nearly identical, suggesting that an apparently optimal program to construct the body plan of nematodes has been conserved for at least 20 million years. This contrasts the levels of divergence between the genomes and the protein orthologs of the Caenorhabditis species, which is comparable to the level of divergence between mouse and human. This indicates an intricate relationship between the structure of genomes and the morphology of animals.

Consortium Wormbase et al. (2000) West Coast Worm Meeting "From ACeDB to a more complete and usable database"

Consortium Wormbase, Foltz NL, Schwarz EM, Sternberg PW

[West Coast Worm Meeting, 2000]

We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.

Sheldon J McKay et al. (2005) International Worm Meeting "Genome organization and colinearity in three Caenorhabditis species"

Sheldon J McKay, Lincoln D Stein

[International Worm Meeting, 2005]

C. elegans and C. briggsae are morphologically similar but their genomes have had about 100 million years to diverge. Examples of ways in which the two genomes have diverged include not only nucleotide substitutions but also species-specific expansion of gene families and many inter- and intra-chromosomal rearrangements (1). In addition to coding DNA and other functional sequences, higher order chromosome structure is also under selective constraints, for example against loss of genetic material due to non-reciprocal chromosome rearrangements. Conservation of regions of colinearity between divergent genomes suggests that gene order is also important. A striking example of this is the high degree inter-species conservation of gene order and composition of operons. We are building on the previously described comparison of the C. elegans and C. briggsae genomes using a global analysis of conservation of syntenic blocks in the genomes of these two species as well as that of C. remanei. The foundation of these comparisons is sequence similarity-based genome alignments performed by WABA(2) and blastz(3). Although conservation at the nucleotide sequence level is helpful in understanding genome evolution, global application of DNA sequence alignments in divergent genomes can be confounded by multiple rearrangements affecting the same region of the chromosome. Disruption in alignable sequences caused by a complex history of local rearrangements can mask larger blocks of colinearity that may be functionally significant. To identify such regions in these three species and, hopefully, unravel some of the complexity of nested chromosome rearrangements, we are applying a method based on the dynamic programming algorithm described in Stein et al. (1) and comparing it to the approach developed by Kent et al. (4) for the mouse and human genomes. We will discuss our findings in relation to the existing body of knowledge on C. elegans and C. briggsae genome organization and the impact of adding an additional species on our understanding of Caenorhabditis genome evolution. 1. Stein, L. D. et al., PLoS Biology 1:166-192 2. Kent, W. J. and A. M. Zahler, Genome Res 10:1115-1125 3. Schwartz, S. et al., Genome Res 13:103-107 4. Kent, W. J. et al., PNAS 100:11484-11489

Shakes, Diane et al. (2009) International Worm Meeting "EMB-1 is a novel protein involved in the metaphase-to-anaphase transition."

Golden, Andy, Shakes, Diane

[International Worm Meeting, 2009]

The Anaphase Promoting Complex (APC) is a multi-subunit E3 ubiquitin ligase that promotes the metaphase-to-anaphase transition during meiotic and mitotic divisions. Temperature-sensitive (ts) mutants in mat-1, mat-2, mat-3, emb-27, and emb-30 arrest as 1-cell embryos, stuck in metaphase of meiosis I. These five genes code for five subunits of the APC. The ts alleles of emb-1 have grabbed our attention because their arrest phenotype is indistinguishable from the APC mutants. Furthermore, genetic doubles constructed between emb-1(hc62) and the APC mutants cannot be maintained at the permissive temperature, a common feature of any APC double mutant. Additionally, suppressors that suppress the APC mutants (Stein et al., 2007) also suppress emb-1. What is EMB-1 you may ask? We mapped emb-1 to a tiny interval on LG III and used RNAi to phenocopy the 1-cell arrest phenotype. Rescue and sequencing confirmed that emb-1 codes for a novel protein with no known homologies outside of Caenorhabditis species. Localization studies are underway. We propose that EMB-1 is a novel subunit or regulator of the APC in C. elegans.

Bhaskar Reddy Gavinolla et al. (2007) International Worm Meeting "Interactions between the microtubule severing protein MEI-2 and spindle checkpoints."

