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Precise estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. We present here a fast, easy-to-implement and precise method to estimate genome size from the number of bases sequenced and the mean sequence coverage. To estimate the latter, we take advantage of the fact that a precise estimation of the Poisson distribution parameter lambda is possible from truncated data, restricted to the part of the coverage distribution representing the true underlying distribution. With simulations we could show that reasonable genome size estimates can be gained even from low-coverage (10X), highly discontinuous genome drafts. Comparison of estimates from a wide range of taxa and sequencing strategies with flow-cytometry estimates of the same individuals showed a very good fit and suggested that both methods yield comparable, interchangeable results.
Background: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non–genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step.
Results: The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life.
Conclusions: It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are non-reducing polyketide synthases (NR-PKSs), and cytochrome P450s. However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acid synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for olivetoric acid and physodic acid biosynthesis, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for the olivetoric acid and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for olivetoric acid and physodic acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.
The evolution and interrelationships of carnivorous squamates (mosasaurs, snakes, monitor lizards, Gila Monsters) are a contentious part of reptile systematics and go to the heart of conflict between morphological and molecular data in inferring evolutionary history. One of the best-preserved fossils in this motley grouping is “Saniwa” feisti Stritzke, 1983, represented by complete skeletons from the early-middle Eocene of Messel, Germany. We re-describe it on the basis of superficial examination, stereoradiography, and high-resolution X-ray computed tomography of new and published specimens. The scalation of the lizard is unique, consisting of small, keeled scales on the head (including a row of enlarged medial supraorbitals) and large, rhomboidal, keeled scales (invested by osteoderms) that covered the rest of the body. Two paired longitudinal rows of enlarged scales ran down the neck. The head was laterally compressed and box-shaped due to the presence of a strong canthal-temporal ridge; the limbs and tail were very long. Notable osteological features include: a toothed, strap-like vomer; septomaxilla with a long posterior process; palpebral with a long posterolateral process; a lacrimal boss and a single lacrimal foramen; a well-developed cultriform process of the parabasisphenoid; two hypoglossal (XII) foramina in addition to the vagus; a lack of resorption pits for replacement teeth; and possibly the presence of more than one wave of developing replacement teeth per locus. There are no osteological modifications suggestive of an intramandibular hinge, but postmortem displacement of the angular-prearticular-surangular complex in multiple specimens suggests that there might have been some degree of mobility in the lower jaw based on soft-tissue modifications. Using phylogenetic analyses on a data-set comprising 473 morphological characters and 46 DNA loci, we infer that a monophyletic Palaeovaranidae Georgalis, 2017, including Eosaniwa Haubold, 1977, lies on the stem of Varanidae Merrem, 1820, basal to various Cretaceous Mongolian taxa. We transfer feisti to the new genus Paranecrosaurus n. gen. Analysis of gut contents reveals only the second known specimen of the cryptozoic lizard Cryptolacerta hassiaca Müller, Hipsley, Head, Kardjilov, Hilger, Wuttke & Reisz, 2011, confirming a diet that was at least partly carnivorous; the preservation of the teeth of C. hassiaca suggests that the gastric physiology of Paranecrosaurus feisti (Stritzke, 1983) n. comb. had high acidity but low enzyme activity. Based on the foregoing and linear discriminant function analysis, we reconstruct P. feisti n. comb., as a powerful, widely roaming, faunivorous-carnivorous stem monitor lizard with a sensitive snout. If the molecular phylogeny of anguimorphs is correct, then many of the features shared by Helodermatidae Gray, 1837 and Varanidae must have arisen convergently, partly associated with diet. In that case, a reconciliation of morphological and molecular data would require the discovery of equally primitive fossils on the helodermatid stem.
Tree water relations of mature oaks in southwest Germany under extreme drought stress in summer 2018
(2021)
Mature oak stands of different tree height at four sandy valley river sites (Quercus robur) and one south-exposed schist slope (Qu. petraea) in the middle Rhine and lower Main valley were studied from early summer 2017 (normal wet year) until the end of 2018 (extremely hot and dry year). Tree water relations (ΨPD, RWC, sap flow rates) were monitored together with soil water relations, LAI and leaf chl content. In two sandy sites with presumed continuous capillary water access from the groundwater aquifer, sap flow rates of the large trees (30 m) and estimated canopy conductance decreased to about 50% of the maximum value in the course of summer 2018, but recovered in autumn. At two other sites, with smaller trees (14–24 m) and presumed interrupted capillary water access during mid-summer 2018, sap flow rates and canopy conductance broke down completely and trees shed a large proportion of leaves in summer. In one of these sites, ΨPD decreased (reversibly) to -4 MPa, one of the lowest values reported in the literature for central Europe, and tree damage resulted not only in extreme leaf shedding, but also in susceptibility to uprooting (in 2 out of 5 measured trees) by thunderstorm gusts in autumn 2018. At the schist slope site, where oaks reached the lowest height and stand density of all sites, sap flow rates remained similar to the values found at the presumed capillary-water supplied sandy sites, indicating access to rock fissure water even at the peak of the drought period. Our findings corroborate the prediction from vegetation modelling that several Qu. robur stands in the Rhine-Main valleys will be prone to severe forest dieback in the forthcoming decades.