TY - JOUR A1 - Muiño, Jose M. A1 - de Bruijn, Suzanne A1 - Pajoro, Alice A1 - Geuten, Koen A1 - Vingron, Martin A1 - Angenent, Gerco C. A1 - Kaufmann, Kerstin T1 - Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor JF - Molecular biology and evolution : MBE N2 - lower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. KW - MADS-domain transcription factor KW - plant development KW - cis-regulatory evolution Y1 - 2015 U6 - https://doi.org/10.1093/molbev/msv210 SN - 1537-1719 SN - 0737-4038 VL - 33 IS - 1 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Wha Lee, Young A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella JF - Nature Communications N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. Y1 - 2015 U6 - https://doi.org/10.1038/ncomms8960 SN - 2041-1723 VL - 6 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Valente, Luis M. A1 - Phillimore, Albert B. A1 - Etienne, Rampal S. T1 - Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands JF - Ecology letters N2 - Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms. KW - Community assembly KW - diversification KW - dynamic equilibrium KW - island biogeography KW - phylogeny Y1 - 2015 U6 - https://doi.org/10.1111/ele.12461 SN - 1461-0248 SN - 1461-023X VL - 18 SP - 844 EP - 852 PB - Wiley-Blackwell CY - Oxford ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) JF - BMC Genomics N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1858-9 SN - 1471-2164 VL - 16 IS - 668 PB - Biomed Central CY - London ER - TY - JOUR A1 - Sbragaglia, Valerio A1 - Lamanna, Francesco A1 - Mat, Audrey M. A1 - Rotllant, Guiomar A1 - Joly, Silvia A1 - Ketmaier, Valerio A1 - de la Iglesia, Horacio O. A1 - Aguzzi, Jacopo T1 - Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk JF - PLoS one N2 - The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12–12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47%, timeless: 59%, bmal1: 79%) and Macrobrachium rosenbergii (clock: 100%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0141893 SN - 1932-6203 VL - 10 IS - 11 PB - Public Library of Science CY - Lawrence ER - TY - JOUR A1 - Pietra, Stefano A1 - Lang, Patricia A1 - Grebe, Markus T1 - SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana JF - Physiologia Plantarum N2 - Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning. Y1 - 2015 UR - http://onlinelibrary.wiley.com/doi/10.1111/ppl.12257/epdf U6 - https://doi.org/DOI: 10.1111/ppl.12257 VL - 153 IS - 3 SP - 440 EP - 453 ER - TY - JOUR A1 - Kiefer, Christian S. A1 - Claes, Andrea R. A1 - Nzayisenga, Jean-Claude A1 - Pietra, Stefano A1 - Stanislas, Thomas A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity JF - Development N2 - The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. KW - AIP1 KW - Actin KW - Arabidopsis KW - Patterning KW - Planar polarity Y1 - 2015 UR - http://dev.biologists.org/content/142/1/151.long U6 - https://doi.org/doi: 10.1242/dev.111013 IS - 142 SP - 151 EP - 161 ER -