Genome: Schmidtea mediterranea

Freshwater Planarian (S. mediterranea).

Category
Invertebrates
Taxonomy
Flatworm
Scientific Name
Schmidtea mediterranea
Common Name
Planarian

Biology

Planarians are free-living representatives of the phylum Platyhelminthes, a group of some 50,000 species of flatworms. Flatworms are among the simplest animals with similar right and left sides: they have no body cavity, yet they possess derivatives of all three germ layers organized into complex organ systems. Thus, Platyhelminthes have been thought to occupy an important position in Metazoan evolution. Planarians are best known for their capacity to regenerate complete individuals from minuscule body parts, as well as for their ability to 'de-grow' when starved. Such extraordinary plasticity in the adult is in direct contrast to the rigidity displayed by currently used invertebrate models such as Caenorhabditis elegans and Drosophila melanogaster. The difference lies in a population of adult somatic (body) stem cells, called neoblasts, which are distributed throughout the planarian body. Neoblasts are the only cells that divide in planarians, and their division progeny generate the 30-40 different cell types found in these organisms. In intact planarians, these stem cells replace cells lost to normal turnover; whereas, in amputated animals, they give rise to the regeneration blastema, the structure in which missing tissues are regenerated. The successful introduction of cell, molecular, and RNAi techniques in planarians, along with heightened interest in stem-cell biology and the plasticity of the differentiated state, has re-kindled interest in these fascinating organisms. Sequencing the 4.8x108 bp genome of the sexual, diploid planarian S. mediterranea will provide a vital resource for the development of a unique model to study metazoan evolution, regeneration, and the regulation of the ability to differentiate into several types of cells. Insights into these basic biological problems will have deep and obvious implications for the improvement of human health.

-- Adapted from the attached whitepaper and courtesy of Dr. Sanchez Alvarado

Habitat

Freshwater planarians are constant and characteristic inhabitants of a wide range of aquatic environments. Most freshwater planarians can tolerate large fluctuations in temperature. As such, they are frequently found in running water communities ranging from alpine streams, springs or spring-fed ponds, as well as subterranean bodies of water. In these habitats, they are normally found living at the bottom on hard surfaces such as under rocks and/or gravel. There are as many species as there are habitats, since planarians, in particular, and playhelminthes, in general, are a very successful group of animals. The genus Schmidtea is common to countries around the Mediterranean Sea, from which the name of the species (mediterranea) originates. The clonal inbred line being utilized for this sequencing project was derived from a wild type population of sexual animals collected by Dr. Maria Pala on the Mediterranean island of Corsica and sent to the laboratory of Dr. Sanchez Alvarado in 1999.

Sequencing Plan

For this estimated 480 Mb genome, fosmid and plasmid libraries were constructed using genomic DNA purified from whole animals of the S2F2 line, which was clonally derived from a single animal. For WGS sequencing, we generated read pairs from the plasmid and fosmid libraries equivalent to 7X sequence coverage of the genome, with the bulk of the reads (6.7X) deriving from the plasmid library. In addition, we will produce ~50,000 Expressed Sequence Tags (ESTs) from cDNA libraries. This genome has proven to be A/T rich, and very repetitious, heterozygous (even though the animals used for DNA preparation were clonally derived) having portions that recombine, making automated assembly of the genome very difficult. The final assembly will be posted to the GSC ftp site for download, and the EST data will be available from the dbEST database in GenBank once it is generated. All trace files are available from the NCBI Trace Archive and the WGS data generated is available from the GSC ftp site. Funding for the sequence characterization of the planarian genome is being provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

Publications

None found.

Data Links

Species Name Data Type
Schmidtea mediterranea FTP Link
Schmidtea mediterranea NCBI Genome Page Link
Schmidtea mediterranea NCBI Trace Archive Link