Co-Variation between Seed Dormancy, Growth Rate and Flowering Time Changes with Latitude in Arabidopsis thaliana

Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.<br

The evolution and mutational robustness of chromatin accessibility in Drosophila

Abstract Background The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila. Results We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that our models generalize well across substantially evolutionarily diverged species of insects, implying that the sequence determinants of accessibility are highly conserved. Using our model to examine species-specific gains in accessibility, we find evidence suggesting that these regions may be ancestrally poised for evolution. Using in silico mutagenesis, we show that accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that accessibility is mutationally robust. Subsequently, we show that accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. Conversely, simulations under strong selection demonstrate that accessibility can be extremely malleable despite its robustness. Finally, we identify motifs predictive of accessibility, recovering both novel and previously known motifs. Conclusions These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks to explore fundamental questions in regulatory genomics and evolution

The Conserved RNA Exonuclease Rexo5 Is Required for 3′ End Maturation of 28S rRNA, 5S rRNA, and snoRNAs

Non-coding RNA biogenesis in higher eukaryotes has not been fully characterized. Here, we studied the Drosophila melanogaster Rexo5 (CG8368) protein, a metazoan-specific member of the DEDDh 3′-5′ single-stranded RNA exonucleases, by genetic, biochemical, and RNA-sequencing approaches. Rexo5 is required for small nucleolar RNA (snoRNA) and rRNA biogenesis and is essential in D. melanogaster. Loss-of-function mutants accumulate improperly 3′ end-trimmed 28S rRNA, 5S rRNA, and snoRNA precursors in vivo. Rexo5 is ubiquitously expressed at low levels in somatic metazoan cells but extremely elevated in male and female germ cells. Loss of Rexo5 leads to increased nucleolar size, genomic instability, defective ribosome subunit export, and larval death. Loss of germline expression compromises gonadal growth and meiotic entry during germline development

Life history traits as a function of the gradients in latitude (expressed in °North) and/or population structure (measured as the relative contribution to the first population structure group).

<p>Only significant effects reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061075#pone-0061075-t002" target="_blank">Table 2</a> are shown with the percentage of variance explained associated. (a) Latitude has a significant effect on primary dormancy and flowering time, p<0.05 and p<0.001, respectively. (b) Population structure estimated by the probability to belong to one of the two clusters, has a significant effect on primary and secondary dormancy, p<0.01 and p<0.1, respectively.</p

Histograms showing natural genetic variation of life history traits using adjusted means.

<p>(a) Primary dormancy (days): measured by number of days required to reach 50% of germination (DSDS50). (b) Secondary dormancy (% of germination decrease per day): measured by the reduction in germination rate of fully after-ripened seed after a 6-week long exposure to 4°C in darkness. (c) Vegetative growth rate (cm²/day): measured by increase of leaf area during one week in the greenhouse. (d) Flowering time (days): number of days until opening of the first flower.</p

Pairs of trait with a latitudinal gradient of co-variation.

<p>Significance was tested with a linear regression model, with latitude as a dependent variable (see methods). p-values associated to the interaction between the traits and the percentage of the latitudinal variation explained by the interaction are shown below and above the diagonal, respectively.</p

Major life-history traits and their effect on fitness in annual plant species.

<p>Green triangle: plant, yellow circle: seed, green sector: conditions favourable for growth, grey sector: adverse conditions. Red arrows show the participation of each trait to lifetime fitness, via their effect on survival, resource acquisition or fecundity.</p