Bhaskar Reddy Gavinolla, Paul E. Mains

[International Worm Meeting, 2007]

The spindle checkpoint protein, SAN-1/MDF-3 is expressed on mitotic centromeres. During anoxia, mutants fail to arrest the cell cycle, leading to chromosome mis-segregation and reduced viability (Nystul et. al 2003). Checkpoint proteins arrest the cell cycle by inhibiting the Anaphase Promoting Complex (APC) and san-1/mdf-3 mutants suppress APC mutants (Stein et al. 2007). We have uncovered a possible link between the microtubule severing complex MEI-1/MEI-2 and the meiotic spindle checkpoint. Like SAN-1/MDF-3, MEI-1 and MEI-2 localize to chromatin and genetically interact with APC mutants. Furthermore, yeast two hybrid data (Li et al. 2004) shows that MEI-2 and SAN-1 interact physically. Both the similar expression patterns and the yeast two-hybrid binding suggested possible genetic interaction between them, so we made double mutants of san-1 and mei-2. This resulted in increased lethality, low brood sizes and spontaneous males, indications of meiotic failure. While enhancement of mei-2 spindle formation defects might be expected by the presence of a compromised spindle checkpoint, the physical interaction and colocalization might indicate a more specific role for MEI-1/MEI-2 in monitoring spindle quality.

Nansheng Chen et al. (2005) International Worm Meeting "Conservation and Functional Significance of Overlapping Genes in Caenorhabditis elegan"

Nansheng Chen, Lincoln Stein

[International Worm Meeting, 2005]

We have systematically examined the overlapping genes in the Caenorhabditis elegans genome. There exist over one thousand such gene pairs in the entire C. elegans genome and can be subdivided into six major categories based on the overlap topology. We demonstrate that some categories of overlapping genes are bipolarized in terms of gene evolution. Some types of overlapping genes are strongly and significantly more conserved than the genome as a whole when compared to Caenorhabditis briggsae, a nematode that split from C. elegans about 100 million years ago (1), while other types of overlapping genes, the nested genes that reside within introns of other genes in particular, are significantly less conserved compared with other genes in the genome. We have also found that although overlapping gene pairs tend not to share common functional motifs, they are enriched with essential genes and genes that cause various defined phenotypes revealed by RNAi trials, indicating the functional significance of these genes. Tissue-specific SAGE library datasets analysis suggests that the flanking genes and their corresponding nested genes are not as strongly positively correlated in gene expression pattern as tandem gene pairs, suggesting that the flanking / nested gene pair arrangement interferes with coexpression among the members of the gene pairs. 1. L. D. Stein et al., PLoS Biol 1, E45 (Nov, 2003).

Scott E. Baird et al. (2007) International Worm Meeting "Available genetic and genomic resources for C. briggsae."

Daniel C. Koboldt, Raymond D. Miller, Bhagwati P. Gupta, Helen M. Chamberlin, Scott E. Baird, Eric S. Haag

[International Worm Meeting, 2007]

The draft genomic assembly of C. briggsae (Stein et al., 2003) has enabled detailed comparisons of specific gene sequences from C. elegans with a relative. However, C. briggsae has characteristics suggesting that more extensive comparisons of it with C. elegans are useful and further, that it is a useful model organism in its own right. We report here a number of recent accomplishments that will further facilitate research in C. briggsae. 1) A SNP-based genetic map of 6 chromosomes that links most of the draft sequence has been developed from recombinant inbred lines. 2) Over 24,000 SNPs have been identified from mapping strain HK104. 3). Insertion/deletion events useful for mapping have been identified including >7,000 that are short (<50 bp) and >600 candidates that are long (>50 bp). 4). A set of 50 phenotypic mutants are in various stages of localization to chromosomes. 5). A new set of 181 recombinant inbred lines useful for quantitative genetics has been developed. 6). New information on C. briggsae is available at http://www.wormbase.org and http://snp.wustl.edu. C. briggsae harbors considerable genetic diversity with a SNP detected on average every 115 bp between the canonical strain AF16 and the mapping strain HK104. C. briggsae is now a very attractive research model organism for forward genetics and the genetics of quantitative traits.

McKay SJ et al. (2010) Curr Protoc Bioinformatics "Using the Generic Synteny Browser (GBrowse_syn)."

Vergara IA, Stajich JE, McKay SJ

[Curr Protoc Bioinformatics, 2010]

Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open-source genome browser package developed as part of the Generic Model Database Project (see UNIT ; Stein et al., 2002). The increasing number of sequenced genomes has led to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of colinear regions of multiple genomes using the familiar GBrowse-style Web page. Like GBrowse, GBrowse_syn can be configured to display any organism, and is currently the synteny browser used for model organisms such as C. elegans (WormBase; http://www.wormbase.org; see UNIT 1.8) and Arabidopsis (TAIR; http://www.arabidopsis.org; see UNIT 1.1). GBrowse_syn is part of the GBrowse software package and can be downloaded from the Web and run on any Unix-like operating system, such as Linux, Solaris, or MacOS X. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v. 1.71).