Description

This track shows the Tetraodon nigroviridis V8 assembly (March 2007) provided by Genoscope, Evry, France. The assembly has a sequence coverage of about 7.9X and contains 1,849 placed scaffolds (15,206 unplaced scaffolds) and covers >90% of the genome which is estimated to be 350 million base pairs.

In dense mode, this track depicts the path through the draft (aka the golden path) used to create the assembled sequence. Clone boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist in the path, spaces are shown between the gold and brown blocks. If the relative order and orientation of the supercontigs between the two blocks is known, a line is drawn to bridge the blocks.

The Genome Browser depicts the Tetraodon genome as 21 chromosomes, 5 random chromosomes in which scaffolds and ultracontigs are not ordered/oriented, and 1 chromosome of unmapped scaffolds and ultracontigs (chrUn_random).

All components within this track are of fragment type "W" (WGS supercontig).

Methods

This assembly was constructed using the whole genome shotgun (WGS) approach, resulting in a sequence coverage of about 7.9X. The assembly contains 1,849 placed scaffolds (N50 size 1349163) and 15,296 unplaced scaffolds (N50 size 54038) generated by the Arachne program and covers more than 90% of the genome. Additional linking data were used to build ultracontigs and to organize the assembly into chromosomes. Genoscope estimates the size of the Tetraodon genome to be about 350 Mb.

The Tetraodon WGS project may be found in GenBank as accession number CAAE01000000, consisting of sequences CAAE01000001-CAAE01025773.

Credits

The Tetraodon V8 release of the genome sequence was produced by a collaboration between Genoscope and the Center for Genome Research at the Broad Institute of MIT and Harvard.