Status
The genome sequence and gene models of Porphyra umbilicalis were downloaded from NCBI, on March 27, 2018. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. The latest data is available at Phytozome.
Summary statistics for the Porphyra umbilicalis release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 87.89 |
| Sequencing read coverage depth | |
| # of contigs | 2184 |
| # of scaffolds | 2126 |
| # of scaffolds >= 2Kbp | 1418 |
| Scaffold N50 | 130 |
| Scaffold L50 (Mbp) | 0.20 |
| # of gaps | 58 |
| % of scaffold length in gaps | 0.1% |
| Three largest Scaffolds (Mbp) | 0.97, 0.80, 0.73 |
| Gene Models | ExternalModels | |
| length (bp) of: | average | median |
| gene | 1826 | 1488 |
| transcript | 1582 | 1290 |
| exon | 814 | 574 |
| intron | 261 | 207 |
| description: | ||
| protein length (aa) | 444 | 350 |
| exons per gene | 1.94 | 1 |
| # of gene models | 13567 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE
Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).
Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6361-E6370. doi: 10.1073/pnas.1703088114
Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE
Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).
Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6361-E6370. doi: 10.1073/pnas.1703088114
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.
