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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.
Coronuloid barnacles are epibionts of several marine vertebrates (including cetaceans and sea turtles) as well as invertebrates, and are assigned to two families of turtle barnacles (Chelonibiidae Pilsbry, 1916 and Platylepadidae Newman & Ross, 1976) and one family of whale barnacles (Coronulidae Leach, 1817). Chelonibiids and coronulids have a scanty, albeit significant fossil record extending back to the Eocene and Pliocene, respectively; in turn, the fossil record of platylepadids is limited to a single record from the Upper Pleistocene. Here we report on an isolated carinolateral compartment of Platylepas Gray, 1825, the type genus of the family, from Lower Pleistocene (Gelasian) epibathyal deposits exposed at Milazzo (Sicily, Italy). This specimen is here designated holotype of a new species, †Platylepas mediterranea sp. nov. We argue that, like most extant members of Platylepas, †P. mediterranea sp. nov. lived partially embedded in the skin of a sea turtle. This record of an extinct platylepadid – the first from the Mediterranean region and the second worldwide – pushes back the fossil record of Platylepadidae to the lowermost Quaternary, thus possibly supporting an even earlier (e.g., Neogene) timing for the origin of this family and adding a new chapter to the evolutionary history of one of the most diverse and successful lineages of epizoic crustaceans.
The article presents a potentially obligate association of a pleustid amphipod of the genus Pleusymtes (Crustacea: Amphipoda: Pleustidae) with the large sea anemone Urticina eques (Gosse, 1858) (Anthozoa: Actiniaria: Actiniidae) from shallow waters of the Barents Sea. The new species shows a conspicuously striped (disruptive or aposematic) colouration, unlike other Arctic species of the genus, which shows a potential for its permanent connection with anemones. It is possible that this is the first known possibly obligatory anemone-associated species, within the genus and the family Pleustidae. The article discusses the taxonomy, morphological differences from congeners and ecological features of the new species, as well as the known symbiotic associations of sea anemones (as hosts) in Arctic and sub-Arctic waters.
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.
A new alpheid shrimp, Aretopsis sandybrucei sp. nov., is described on the basis of three specimens collected from three deep-water banks in the Chesterfield Plateau of the Coral Sea, between New Caledonia and Queensland, Australia, at a depth range of 280–550 m. The new species is the first known deep-water species of the genus Aretopsis De Man, 1910, with its two congeners, A. amabilis De Man, 1910 and A. manazuruensis Suzuki, 1971, being confined to the lower intertidal and shallow subtidal areas, to a maximum depth of 50 m. Based on morphological grounds, A. sandybrucei sp. nov. can be easily separated from A. amabilis and A. manazuruensis by the generally much stouter third to fifth pereiopods, with their dactyli each bearing a very small secondary unguis on the flexor margin, in comparison to a much stronger one in the other two species. Aretopsis sandybrucei sp. nov. also differs from A. amabilis and A. manazuruensis by the less contrasting colour pattern, including the more translucent, dull yellowish chelae and tail fan. An association of A. sandybrucei sp. nov. with a deep-water hermit crab appears to be highly likely due to the presence of several large hermit crabs (Paguridae) in at least one of the three dredge/bottom trawl hauls, which was also containing a paratype of the new species. The taxonomic status of A. amabilis and A. manazuruensis is discussed.