Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the "abominable mysteries" of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. METHODOLOGY/PRINCIPAL FINDINGS:We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. CONCLUSIONS/SIGNIFICANCE:This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family

The Domestication of Annatto (Bixa orellana) from Bixa urucurana in Amazonia

Annatto (Bixa orellana) is an important colorant domesticated in theNeotropics, although it is not clear where or from which wild populations. We reviewed the available biological, archaeological, and ethnographic information about annatto, and integrated this with our recent ethnobotanical observations of cultivated and non-cultivated populations in order to evaluate the hypothesis thatwhat is classified as Bixa urucurana is the wild ancestor of cultivated annatto, Bixa orellana. Most B. urucurana populations we found in Amazonia occurred in open forests or anthropogenic landscapes, although never cultivated, and always associated with riparian environments. While cultivated annatto always produces abundant pigment, B. urucurana populations that we observed contained variable amounts of pigment, fromvery little to nearly the amount of cultivated annatto, suggesting gene flow fromcultivated to non-cultivated. Bixa urucurana has indehiscent fruits, which indicate changes in dehiscence during annatto domestication, a notable feature rarely found in other tree species. Local residents identified the non-cultivated populations aswild annatto (urucum bravo), and they emphasized their smaller fruits with less pigment, their spontaneous regeneration, their non-use, and that they hybridize with cultivated annatto. Ethnography identified the symbolic importance of annatto, but an explicit mention of origin only comes from southern Amazonia. Although the oldest annatto archaeological record came from the Caribbean, domestication occurred in northern South America, since B. urucurana does not occur in the Caribbean. Traditional ecological knowledge and morphology identified the close relationship between B. urucurana (never cultivated) and B. orellana (always cultivated). Evidence reported here strongly supports Kuntze's (1925) suggestion that Bixa urucurana Willd. is a variety of B. orellana L., thus identifying the wild ancestor of cultivated annatto. © 2015, by The New York Botanical Garden Press, Bronx, NY 10458-5126 U.S.A

Mutation in the c-di-amp cyclase daca affects fitness and resistance of methicillin resistant staphylococcus aureus

Faster growing and more virulent strains of methicillin resistant Staphylococcus aureus (MRSA) are increasingly displacing highly resistant MRSA. Elevated fitness in these MRSA is often accompanied by decreased and heterogeneous levels of methicillin resistance; however, the mechanisms for this phenomenon are not yet fully understood. Whole genome sequencing was used to investigate the genetic basis of this apparent correlation, in an isogenic MRSA strain pair that differed in methicillin resistance levels and fitness, with respect to growth rate. Sequencing revealed only one single nucleotide polymorphism (SNP) in the diadenylate cyclase gene dacA in the faster growing but less resistant strain. Diadenylate cyclases were recently discovered to synthesize the new second messenger cyclic diadenosine monophosphate (c-di-AMP). Introduction of this mutation into the highly resistant but slower growing strain reduced resistance and increased its growth rate, suggesting a direct connection between the dacA mutation and the phenotypic differences of these strains. Quantification of cellular c-di-AMP revealed that the dacA mutation decreased c-di-AMP levels resulting in reduced autolysis, increased salt tolerance and a reduction in the basal expression of the cell wall stress stimulon. These results indicate that c-di-AMP affects cell envelope-related signalling in S. aureus. The influence of c-di-AMP on growth rate and methicillin resistance in MRSA indicate that altering c-di-AMP levels could be a mechanism by which MRSA strains can increase their fitness levels by reducing their methicillin resistance levels