Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics

Currently only four genome sequences for Limnothrix spp. are publicly available, and information on the genetic properties of cyanobacteria belonging to this genus is limited. In this study, we report the draft genome of Limnothrix sp. CACIAM 69d, isolated from the reservoir of a hydroelectric dam located in the Amazon ecosystem, from where cyanobacterial genomic data are still scarce. Comparative genomic analysis of Limnothrix revealed the presence of key enzymes in the cyanobacterial central carbon metabolism and how it is well equipped for environmental sulfur and nitrogen acquisition. Additionally, this work covered the analysis of Limnothrix CRISPR-Cas systems, pathways related to biosynthesis of secondary metabolites and assembly of extracellular polymeric substances and their exportation. A trans-AT PKS gene cluster was identified in two strains, possibly related to the novel toxin Limnothrixin biosynthesis. Overall, the draft genome of Limnothrix sp. CACIAM 69d adds new data to the small Limnothrix genome library and contributes to a growing representativeness of cyanobacterial genomes from the Amazon region. The comparative genomic analysis of Limnothrix made it possible to highlight unique genes for each strain and understand the overall features of their metabolism

Twelve polymorphic microsatellite loci developed and optimized from the Leptodactylus chaquensis

We isolated and characterized twelve polymorphic microsatellite loci for Leptodactylus chaquensis. Levels of polymorphism of the microsatellite loci measured in twenty individuals showed two to 7 alleles per locus with observed heterozygosity ranging from 0.20 to 0.75 and polymorphic information content ranging from 0.1736 to 0.7431. No evidence for linkage disequilibrium was detected between all pairs of loci and deviations from Hardy-Weinberg expectations were not significant for any loci. These microsatellite markers reported here can be used in genetic analysis of populations and contribute to a better understanding of the taxonomy of the ocellatus group verifying the occurrence of reproductive isolation of species (or subspecies) closely related to L. chaquensis.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Morphological aspects of Henneguya aequidens n. sp (Myxozoa: Myxobolidae) in Aequidens plagiozonatus Kullander, 1984 (Teleostei: Cichlidae) in the Amazon region, Brazil

A new species of Myxosporea, Henneguya aequidens sp. n. (Myxozoa: Myxobolidae), was described based on its ultrastructural features. This is a parasite of the freshwater fish Aequidens plagiozonatus, in the Peixe-boi River, Para, Brazil. This parasite was found in the gills, in the form of whitish ellipsoid cysts with mature spores inside them. The average spore body was 15 +/- 0.9 mu m in length (n = 30) and 6 +/- 0.8 mu m in width (n = 30), and the tail measured 27 +/- 0.5 mu m in length (n = 15). The spores showed typical features of the genus Henneguya with two valves of equal size and two symmetrical polar capsules of 3 +/- 0.3 mu m in length and 2 +/- 0.3 mu m in width. Each polar capsule had a polar filament forming a helix from the apical region to the polar caps, with four to six turns. Based on the ultrastructural differences in morphology of these spores, the location of the parasite, and its host specificity, this parasite was described as a new species

Development of eleven polymorphic microsatellite markers for the Chaco Treefrog, Hypsiboas raniceps

We report the characterization of eleven polymorphic microsatellite loci for Hypsiboas raniceps in 20 individuals collected in the northwest of São Paulo State, Brazil. The number of alleles per locus, observed heterozygosity and polymorphic information content ranged from 2 to 16, 0.05 to 0.90 and 0.048 to 0.905, respectively. Linkage equilibrium was observed for all loci and only one locus showed significant deviation from Hardy-Weinberg equilibrium with evidence of null alleles. The remaining ten loci will be useful for population genetic studies and revealing population structure in this species.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Contemporary gene flow and weak genetic structuring in Rococo toad (Rhinella schneideri) populations in habitats fragmented by agricultural activities

The reduced vagility and philopatric behaviour of most amphibians make them especially vulnerable to the effects of habitat fragmentation, in particular the loss of genetic variation. However, almost no data are available on the effects of agricultural practices on populations of Neotropical amphibians. Here, the genetic diversity of Rococo toad (Rhinella schneideri) populations in the highly disturbed landscape of the north-western region of the Brazilian state of São Paulo was analysed using microsatellite markers. Two areas were sampled - one dominated by open pastures (four populations) and the other by sugar cane plantations (two populations) - in an attempt to evaluate the possible influence of the type of anthropogenic matrix on genetic variability and gene flow (dispersion). The populations presented a relatively uniform genetic stock, with low levels of inbreeding (Fis) and high levels of admixture between localities (Fst, Rst, STRUCTURE) indicating no genetic subdivision. The results indicated relatively high levels of recent migration among sites (m) and no isolation by distance. The analyses also found that historical and contemporary rates of migration among populations were broadly similar. Overall, then, neither type of matrix appeared to have an effect on the connectivity of the Rococo toad populations. This suggests that the species has a considerable capacity for dispersal, allowing it to maintain a relatively homogeneous population, even under intense human pressure.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Comparative Genetic Diversity of Wild and Captive Populations of the Bare-Faced Curassow (Crax fasciolata) Based on Cross-Species Microsatellite Markers: Implications for Conservation and Management

The bare-faced curassow (Crax fasciolata) is a large Neotropical bird that suffers anthropogenic pressure across much of its range. A captive population is maintained for conservation management, although there has been no genetic screening of stocks. Based on the six microsatellite markers developed for Crax globulosa, the genetic variability of C. fasciolata and possible differences between a wild and a captive population were investigated. Only three loci were polymorphic, with a total of 27 alleles. More than half of these alleles were private to the wild (n = 8) or captive (n = 7) populations. Significant deviations from Hardy-Weinberg equilibrium were restricted to the captive population. Despite the number of private alleles, genetic drift has probably promoted differentiation between populations. Our results indicate that wild C. fasciolata populations are genetically impoverished and structured, but species-specific microsatellite markers will be necessary for a more reliable assessment of the species` genetic diversity.BIRDBIRDConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CNPq[152757/2007-4]CNPq[302747/2008-7]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CNPq[476212/2007-3

An alternative genotyping method using dye-labeled universal primer to reduce unspecific amplifications

We proposed a modification the procedure of genotyping based in labeled universal primer and tailed primer. In the standard protocol, three primers are used in the same PCR reaction, a forward primer with tail added at the 5' end of the identical sequence to labeled universal primer with dye-fluorescent and a reverse primer. Unfortunately, the choice of a labeled primer characterized by a large number of complementary sequences in target genomes (which is more probable in larger genomes) result in unspecific amplifications (false positive) can cause absence or decrease amplification of the locus of interest and also false interpretation of the analysis. However, identification of possible homologies between the primer chosen for labelling and the genome is rarely possible from the available DNA data bases. In our approach, cycling is interrupted for the addition of the labeled primer only during the final cycles, thus minimizing unspecific amplification and competition between primers, resulting in the more fidelity amplification of the target regions.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

High-Quality Draft Genome Sequence of Pantanalinema sp. GBBB05, a Cyanobacterium From Cerrado Biome

Peer reviewe

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009–31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.This article is from Molecular Ecology Resources 9 (2009): 1460, doi:10.1111/j.1755-0998.2009.02759.x.</p

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle, Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium alboatrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.Glenn R. Almany...Rohan Mellick...Maurizio Rossetto...et al