Status
[September 2023] The metagenome, from freshwater lake microbial communities collected in Wisconsin, United States, was sequenced using Illumina NovaSeq and assembled using MetaHipMer. Contigs were binned and high quality eukaryotic bins were identified using EukCC version 2.0. Metagenome bin 3300059473_4966, representing an unknown Trebouxiophyceae sp., was identified as highly complete and therefore annotated using the JGI Annotation Pipeline.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 14.82 |
| Sequencing read coverage depth | NA |
| # of contigs | 1108 |
| # of scaffolds | 1108 |
| # of scaffolds >= 2Kbp | 1108 |
| Scaffold N50 | 228 |
| Scaffold L50 (Mbp) | 0.02 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.18, 0.13, 0.09 |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1371 | 1101 |
| transcript | 1215 | 993 |
| exon | 632 | 396 |
| intron | 171 | 124 |
| description: | ||
| protein length (aa) | 405 | 331 |
| exons per gene | 1.92 | 2 |
| # of gene models | 8098 |
Collaborators
- Katherine McMahon at University of Wisconsin, Madison
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Oliver T, Varghese N, Roux S, Schulz F, Huntemann M, Clum A, Foster B, Foster B, Riley R, LaButti K, Egan R, Hajek P, Mukherjee S, Ovchinnikova G, Reddy TBK, Calhoun S, Hayes RD, Rohwer RR, Zhou Z, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Mouncey NJ, Del Rio TG, Grigoriev IV, Hofmeyr S, Oliker L, Yelick K, Anantharaman K, McMahon KD, Woyke T, Eloe-Fadrosh EA
Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.
Sci Data. 2024 Sep 4;11(1):966. doi: 10.1038/s41597-024-03826-8
Oliver T, Varghese N, Roux S, Schulz F, Huntemann M, Clum A, Foster B, Foster B, Riley R, LaButti K, Egan R, Hajek P, Mukherjee S, Ovchinnikova G, Reddy TBK, Calhoun S, Hayes RD, Rohwer RR, Zhou Z, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Mouncey NJ, Del Rio TG, Grigoriev IV, Hofmeyr S, Oliker L, Yelick K, Anantharaman K, McMahon KD, Woyke T, Eloe-Fadrosh EA
Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.
Sci Data. 2024 Sep 4;11(1):966. doi: 10.1038/s41597-024-03826-8
Links
- IMG study: Freshwater microbial communities from Lake Mendota, Crystal Bog Lake, and Trout Bog Lake in Wisconsin, United States
- JGI PhyloGroup Portals: Archaeplastida Viridiplantae Chlorophyta Trebouxiophyceae Chlorellaceae
- JGI EcoGroup Portals: Algae
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.
