What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen

  • 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.
Author:Bastian Greshake TzovarasORCiDGND, Francisca H. I. D. Segers, Anne Bicker, Francesco Dal GrandeORCiD, Jürgen OtteORCiDGND, Seyed Yahya Anvar, Thomas HankelnORCiDGND, Imke SchmittORCiDGND, Ingo EbersbergerORCiDGND
Parent Title (English):Genome biology and evolution
Publisher:Oxford University Press
Place of publication:Oxford
Document Type:Article
Date of Publication (online):2020/03/12
Date of first Publication:2020/03/12
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2021/08/19
Tag:SPAdes; chlorophyta; gene loss; metagenome assembly; microbiome; organellar ploidy levels; sequencing error; symbiosis
Page Number:16
First Page:309
Last Page:324
This study was funded through the programme “LOEWE – Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse's Ministry of Higher Education, Research, and the Arts.
Institutes:Biowissenschaften / Biowissenschaften
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (English):License LogoCreative Commons - Namensnennung-Nicht kommerziell 4.0