Ciona Project Information

Contents

Who are we?

The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

What is Ciona savignyi?

Ciona savignyi

Ciona savignyi is a Pacific species of the order Ascidia (sea squirts), marine organisms which are sessile filter feeders as adults. C. savignyi has recently spread from Japan and can now be found in large numbers in protected waters, especially yacht harbors, along the West coast of the US. Development from the fertilized egg to the adult proceeds in three stages.

As urochordates, ascidians occupy a special position in the phylogenetic tree of biomedicine's model organisms: They are chordates (and as such share many fundamental aspects of the chordate body plan with vertebrates, in contrast to, for example, Drosophila), but they diverged from the other chordates just before the large scale gene duplications that occurred in the lineage of vertebrates. Thus, urochordates possess a unique combination of two highly desirable properties of experimental model organisms:

  1. Genetic and developmental simplicity that greatly facilitates experimental studies, and
  2. homologies with vertebrates that extend to high levels of development and tissue organization

Of the two invertebrate chordate phyla (cephalochordata and urochordata), which both occupy this early phylogenetic position, urochordata is the only one with representative species that can easily be cultured in the laboratory. Attempts have been made in several labs to culture amphioxus, with no success.

Ascidians are among the simplest chordates but their developmental mechanisms are largely conserved with those of vertebrates. Many structural features of morphogenesis in ascidians parallel those which are seen in higher vertebrates. To a large extent, the fate map and basic body plan of ascidians are superimposable with those of higher vertebrates. Most notably, the ascidian tadpole larva has a dorsal nerve cord and notochord.

A century of research has showcased the ascidianís ease of manipulation in the laboratory, as well as their scientific importance as simple chordate models. Ascidians have been studied as developmental models since the early twentieth century, when Conklin characterized the dramatic segregation of Cynthia (Styela) partita cytoplasm following fertilization. Since then, ascidians have remained favored model organisms for embryologists and developmental biologists, who have characterized mechanisms of ascidian fertilization, embryogenesis, and metamorphosis. A host of modern techniques and manipulations have been used to study ascidian development, including cell ablation, electroporation of eggs and embryos, antisense inactivation of mRNA, whole mount in situ hybridization, and overexpression of genes.

The genome size of Ciona sp. has been estimated to be 180 Mbp/haploid genome with 15,000 genes, less than one half of the number estimated for vertebrates. This is consistent with the tree-based prediction that ascidians have smaller gene families and less genetic redundancy because their lineage diverged from the chordates before the vertebrate genome duplications.

Sequencing Ciona

We have been funded by the National Human Genome Research Institute (NHGRI) to produce a high quality assembly of Ciona savignyi genome. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Whole genome shotgun libraries were prepared from Ciona genomic DNA obtained from the laboratory of Arend Sidow at Stanford. A plasmid library with an average insert size of 4 kb was prepared from randomly sheared and sized-selected DNA. Both ends of each plasmid were sequenced.

Data releases

In advance of a completed assembly of the Ciona data, we are making sequence and quality files for the individual reads available for download.

Data Version 9/20/01: 4,386,738 reads (estimated 14X genome coverage)

Data Version 6/14/01: 2,250,814 reads (estimated 7X genome coverage)