Scleractinian corals represent the foundation species of one of the most diverse and productive ecosystem on earth, coral reefs. Corals not only constitute the trophic basis of these ecosystems, but also provide essential habitats and shelter for a wide variety of marine species, many of which are commercially relevant. They also provide other important ecosystem services such as food provision, shoreline protection and opportunities for ecotourism. Despite the ecological importance of corals, very little is known about how their soft-bodied ancestor evolved the ability to form a calcified skeleton and became the ecosystem builders they are today. Corallimorpharia are closely related to reef-building corals but lack the ability to form calcified skeletons. Here we assembled and annotated two draft genomes of the corallimorpharians, Amplexidiscus fenestrafer and Discosoma sp., and further provided an online interface to facilitate the use of these resources. The two genomes can not only inform on the current evolutionary gap in genomic resources for the subclass of Hexacorallia but also provide important resources for comparative genomic studies aiming at understanding the evolution of coral specific traits. Our broad phylogenomic approach using whole genome data, including phylogenetic analyses of nuclear encoding genes as well as genome-wide presence/absence information and synteny conservation from six hexacorallian species, provides robust evidence that corallimorpharians are a monophyletic sister group of scleractinians, therefore rejecting the “naked coral” hypothesis. Being the closest non-calcifying relative of scleractinian corals, corallimorpharians appear to be the best candidates to understand the evolutionary origin of coral calcification. Molecular divergence analysis of scleractinian coral and Corallimorpharia genes suggests that the soft-bodied ancestor of corals evolved the ability to calcify within approximately 80 million years after the divergence of these two orders. To uncover the molecular basis of coral skeletal formation and growth, we integrate genomic and transcriptomic data as well as skeletal proteomic data, and show that gene and domain duplications have been the main evolutionary mechanisms underlying the evolution of calcification in scleractinian corals.

The exact origin of the peculiar naked barley is somewhat illusive. There   is a debate whether it has a single, monophyletic origin or a multiple, paraphyletic origin. It is from previous Asian studies on naked   barley known that a mutation   or a deletion of the nud gene expresses the   naked seed phenotype. Not much   investigation has been done outside of   Asia, least of all in the Nordic countries, on what gives naked   barley its character. Therefore this   study was set up to examine if   the Nordic variant of naked barley shares   the same nud allele as the Asian   and thus has a   close connection with it, or   if they have independent mutations. I   could confirm that the known alleles of the nud gene do determine the seed character of barley. Most of the   results of the PCR genotyping confirmed the phenotype of the tested   accessions, both naked and hulled barleys. However, one visually phenotyped naked   barley cultivar (NGB4580) still amplified with the known primers that would   match the Asian hulled allele, meaning that the Nordic accession NGB4580 of   naked barley did not carry the known nud   deletion. This suggests that naked barley has arisen independently in Asia   and in the Nordic countries.

Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-05-18T18:34:42Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Albuquerque DL_2104_Revisão de Neogonodactylus e análise filogenética de Gonodactyloidea_Crustacea-Stomatopoda.pdf: 6978022 bytes, checksum: df08f84986a54d4e765d49fbd8ce24ea (MD5) / Made available in DSpace on 2017-05-18T18:34:42Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Albuquerque DL_2104_Revisão de Neogonodactylus e análise filogenética de Gonodactyloidea_Crustacea-Stomatopoda.pdf: 6978022 bytes, checksum: df08f84986a54d4e765d49fbd8ce24ea (MD5) Previous issue date: 2014-02 / Gonodactyloidea é considerada a segunda maior superfamília de Stomatopoda em número de espécies. A complexidade morfológica e a grande representatividade de exemplares, principalmente do gênero Neogonodactylus, em águas brasileiras, chamou a atenção para importância de estudar este grupo. Este gênero possui distribuição anfi-americana e é registrado em ambos os hemisférios. A monofilia da superfamília, família e gênero ainda não havia sido comprovada, o que gerou o interesse e necessidade de reavaliar o grupo. Portanto, o presente trabalho teve como objetivo testar a monofilia da superfamília, bem como da família Gonodactylidae, com enfoque principal no gênero Neogonodactylus, que foi analisado quanto à sua taxonomia, sistemática e filogenia. O material utilizado proveio principalmente das coleções carcinológicas do Museu de Oceanografia Petrônio Alves Coelho (Brasil) e National Museum of Natural History (EUA), abrangendo mais de mil exemplares de 38 espécies. O presente trabalho foi realizado a partir da construção de duas matrizes de caracteres geradas no programa DELTA 1.0-RC4, uma para avaliação da superfamília e família, contendo dezoito taxa e 59 caracteres; e outra para análise de Neogonodactylus, incluindo suas 22 espécies mais uma de Gonodactylus como grupo externo com 54 caracteres. As análises filogenéticas foram geradas com base nessas matrizes, através do programa PAUP 4.0, pelo método de busca heurística, com 1000 réplicas, onde os caracteres não foram pesados nem ordenados. Os índices de Bremer e Bootstrap foram utilizados para avaliar a consistência dos ramos. Apesar dos índices filogenéticos não apresentarem valores altos, a monofilia da superfamília Gonodactyloidea surge com a retirada de Alainosquillidae da mesma. Esta era a única família a possuir espécies do grupo funcional spearers, porém a posição desta família não ficou clara na presente análise. Desta forma, o presente trabalho traz uma proposta de monofilia tanto de Gonodactyloidea, quanto de Gonodactylidae. Pela primeira vez foi realizada a filogenia do gênero Neogonodactylus englobando todas as espécies existentes, desta forma o gênero começa a ser mais bem compreendido. Redescrições, desenhos e chave de identificação para o gênero Neogonodactylus foram confeccionados. Variações e informações adicionais também foram analisadas e fornecidas para cada espécie. Assim o presente trabalho contribuiu de forma inédita para a melhor compreensão de Gonodactyloidea, da família Gonodactylidae e de Neogonodactylus. / Gonodactyloidea is considered the second largest superfamily within Stomatopoda regarding the number of species. The morphological complexity and the representativeness of specimens, mainly of the genus Neogonodactylus, in Brazilian waters brought attention to the importance of studying this group. Neogonodactylus has an amphi-american distribution and it has been registered in both hemispheres. The monophyly of the superfamily, family and genus have not been proved yet, generating the interest and the necessity to review the group. Therefore, the present work aimed to test the monophyly of the superfamily Gonodactyloidea, as well as of the family Gonodactylidae, with a main focus on the genus Neogonodactylus, which was analyzed based on its taxonomy, systematic and phylogeny. The material was mainly provided from the carcinological collections of Museu de Oceanografia Petrônio Alves Coelho (Brazil) e National Museum of Natural History (EUA), covering more than one thousand specimens of 38 species. The present work was based on two characters matrixes, generated on DELTA 1.0-RC4 program, one to evaluate the superfamily and family based on eighteen taxa and 59 characters; and the other to analyze the Neogonodactylus genus, including their own 22 species and one Gonodactylus as out group with 54 characteres. Phylogenetic analysis were based on these matrixes, through the PAUP 4.0 program, with heuristic source method, with 1000 replicates, with characters not weighted neither ordinated. The Bremer and Bootstrap indexes were used to evaluate the branch consistency. Despite the fact that phylogenetic indexes did not present high values, the monophyly of the superfamily Gonodactyloidea raised with the exclusion of the family Alainosquillidae. This was the only family to bear species from the functional group spearers; however, the position of this family was still not clear in the current analysis. Thus the present thesis proposes the monophyly of the Gonodactyloidea and Gonodactylidae. For the first time, the phylogeny of the genus Neogonodactylus was performed, and since it encompassed all the extant species, the genus began to be more understood. Redescriptions of species, figures and a key for the genus Neogonodactylus were made. Variations and additional information were also studied and released for each species. Thereby the present work contributed in a unique way to a better understanding of Gonodactyloidea, Gonodactylidae and Neogonodactylus.

Yes / Recent studies portend a rising global spread and adaptation of human- or healthcare- associated pathogens. Here, we analyse an international collection of the emerging, multi-drug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals.