-
[
Annu Rev Genomics Hum Genet,
2015]
The modENCODE (Model Organism Encyclopedia of DNA Elements) Consortium aimed to map functional elements-including transcripts, chromatin marks, regulatory factor binding sites, and origins of DNA replication-in the model organisms Drosophila melanogaster and Caenorhabditis elegans. During its five-year span, the consortium conducted more than 2,000 genome-wide assays in developmentally staged animals, dissected tissues, and homogeneous cell lines. Analysis of these data sets provided foundational insights into genome, epigenome, and transcriptome structure and the evolutionary turnover of regulatory pathways. These studies facilitated a comparative analysis with similar data types produced by the ENCODE Consortium for human cells. Genome organization differs drastically in these distant species, and yet quantitative relationships among chromatin state, transcription, and cotranscriptional RNA processing are deeply conserved. Of the many biological discoveries of the modENCODE Consortium, we highlight insights that emerged from integrative studies. We focus on operational and scientific lessons that may aid future projects of similar scale or aims in other, emerging model systems.
-
[
Cell,
2001]
In 1998, The C. elegans Sequencing Consortium (1998) announced the essentially complete Caenorhabditis elegans genomic sequence, setting a high standard for sequencing multicellular genomes. As of April 2001, the C. elegans genome, including repetitive regions, is >99.6% complete with sequence equivalent to what many genome projects call phase III. How has this changed the lives of C. elegans researchers, and our view of the worm?
-
[
Genome Res,
1995]
Caenorhabditis elegans, a free-living nematode worm, has proved a particularly useful model organism for studying the anatomy, behavior, genetics, and development of a metazoan. It also has one of the smallest genomes of the higher eukaryotes (100 Mb distributed over six chromosomes), making it an ideal candidate for detailed molecular analysis. The C. elegans genome project began over 10 years ago and is a collaberative effort between two laboratories (St. Louis, MO, USA and Cambridge, UK), with the ultimate aim of mapping and sequencing the whole of the 100-Mb genome. The consortium has now completed the sequence of approximately one-fifth of the genome and plans to have sequenced more than half the genome before the end
-
[
WormBook,
2007]
The soil nematode Caenorhabditis briggsae is an attractive model system for studying evolution of both animal development and behavior. Being a close relative of C. elegans, C. briggsae is frequently used in comparative studies to infer species-specific function of the orthologous genes and also for studying the dynamics of chromosome evolution. The genome sequence of C. briggsae is valuable in reverse genetics and genome-wide comparative studies. This review discusses resources and tools, which are currently available, to facilitate study of C. briggsae in order to unravel mechanisms of gene function that confer morphological and behavioral diversity.
-
[
Curr Biol,
2004]
The recently published genome of the nematdoe Caenorhabditis briggsae provides a drastic improvement in structural annotation of the C. elegans genome, as well as a promising source of evolutionary comparisons.
-
[
Genome Biol,
2003]
The publication of the draft genome sequence of Caenorhabditis briggsae improves the annotation of the genome of its close relative Caenorhabditis elegans and will facilitate comparative genomics and the study of the evolutionary changes during development.
-
[
Methods Mol Biol,
2006]
The genome of the nematode Caenorhabditis elegans was the first animal genome sequenced. Subsequent sequencing of the Caenorhabditis briggsae genome enabled a comparison of the genomes of two nematode species. In this chapter, we describe the methods that we used to compare the C. elegans genome to that of C. briggsae. We discuss how these methods could be developed to compare the C. elegans and C. briggsae genomes to those of Caenorhabditis remanei, C. n. sp. represented by strains PB2801 and CB5161, among others (1), and Caenorhabditis japonica, which are currently being sequenced.
-
[
Parasitology,
1999]
The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple DNA libraries representing the complete filarial nematode lifecycle, and comparative analysis of the sequence dataset, particularly using the complete genome sequence of the model nematode C. elegans, has proved very effective in gene discovery.
-
[
WormBook,
2005]
The C. elegans genome contains approximately 1300 genes that produce functional noncoding RNA (ncRNA) transcripts. Here we describe what is currently known about these ncRNA genes, from the perspective of the annotation of the finished genome sequence. We have collated a reference set of C. elegans ncRNA gene annotation relative to the WS130 version of the genome assembly, and made these data available in several formats.
-
[
Trends in Genetics,
1998]
On 1 August 1997, US Vice President Gore officially announced the creation of a new World Wide Web database which aims to provide powerful new resources to researchers investigating the molecular basis of cancer...