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"Donovan, C"
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Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity
The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research.
Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family.
Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae.
Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.
Journal Article
Living with obesity in Ireland: determinants, policy and future perspectives
Globally, the prevalence of those living with obesity (≥30 kg/m 2 ) is rising, with this trend expected to continue if firm and decisive policy interventions are not introduced. Across Europe, despite many consecutive policies aiming to reverse rising trends in weight status over recent decades, no country is currently on track to halt and reverse current trends in the coming years. This is evident in Ireland too, whereby the reporting of nationally representative weight status data show that targets have not been achieved since reporting began. The aim of this review is to critically appraise recent evidence relating to the key determinants of obesity including weight status, diet quality and physical activity with an emphasis on socioeconomic inequalities. And to consider these in the context of respective policy measures and propose future-focused recommendations. Furthermore, as with the complex nature of obesity, multifaceted approaches that shift the focus from the individual and place responsibility at a societal level will be reviewed.
Journal Article
Visual recognition of social signals by a tectothalamic neural circuit
Social affiliation emerges from individual-level behavioural rules that are driven by conspecific signals
1
–
5
. Long-distance attraction and short-distance repulsion, for example, are rules that jointly set a preferred interanimal distance in swarms
6
–
8
. However, little is known about their perceptual mechanisms and executive neural circuits
3
. Here we trace the neuronal response to self-like biological motion
9
,
10
, a visual trigger for affiliation in developing zebrafish
2
,
11
. Unbiased activity mapping and targeted volumetric two-photon calcium imaging revealed 21 activity hotspots distributed throughout the brain as well as clustered biological-motion-tuned neurons in a multimodal, socially activated nucleus of the dorsal thalamus. Individual dorsal thalamus neurons encode local acceleration of visual stimuli mimicking typical fish kinetics but are insensitive to global or continuous motion. Electron microscopic reconstruction of dorsal thalamus neurons revealed synaptic input from the optic tectum and projections into hypothalamic areas with conserved social function
12
–
14
. Ablation of the optic tectum or dorsal thalamus selectively disrupted social attraction without affecting short-distance repulsion. This tectothalamic pathway thus serves visual recognition of conspecifics, and dissociates neuronal control of attraction from repulsion during social affiliation, revealing a circuit underpinning collective behaviour.
A tectothalamic pathway for social affiliation in developing zebrafish dissociates neuronal control of attraction from repulsion during affiliation, revealing a circuit underpinning of collective behaviour
Journal Article
Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene
In this work, we investigate morphological differences between Arabidopsis thaliana, which has simple leaves, and its relative Cardamine hirsuta, which has dissected leaves comprising distinct leaflets. With the use of genetics, interspecific gene transfers, and time-lapse imaging, we show that leaflet development requires the REDUCED COMPLEXITY (RCO) homeodomain protein. RCO functions specifically in leaves, where it sculpts developing leaflets by repressing growth at their flanks. RCO evolved in the Brassicaceae family through gene duplication and was lost in A. thaliana, contributing to leaf simplification in this species. Species-specific RCO action with respect to its paralog results from its distinct gene expression pattern in the leaf base. Thus, regulatory evolution coupled with gene duplication and loss generated leaf shape diversity by modifying local growth patterns during organogenesis.
Journal Article
Radiation exposure induces genome-wide alternative splicing events in Aedes aegypti mosquitoes
Sterile insect technique is a method to control insect pest populations by sterilizing males with ionizing radiation. However, radiation sickness lowers the fitness of sterilized males. In this study, we investigate impacts of ionizing radiation on gene transcription, specifically alternative splicing events in irradiated male
Aedes aegypti
mosquitoes. We compared RNA sequencing data from mosquitoes irradiated with a single standard X-ray dose of 50 Grey and un-irradiated control mosquitoes using the Multivariate Analysis of Transcript Splicing computational tool. We found that radiation exposure caused alternative splicing events in 197 genes that are involved in a variety of biological processes including the Hippo and Notch cell signaling pathways. Our results suggest that radiation damage produced by ionizing radiation can alter the splicing of genes involved in important biological functions in male
Ae. aegypti
mosquitoes. These findings identify several new leads for new projects aimed at understanding the impact of radiation-induced alternative splicing on mosquito fitness and improving sterile insect technique by the development of radio-resistant mosquito strains.
Journal Article
Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis
This study was conducted to explore specific chill models and the mechanisms underlying rhizome bud dormancy break in Polygonatum kingianum. Rhizome buds were subjected to various chilling temperatures for different duration and then transferred to warm conditions for germination and subsequent evaluation of their response to temperature and chilling requirements. A CUkingianum model was constructed to describe the contribution of low temperature to the chill unit, and it was suggested that 2.97°C was the optimum temperature and that 11.54°C was the upper limit for bud release. The CASkingianum model showed the relationship between chilling accumulation and sprouting percentage; therefore, rhizome bud development could be predicted through the model. Weighted correlation network analysis (WGCNA) of transcriptomic data of endo-, eco- and nondormant rhizome buds generated 33 gene modules, 6 of which were significantly related to bud sprouting percentage. In addition, 7 significantly matched transcription factors (TFs) were identified from the promoters of 17 \"real\" hub genes, and DAG2 was the best matched TF that bound to AAAG element to regulate gene expression. The current study is valuable for developing a highly efficient strategy for seedling cultivation and provides strong candidates for key genes related to rhizome bud dormancy in P. kingianum.
Journal Article
Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (
Inga
and
Leucaena
) and two recently published plastomes (
Acacia
and
Prosopis
) and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in
Acacia
and
Inga
. Mimosoid plastomes harbor additional interesting features, including loss of
clpP
intron1 in
Inga
, accelerated rates of evolution in
clpP
for
Acacia
and
Inga
and
dN/dS
ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.
Journal Article
Toward a Global Phylogeny of the Brassicaceae
The Brassicaceae is a large plant family (338 genera and 3,700 species) of major scientific and economic importance. The taxonomy of this group has been plagued by convergent evolution in nearly every morphological feature used to define tribes and genera. Phylogenetic analysis of 746 nrDNA internal transcribed spacer (ITS) sequences, representing 24 of the 25 currently recognized tribes, 146 genera, and 461 species of Brassicaceae, produced the most comprehensive, single-locus–based phylogenetic analysis of the family published to date. Novel approaches to nrDNA ITS analysis and extensive taxonomic sampling offered a test of monophyly for a large complement of the currently recognized tribes and genera of Brassicaceae. In the most comprehensive analysis, tribes Alysseae, Anchonieae plus Hesperideae, Boechereae, Cardamineae, Eutremeae, Halimolobeae, Iberideae, Noccaeeae, Physarieae, Schizopetaleae, Smelowskieae, and Thlaspideae were all monophyletic. Several broadly defined genera (e.g., Draba and Smelowskia) were supported as monophyletic, whereas others (e.g., Sisymbrium and Alyssum) were clearly polyphyletic. Analyses of ITS data identified several problematic sequences attributable to errors in sample identification or database submission. Results from parsimony ratchet and Bayesian analyses recovered little support for the backbone of the phylogeny, suggesting that many lineages of Brassicaceae have undergone rapid radiations that may ultimately be difficult to resolve with any single locus. However, the development of a preliminary supermatrix including the combination of 10 loci for 65 species provides an initial estimate of intertribal relations and suggests that broad application of such a method will provide greater understanding of relationships in the family.
Journal Article