Info • Zygnema circumcarinatum UTEX 1560

Status

The Zygnema circumcarinatum UTEX 1560 genome assembly and gene models have not been determined by the JGI, but were downloaded from https://bcb.unl.edu/Zygnema_4genomes/ (Yanbin Yin Lab, University of Nebraska - Lincoln) on January 24, 2023. Please note that this copy of the genome is not maintained by the Yin Lab and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.

Please note: the full set of published MAKER-P models are included as the ExternalsModels gene track. Prior v1 gene models were mapped to this v2 assembly. The v1 assembly and annotation are available separately in the downloads section.

Genome Assembly
Genome Assembly size (Mbp) 67.28
Sequencing read coverage depth 103.4x
# of contigs 4336
# of scaffolds 514
# of scaffolds >= 2Kbp 200
Scaffold N50 7
Scaffold L50 (Mbp) 3.79
# of gaps 3822
% of scaffold length in gaps 2.3%
Three largest Scaffolds (Mbp) 8.43, 4.99, 4.79


Gene Models FilteredModels1
length (bp) of: average median
gene 4016 3138
transcript 1860 1485
exon 253 141
intron 342 255
description:
protein length (aa) 491 370
exons per gene 7.35 6
# of gene models 12436


Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Feng Xuehuan, Zheng Jinfang, Irisarri Iker, Yu Huihui, Zheng Bo, Ali Zahin, de Vries Sophie, Keller Jean, Fürst-Jansen Janine M.R., Dadras Armin, Zegers Jaccoline M.S., Rieseberg Tim P., Ashok Amra Dhabalia, Darienko Tatyana, Bierenbroodspot Maaike J., Gramzow Lydia, Petroll Romy, Haas Fabian B., Fernandez-Pozo Noe, Nousias Orestis, Li Tang, Fitzek Elisabeth, Grayburn W. Scott, Rittmeier Nina, Permann Charlotte, Rümpler Florian, Archibald John M., Theißen Günter, Mower Jeffrey P., Lorenz Maike, Buschmann Henrik, von Schwartzenberg Klaus, Boston Lori, Hayes Richard D., Daum Chris, Barry Kerrie, Grigoriev Igor V., Wang Xiyin, Li Fay-Wei, Rensing Stefan A., Ari Julius Ben, Keren Noa, Mosquna Assaf, Holzinger Andreas, Delaux Pierre-Marc, Zhang Chi, Huang Jinling, Mutwil Marek, de Vries Jan, Yin Yanbin
Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution
biorxiv.org

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.