Caenorhabditis briggsae
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| Caenorhabditis briggsae | ||||||||||||||
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| Caenorhabditis briggsae |
Caenorhabditis briggsae is a small nematode, closely related to Caenorhabditis elegans. The differences between the two species are subtle. The male tail in C. briggsae has a slightly different morphology than C. elegans. C. briggsae is used primarily to study the differences between it and the more intimately understood C. elegans, especially at the DNA and protein sequence level. C. briggsae, like C. elegans, is a hermaphrodite. [1] The genome sequence for C. briggsae was determined in 2003 [2].
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[edit] History
Ellsworth C. Dougherty first recognized the potential of C. briggsae, which had been found by Margaret Briggs in a pile of leaves on the campus of Stanford University in Palo Alto, California, in 1944 and used in her MS studies under the direction of Dr. Arthur C. Giese (Briggs, 1946; Gochnauer, 2004). Briggs studied the lifecycle of what she identified as Rhabditis sp. in association with bacteria and in various culture media devoid of other organisms. She showed that the population could not be sustained in the absence of bacteria or even on dead bacterial cells; living bacteria were a necessary food source. However, survival of individuals was greater on some bacteria-free media than others. [3]
[edit] Habitat
Caenorhabditis briggsae can often be found in compost, garden beds, or moist mushroom beds rich with microorganisms and various nutrients. The organism's main habitat is often considered to be the temperate regions of the globe, often accompanying its relatives C. elegans and C. remanei. [4]
[edit] Overview of Genome
The whole genome sequencing project (Stein et al., 2003) revealed that the genomes of C. briggsae and C. elegans have much in common (Summarized in Table 1). For example, both worms have the same number of chromosomes (six chromosomes each), similar genome size, and similar numbers of protein coding and non-protein coding genes. Further analysis demonstrated that about 62% of the protein coding genes in C. briggsae have orthologs in C. elegans. Nevertheless, many interesting species-specific features including species-specific genes exist, which serve as the foundation for comparative analysis. In the following subsections, we will describe the C. briggsae genome and compare it with the C. elegans genome. [5]
[edit] Comparative genomics with C.elegans
Caenorhabditis briggsae is a soil nematode estimated to have diverged from C. elegans approximately 80-100 million years ago, and yet is morphologically almost indistinguishable from it. Areas of sequence encoding proteins are mostly conserved between the two species while most intergenic and intronic sequence are divergent. Areas of similarity between the sequence of the two organisms can suggest coding exons or point to regulatory regions and to RNA genes missed in standard analysis. [6]
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.[7]
[edit] References
- ^ Haag, Eric S.. The evolution of nematode sex determination: C. elegans as a reference point for comparative biology. WormBook.
- ^ Stein, L. D. et al. (2003). The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biology 1: 166–192. doi:.
- ^ Ellsworth C Dougherty
- ^ Watson L. D. et al. (2007). Caenorhabditis briggsae.
- ^ Genomics and biology of the nematode Caenorhabditis briggsae
- ^ C. briggsae Project
- ^ To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently. <ref>To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.<ref>[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1914384#id2806222 Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny<!-- Bot generated title -->]</li></ol></ref>
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