Status
v1.0 (July 24, 2007): This Lottia gigantea genome sequence was assembled using the JGI assembler, Jazz, constructed from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from the finished assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses, reported here as the Lotgi1 annotation.
Summary statistics for the 1.0 release (Lotgi1):
| Nuclear Genome Assembly: | Lotgi1 |
| Nuclear genome size (Mbp) | 359.5 |
| Sequencing read coverage depth | 8.87x |
| Reported # of contigs | 20,146 |
| # of nuclear scaffolds | 4,475 |
| # of nuclear scaffolds >2 Kbp | 2,631 |
| Nuclear scaffold N/L50 | 51/1.87 Mbp |
| Three largest Scaffolds (Mbp) |
9.4
7.1
6.4
|
| ESTs: | Data set | # sequences total | # mapped to genome | # not mapped to genome | % mapped to genome |
| EST clusters | EstClusters_naClusterCr705LottiaJgi20060727 | 38,599 | 35,832 | 2,767 | 93% |
| ESTs | Ests_naEstLottiaJgi20060727 | 252,091 | 231,940 | 20,151 | 92% |
| Gene Models: | Lotgi11 |
| length (bp) of: average | |
| gene | 5,234 |
| transcript | 1,286 |
| exon | 213 |
| intron | 787 |
| description: | |
| protein length (aa) | 378 |
| exons per gene | 6.0 |
| # of gene models | 23,851 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS
Insights into bilaterian evolution from three spiralian genomes.
Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696
Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS
Insights into bilaterian evolution from three spiralian genomes.
Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
