Status
v1.0 (December 20, 2007): The Selaginella moellendorffii genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses.
Summary statistics for the S. moellendorffii v1.0 release:
| Nuclear Genome Assembly1 | v1.0 |
| Nuclear genome size (Mbp) | 212.5 |
| Sequencing read coverage depth | 7.0x |
| Reported # of contigs | 5,156 |
| # of nuclear scaffolds | 759 |
| # of nuclear scaffolds >2 Kbp | 726 |
| Nuclear scaffold N/L50 | 38/1.7 Mbp |
| Three largest Scaffolds (Mbp) | 7.0 6.2 4.5 |
| ESTs: | Data set | # sequences total | # mapped to genome | # not mapped to genome | % mapped to genome |
| EST clusters | EstClusters_556_S_moellendorffii_Jgi20060227 | 19,871 | 17,514 | 2,357 | 88% |
| ESTs | Ests_naEstSelaginella_moellendorffiiAll20060227 | 93,812 | 89,049 | 4,763 | 95% |
| Gene Models2 | v1.0 all scaffolds2 | v1.0 non-redundant3 |
| length (bp) of: average | ||
| gene | 1711.37> | 1701.63 |
| transcript | 1229.57 | 1193.81 |
| exon | 213.66 | 213.44 |
| intron | 103.33 | 112.56 |
| description: | ||
| protein length (aa) | 392.04 | 381.85 |
| exons per gene | 5.75> | 5.59 |
| # of gene models | 34,697 | 22,285 |
[2] FilteredModels2 gene model track
[3] FilteredModels3 gene model track
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810
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.
