What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Greshake Tzovaras, Bastian; Segers, Francisca H. I. D.; Bicker, Anne; Dal Grande, Francesco; Otte, Jürgen; Anvar, Seyed Yahya; Hankeln, Thomas; Schmitt, Imke; Ebersberger, Ingo

doi:10.1093/gbe/evaa049

What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen

Journal Article · Thu Mar 12 00:00:00 EDT 2020 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evaa049· OSTI ID:1629509

Greshake Tzovaras, Bastian ^[1]; Segers, Francisca H. I. D. ^[2]; Bicker, Anne ^[3]; Dal Grande, Francesco ^[4]; Otte, Jürgen ^[5]; Anvar, Seyed Yahya ^[6]; Hankeln, Thomas ^[3]; Schmitt, Imke ^[7]; ^[8]

Goethe Univ., Frankfurt (Germany). Inst. of Cell Biology and Neuroscience. Applied Bioinformatics Group; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Paris (France). Center for Research & Interdisciplinarity; DOE/OSTI
Goethe Univ., Frankfurt (Germany). Inst. of Cell Biology and Neuroscience. Applied Bioinformatics Group; LOEWE Center for Translational Biodiversity Genomics, Frankfurt (Germany)
Johannes Gutenberg Univ., Mainz (Germany). Inst. for Organismic and Molecular Evolution. Molecular Genetics and Genome Analysis
LOEWE Center for Translational Biodiversity Genomics, Frankfurt (Germany); Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt (Germany)
Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt (Germany)
Leiden Univ. (Netherlands). Medical Center. Dept. of Human Genetics
LOEWE Center for Translational Biodiversity Genomics, Frankfurt (Germany); Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt (Germany); Goethe Univ., Frankfurt (Germany). Inst. for Ecology, Diversity, and Evolution. Molecular Evolutionary Biology Group
Goethe Univ., Frankfurt (Germany). Inst. of Cell Biology and Neuroscience. Applied Bioinformatics Group; LOEWE Center for Translational Biodiversity Genomics, Frankfurt (Germany); Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt (Germany)

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ~20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1629509

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 4 Vol. 12; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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