Status
(October 2016) The Pavlovales sp. CCMP2436 genome was sequenced with Illumina technology, assembled with AllPathsLG, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina technology, and assembled with Rnnotator. The mitochondrial and plastid genomes were sequenced with Illumina technology and assembled with AllPathsLG.
Summary statistics for the Pavlovales sp. CCMP2436 v1.0 release are
below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 165.41 |
| Sequencing read coverage depth | 124.7x |
| # of contigs | 26909 |
| # of scaffolds | 2243 |
| # of scaffolds >= 2Kbp | 1910 |
| Scaffold N50 | 196 |
| Scaffold L50 (Mbp) | 0.25 |
| # of gaps | 24666 |
| % of scaffold length in gaps | 24.3% |
| Three largest Scaffolds (Mbp) | 1.48, 1.42, 1.10 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 207830398 | 189339800 | 91.1% |
| Other | JGI_RNA_contigs | 87591 | 60499 | 69.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1616 | 1184 |
| transcript | 991 | 864 |
| exon | 323 | 174 |
| intron | 305 | 194 |
| description: | ||
| protein length (aa) | 278 | 222 |
| exons per gene | 3.07 | 2 |
| # of gene models | 26034 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C
Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.
Life Sci Alliance. 2023 Mar;6(3):. doi: 10.26508/lsa.202201833
Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C
Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.
Life Sci Alliance. 2023 Mar;6(3):. doi: 10.26508/lsa.202201833
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.
