Status
This v3.0 assembly (22 Aug 2011) is a targeted finishing release with 4 chromosomes completely finished with no gaps: chromosomes: 2,3,18 and 19. The v2.0 release was very complete with 19 chromosomes completed telomere to telomere. There are also 2 additional scaffolds which do not appear to be organelle by BLAST and could fit inside some of the larger gaps in the main genome.
This v3.2 annotation (22 Nov 2013) is improved with RNA-Seq and manual curation.
Summary statistics for the Micromonas pusilla CCMP1545
v3.2 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 21.95 |
| Sequencing read coverage depth | Finished |
| # of contigs | 397 |
| # of scaffolds | 21 |
| # of scaffolds >= 2Kbp | 21 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.18 |
| # of gaps | 376 |
| % of scaffold length in gaps | 1.0% |
| Three largest Scaffolds (Mbp) | 2.21, 2.17, 1.95 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | JGI_ESTs | 29928 | 28556 | 95.4% |
| Other | JGI_EST_cluster_consensi | 12561 | 6782 | 54.0% |
| Gene Models | MBARI_models | |
| length (bp) of: | average | median |
| gene | 2007 | 1596 |
| transcript | 1801 | 1412 |
| exon | 840 | 527 |
| intron | 182 | 180 |
| description: | ||
| protein length (aa) | 551 | 425 |
| exons per gene | 2.14 | 2 |
| # of gene models | 9829 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222
Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222
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.
