Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus) and other eukaryote species revealed by nucleotide and amino acid sequence analyses

Abstract Actin-encoding cDNAs of Nile tilapia (Oreochromis niloticus) were isolated by RT-PCR using total RNA samples of different tissues and further characterized by nucleotide sequencing and in silico amino acid (aa) sequence analysis. Comparisons among the actin gene sequences of O. niloticus and those of other species evidenced that the isolated genes present a high similarity to other fish and other vertebrate actin genes. The highest nucleotide resemblance was observed between O. niloticus and O. mossambicus α-actin and β-actin genes. Analysis of the predicted aa sequences revealed two distinct types of cytoplasmic actins, one cardiac muscle actin type and one skeletal muscle actin type that were expressed in different tissues of Nile tilapia. The evolutionary relationships between the Nile tilapia actin genes and diverse other organisms is discussed

Genetic conservation of Brazilian fishes - Present state and perspectives

Natural environments have been worldwide affected by the growing impact of anthropogenic actions that promote the reduction or the extinction of several vertebrate species. Aquatic ecosystems represent one of the most affected environments and many fish species and/or populations have been increasingly fragmented distributed due to habitat degradation, predatory fishing, introduction of exotic species, river sedimentation, deforestation, pollution, reduction of food resource, and construction of hydroelectric dams. Actually, more than 150 Brazilian fish species, including freshwater, estuary and coastal species, can be considered threatened. Information on the diversity, conservation biology and population analysis on threatened species or populations, with several DNA markers, can be extremely useful for the success of fish species-recovery and maintenance programs. Although DNA analysis in Neotropical fish species are just beginning, they tend to increase with the widespread attention to the use of molecular approaches to minimize problems related to the risk of extinction. The accumulation of information on biology and pattern of genetic variation of fish species, associated with ecological and demographic data, and also education and respect to the nature, constitutes a crucial task to develop efficient conservation strategies in order to preserve the genetic diversity in aquatic environments

Characterization of α-actin isoforms in white and red skeletal muscle types of Leporinus macrocephalus (Characiformes, Anostomidae)

RESUMO Dois genes de α-actina do peixe Leporinus macrocephalus, referindo-se aos tecidos musculares branco e vermelho, foram isolados. Isoformas de actinas, que principalmente diferiram por uma substituição Ser/Ala155, podem ter uma significância funcional relacionada à interação entre actina e ATP. Um resíduo de Ala155, como observado na α-actina esquelética do músculo vermelho, resulta em uma diminuição da afinidade da actina pelo ATP, o que também pode estar associado à ação contrátil lenta desse tecido. Adicionalmente, uma substituição Phe/Ile262 na actina do músculo vermelho leva a uma variação na hidrofobicidade no "plug-D" da proteína, o que pode alterar sua estabilidade. Dados de qRT-PCR evidenciaram significante maior nível de actina RNAm em músculo branco, quando comparado ao músculo vermelho (T=105 Mann Whitney; p=<0,001). Este resultado pode estar relacionado às demandas energéticas do tecido muscular branco, com fibras de contração rápida e metabolismo glicolítico para fornecimento de energia. Os dados disponíveis sobre actinas musculares levam a propor que as α-actinas esqueléticas dos músculos branco e vermelho são geneticamente e funcionalmente distinguíveis em espécies de peixes, uma característica não encontrada em outros grupos de vertebrados

Nucleotide sequence of 5S rDNA and localization of the ribosomal RNA genes to metaphase chromosomes of the Tilapiine cichlid fish, Oreochromis niloticus

In this study, we report the cloning and nucleotide sequence of PCR-generated 5S rDNA from the Tilapiine cichlid fish, Oreochromis niloticus. Two types of 5S rDNA were detected that differed by insertions and/or deletions and base substitutions within the non-transcribed spacer (NTS). Two 5S rDNA loci were observed by fluorescent in situ hybridization (FISH) in metaphase spreads of tilapia chromosomes. FISH using an 18S rDNA probe and silver nitrate sequential staining of 5S-FISH slides showed three 18S rDNA loci that are not syntenic to the 5S rDNA loci

Partial molecular characterization of the Nile tilapia (Oreochromis niloticus) alpha-cardiac muscle actin gene and its relationship to actin isoforms of other fish species

An alpha actin gene segment, isolated from Nile tilapia (Oreochromis niloticus), was characterized by nucleotide sequencing, predicted amino acid sequence and Southern blot hybridization. Genomic DNA amplification resulted in a 1063-bp fragment corresponding to a partial alpha-cardiac muscle actin gene containing exons 3 to 6. Southern blot analysis of the restriction-digested DNA revealed that the Nile tilapia genome contains multiple muscle actin isoforms. Although comparison of the nucleotide sequence, amino acid residues and exon-intron organization of the isolated actin gene with those of other vertebrates showed a high level of identity, diagnostic amino acid residues can still be correlated to distinct actin genes in fish species

Marshes as “Mountain Tops”: Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae)

<div><p>Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (<i>Formicivora paludicola</i>) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250–300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall <i>F</i>_ST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8–99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.</p></div

Novel and cross-amplified microsatellite loci for the critically endangered São Paulo marsh antwren Formicivora paludicola (Aves: Thamnophilidae)

The So Paulo marsh antwren (Formicivora paludicola) is a critically endangered bird endemic to marshes in the metropolitan region of So Paulo city, Brazil. The total population is estimated to be around 300 individuals, distributed among 15 small (&lt; 50 ha) fragments, suggesting that loss of genetic variability may affect the long-term viability of this species. To develop genetic tools for gaining information on effective population sizes, inbreeding and gene flow between populations, we describe nine polymorphic microsatellite loci isolated from a F. paludicola library using next-generation sequencing. We report on levels of variation in these novel microsatellites and eight additional heterologous loci in these birds. Expected (H (E)) and observed (H (O)) heterozygosities averaged 0.72 and 0.70, respectively, and the number of alleles per locus ranged from 3 to 10. These loci will permit evaluation of whether artificial translocations are necessary for long-term viability of this rare bird.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP