Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes

BACKGROUND: Several lines of evidence indicate that polyploidy occurred by around 54 million years ago, early in the history of legume evolution, but it has not been known whether this event was confined to the papilionoid subfamily (Papilionoideae; e.g. beans, medics, lupins) or occurred earlier. Determining the timing of the polyploidy event is important for understanding whether polyploidy might have contributed to rapid diversification and radiation of the legumes near the origin of the family; and whether polyploidy might have provided genetic material that enabled the evolution of a novel organ, the nitrogen-fixing nodule. Although symbioses with nitrogen-fixing partners have evolved in several lineages in the rosid I clade, nodules are widespread only in legume taxa, being nearly universal in the papilionoids and in the mimosoid subfamily (e.g., mimosas, acacias)--which diverged from the papilionoid legumes around 58 million years ago, soon after the origin of the legumes. METHODOLOGY/PRINCIPAL FINDINGS: Using transcriptome sequence data from Chamaecrista fasciculata, a nodulating member of the mimosoid clade, we tested whether this species underwent polyploidy within the timeframe of legume diversification. Analysis of gene family branching orders and synonymous-site divergence data from C. fasciculata, Glycine max (soybean), Medicago truncatula, and Vitis vinifera (grape; an outgroup to the rosid taxa) establish that the polyploidy event known from soybean and Medicago occurred after the separation of the mimosoid and papilionoid clades, and at or shortly before the Papilionoideae radiation. CONCLUSIONS: The ancestral legume genome was not fundamentally polyploid. Moreover, because there has not been an independent instance of polyploidy in the Chamaecrista lineage there is no necessary connection between polyploidy and nodulation in legumes. Chamaecrista may serve as a useful model in the legumes that lacks a paleopolyploid history, at least relative to the widely studied papilionoid models

SENSITIVITY OF RESOLVED MOUNTAIN DRAG TO MODEL RESOLUTION FOR MAP CASE STUDIES

Seven mountain wave case studies from the Mesoscale Alpine Programme (MAP) have been used to investigate the variation in the resolved surface pressure drag due to the Alps with model horizontal resolution. The three independent modelling systems tell the same story. For cases with small southerly (or northerly) wind-speeds near mountain crest level (< 10 m s-1), most of the drag was produced by low-level flow splitting around the Alpine barrier and the drags were converging. For situations where the southerly (or northerly) wind component increased strongly with height due to the location of the jet-stream directly above the Alps, the larger wind-speeds near mountain crest level forced much stronger mountain waves in the flow aloft. For such cases, the drag increased strongly as the grid-spacing was reduced from 12km to 4km. This has important consequences for the use of drag parameterisations

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

Background: Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. Results: Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. Conclusions: Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation

Rapid development and persistence of efficient subglacial drainage under 900 m-thick ice in Greenland

Intensive study of the Greenland Ice Sheet's (GrIS) subglacial drainage has been motivated by its importance for ice dynamics and for nutrient/sediment export to coastal ecosystems. This has revealed consistent seasonal development of efficient subglacial drainage in the lower ablation area. While some hydrological models show qualitative agreement with field data, conflicting evidence (both field- and model-based) maintains uncertainty in the extent and rate of efficient drainage development under thick (∼1 km) ice. Here, we present the first simultaneous time series of directly-observed subglacial drainage evolution, supraglacial hydrology and ice dynamics over 11 weeks in a large GrIS catchment. We demonstrate development of a fast/efficient subglacial drainage system extending from the margin to beneath ice >900 m thick, which then persisted with little response to highly variable moulin inputs including extreme melt events and extended periods (2 weeks) of low melt input. This efficient system evolved within ∼3 weeks at a moulin initiated when a fracture intersected a supraglacial river (rather than hydrofracture and lake drainage). Ice flow response to surface melt inputs at this site follows a pattern commonly observed in the lower GrIS ablation area, and by assuming a strong relationship between ice dynamics and subglacial hydrology, we infer that efficient subglacial drainage evolution is widespread under 900 m-thick ice in west Greenland. This time series of tracer transit characteristics through a developing and then persistent efficient drainage system provides a unique data set with which to validate and constrain existing numerical drainage system models, extending their capability for simulating drainage system evolution under current and future conditionspublishedVersio

E-cadherin can limit the transforming properties of activating β-catenin mutations

Wnt pathway deregulation is a common characteristic of many cancers. But only Colorectal Cancer predominantly harbours mutations in APC, whereas other cancer types (hepatocellular carcinoma, solid pseudopapillary tumours of pancreas) have activating mutations in β-catenin (CTNNB1). We have compared the dynamics and the potency of β-catenin mutations in vivo. Within the murine small intestine (SI), an activating mutation of β-catenin took much longer to achieve a Wnt deregulation and acquire a crypt-progenitor-cell (CPC) phenotype than Apc or Gsk3 loss. Within the colon, a single activating mutation of β-catenin was unable to drive Wnt deregulation or induce the CPC phenotype. This ability of β-catenin mutation to differentially transform the SI versus the colon correlated with significantly higher expression of the β-catenin binding partner E-cadherin. This increased expression is associated with a higher number of E-cadherin:β-catenin complexes at the membrane. Reduction of E-cadherin synergised with an activating mutation of β-catenin so there was now a rapid CPC phenotype within the colon and SI. Thus there is a threshold of β-catenin that is required to drive transformation and E-cadherin can act as a buffer to prevent β-catenin accumulation

Seismic evidence for complex sedimentary control of Greenland Ice Sheet flow

The land-terminating margin of the Greenland Ice Sheet has slowed down in recent decades, although the causes and implications for future ice flow are unclear. Explained originally by a self-regulating mechanism where basal slip reduces as drainage evolves from low to high efficiency, recent numerical modeling invokes a sedimentary control of ice sheet flow as an alternative hypothesis. Although both hypotheses can explain the recent slowdown, their respective forecasts of a long-term deceleration versus an acceleration of ice flow are contradictory. We present amplitude-versus-angle seismic data as the first observational test of the alternative hypothesis. We document transient modifications of basal sediment strengths by rapid subglacial drainages of supraglacial lakes, the primary current control on summer ice sheet flow according to our numerical model. Our observations agree with simulations of initial postdrainage sediment weakening and ice flow accelerations, and subsequent sediment restrengthening and ice flow decelerations, and thus confirm the alternative hypothesis. Although simulated melt season acceleration of ice flow due to weakening of subglacial sediments does not currently outweigh winter slowdown forced by self-regulation, they could dominate over the longer term. Subglacial sediments beneath the Greenland Ice Sheet must therefore be mapped and characterized, and a sedimentary control of ice flow must be evaluated against competing self-regulation mechanismspublishersversionPeer reviewe

The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus

Differential expression analysis between parasitic nematode strains is commonly used to implicate candidate genes in anthelmintic resistance or other biological functions. We have tested the hypothesis that the high genetic diversity of an organism such as Haemonchus contortus could complicate such analyses. First, we investigated the extent to which sequence polymorphism affects the reliability of differential expression analysis between the genetically divergent H. contortus strains MHco3(ISE), MHco4(WRS) and MHco10(CAVR). Using triplicates of 20 adult female worms from each population isolated under parallel experimental conditions, we found that high rates of sequence polymorphism in RNAseq reads were associated with lower efficiency read mapping to gene models under default TopHat2 parameters, leading to biased estimates of inter-strain differential expression. We then showed it is possible to largely compensate for this bias by optimising the read mapping single nucleotide polymorphism (SNP) allowance and filtering out genes with particularly high single nucleotide polymorphism rates. Once the sequence polymorphism biases were removed, we then assessed the genuine transcriptional diversity between the strains, finding ≥824 differentially expressed genes across all three pairwise strain comparisons. This high level of inter-strain transcriptional diversity not only suggests substantive inter-strain phenotypic variation but also highlights the difficulty in reliably associating differential expression of specific genes with phenotypic differences. To provide a practical example, we analysed two gene families of potential relevance to ivermectin drug resistance; the ABC transporters and the ligand-gated ion channels (LGICs). Over half of genes identified as differentially expressed using default TopHat2 parameters were shown to be an artifact of sequence polymorphism differences. This work illustrates the need to account for sequence polymorphism in differential expression analysis. It also demonstrates that a large number of genuine transcriptional differences can occur between H. contortus strains and these must be considered before associating the differential expression of specific genes with phenotypic differences between strains