The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics

By Lincoln D. Stein, Z. Bao, Darin Blasiar, T. Blumenthal, Michael R. Brent, Nansheng Chen, A. Chinwalla, Laura Clarke, C. Clee, Avril Coghlan and 26 more. PLoS Biology, 2003

1,019 citations recorded by the source corpus.

The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.

Subfields: Aging, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/73405320dfc31eb4c9d94a5d4dc3a731868a5e4a

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Citations in the corpus

Rfam: annotating non-coding RNAs in complete genomes (2004, background): “Caenorhabditis briggsae (10), chicken (11) and Erwinia caratova (12)].”
Fast and reliable prediction of noncoding RNAs (2005, neutral): “To date, complete genomic sequences of related species have been sequenced for almost all genetic model organisms as for example bacteria [10, 11], yeasts [12], nematodes [13, 14 ] and even mammals [15, 16, 17].”
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences (2009, methodology): “If working with a genome for which Repbase does not have an appropriate repeat library, RECON (Bao and Eddy, 2002; Stein et al., 2003) or RepeatScout (http://bix.ucsd.edu/repeatscout/; Price et al., 2005) can be used to establish one from scratch.”
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects (2011, neutral): “elegans release WS221 ESTs available from WormBase, and protein homology input consisted of all Caenorhabditis briggsae[30] WS221 proteins from WormBase together with all of the UniProt/Swiss-Prot database proteins (minus Caenorhabditis proteins).”
Systematic analysis and nomenclature of mammalian F-box proteins. (2004, background): “This expansion is species-specific because the Caenorhabditis briggsae genome is predicted to encode a similar number of F-box proteins as found in human and mouse genomes (Stein et al. 2003).”
An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis (2008, background): “…of fixed length L by counting co-occurring substrings in both sequences at the same position: k wd ℓ (x, x ′ ) = 1 L L−l+1 l=1 ℓ d=1 β d I x [l:l+d] = x ′ [l:l+d] (1) where x [l:l+d] is the substring of length d of x at position l and β d = 2 ℓ−d+1 ℓ 2 +ℓ is the weighting of the substring lengths.”
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita (2008, methodology): “Although the model free-living nematodes Caenorhabditis elegans and Caenorhabditis briggsae have been the subjects of intensive stud”
WormBase: a multi-species resource for nematode biology and genomics (2004, background): “elegans by identifying previously missed genes and suggesting many changes to the internal structure of gene models (2).”