Red Algal Resources to Promote Integrative Research in Algal Genomics

    These bioinformatic resources were developed by a global community of scientists working together in the US NSF-supported Porphyra Research Collaboration Network (NSF 0741907: The Porphyra genome: Promoting resource development and integrative research in algal genomics) and by a US DOE Joint Genome Institute (JGI) contract from the JGI Community Science Program for the Porphyra umbilicalis genome. These resources are made available to the scientific community through support of Rutgers University, the University of Maine, and the NSF Porphyra RCN grant. Data generated by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.
    Data from the Porphyra JGI project were deposited to NCBI within the BioProject PRJNA234409 and as Whole Genome Shotgun project MXAK00000000m version MXAK01000000 to DDBJ/ENA/GenBank. The chloroplast genome was assembled and is deposited as GenBank Accession MF385003. The Porphyra genome is also available from the JGI plant genomics portal Phytozome, which has other analysis tools including an assembly browser. The Porphyra umbilicalis genome and associated analyses are published as Brawley, S. H., Blouin, N. A., Ficko-Blean, E., Wheeler, G. L., Lohr, M. et al. 2017. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)
    Transcriptomic and genomic data that are part of this BLAST resource site are from the Porphyra umbilicalis genome (v.1.5), and other algal transcriptomes and genomes, including transcriptomes from the Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biol 12(6): e1001889.. In addition to the primary Porphyra v.1.5 assembly (Brawley et al., 2017), scaffolds belonging to contaminating bacteria (bacterialV1.4) and eukaryotes (eukaryoteOtherV1.4) that were bioinformatically separated from the Porphyra scaffolds are available here, as well as genomic resources from other red algal sequencing projects and some related lineages. These resources are being maintained by Rutgers University, which will add other red algal genomes/transcriptomes as they become available.

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