SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis : from Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, (CIBB 2010), Palermo, Italy, 16 - 18 September 2010

Background: The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods: Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results: We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions: The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops

Estudo in silico de genes que codificam fatores de transcrição responsivos à seca, salinidade e congelamento nos genomas do eucalipto, cana e arroz

Estresses abióticos são os principais responsáveis por provocar alterações no crescimento e desenvolvimento vegetal. As plantas, em contrapartida, lançam mão de uma variedade de respostas a fim de manter seus processos metabólicos e fisiológicos. Uma das principais respostas das plantas às alterações das condições ambientais é a regulação adicional da expressão. Além desta, são de grande importância a síntese de osmoprotetores, transportadores iônicos, chaperonas, proteínas de choque térmico, aquaporinas, proteínas LEA, entre outras. Este trabalho buscou identificar genes que codificam fatores de transcrição (DREB, ERF, MYB, bHLH, bZIP, HSF, WRKY, NAC, ZincFinger e Homeodomínio) em eucalipto, cana-de-açúcar e arroz através de ferramentas in silico. Os resultados obtidos revelaram a presença de fatores de transcrição em todos os genomas estudados, revelando a importância dos mesmos nas respostas aos estresses abióticos. De uma forma geral, as proteínas pertencentes à uma mesma família mostraram características (ponto isoelétrico e massa molecular) bastante similares, indicando o alto grau de conservação das mesmas. Os dendrogramas gerados refletiram uma relação muito mais adaptativa do que filogenética entre os organismos. Além disso, também a estrutura gênica parece ser conservada em eucalipto e cana, como observado nas análises comparativas entre as ORFs destas culturas e as de seqüências genômicas de Arabidopsis e Oryza sativa. O padrão de expressão encontrado reflete o envolvimento destes fatores tanto no estresse biótico, quanto no estresse abiótico, com grande número de transcritos em tecidos infectados por bactérias, caule, raiz e região de transição raiz-caule. Em suma, os resultados apontam para a conservação dos principais mecanismos de controle da transcrição envolvidos na resistência/tolerância aos estresses, como a seca, salinidade e congelamento, em eucalipto, cana e arroz. No entanto, estudos adicionais, in vivo e in vitro, darão maiores subsídios para o melhor esclarecimento da funcionalidade destas proteínas e das vias em que participam estes gene

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data