Refine
Year of publication
- 2020 (2) (remove)
Document Type
- Article (2)
Language
- English (2)
Has Fulltext
- yes (2)
Is part of the Bibliography
- no (2) (remove)
Keywords
- symbiosis (2) (remove)
Institute
Three groups of beetles inhabit cones of cycads (Cycadales) in the northern hemisphere and are believed to be involved in their pollination. The primitive weevil subtribe Allocorynina (Coleoptera: Belidae) is restricted to the New World cycad genera Dioon Lindl. and Zamia L. One group of weevils (Curculionidae), found only in Cycas L., appears to be a relatively recent colonizer of northern hemisphere cycads. Members of the beetle subfamily Pharaxonothinae (Erotylidae) occur in all Asian and New World cycad genera. Phylogenetic trees of these beetles, based on DNA analysis and supported with morphological studies, are compared to patterns of continental drift and cycad phylogenies. Laurasian origins are suggested for these beetle groups with high latitude dispersal for at least one of these groups during periods of global warm climates.
What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen
(2020)
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.