Anotação genômica e caracterização de locos microssatélites em sequências expressas do genoma do camarão marinho Litopenaeus vannamei

• Ano de defesa: 2011
• Autor(a) principal: Santos, Camilla Alves
• Orientador(a): Freitas, Patrícia Domingues de
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso embargado
• Idioma: por
• Instituição de defesa: Universidade Federal de São Carlos
• Programa de Pós-Graduação: Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEv
• País: BR
• Palavras-chave em Português: Genoma; Sequenciamento; Enzimas; Xenobiotica - metabolismo
• Palavras-chave em Inglês: Microsatellites; ESTs; Penaeid; EC numbers; Metabolic pathways
• Área do conhecimento CNPq: CIENCIAS BIOLOGICAS::GENETICA
• Link de acesso: https://repositorio.ufscar.br/handle/ufscar/5489

Litopenaeus vannamei is known as Pacific white shrimp and is the main species marketed worldwide. Its geographical distribution includes the Pacific coast, ranging from Mexico to Peru. Due to its outstanding economic importance, this species has been farmed and showing great adapting levels to captivity, having been introduced in several countries, including Brazil. However, despite all the concern to properly manage the farming populations, many countries have not had a renewal of their breeding herds because of the risk of introduction of exogenous pathogens, which has increased the degree of inbreeding of these stocks and decreased levels of genetic diversity. To monitor this loss, microsatellite markers or SSRs (Simple Sequence Repeats), from genome arbitrary and expressed regions have been used. In the specific case of SSRs present in expressed regions of the genome (ESTs, Expressed Sequence Tags) or SSRs-ESTs, they allow the access to the genetic variability of populations, and the ESTs markers devoid of SSRs may be related to genes of interest, subsidizing the development of breeding programs based on Marker Assisted Selection (MAS). Moreover, EST-SSRs loci may show an excellent rate of transferability in taxonomically related species, since they are in more conserved regions of the genome. Within this context, this study aimed (i) the validation population of EST-SSR loci isolated through dataming from L. vannamei ESTs database (www.shrimp.ufscar.br), (ii) the genomic annotation of ESTs and EST-SSRs markers (iii) the determination of EC numbers (Enzyme Codes), aiming respectively, (i) the characterization of polymorphic markers (ii) the description of genes and their protein products and (iii) the establishment of information to describe the possible pathways for the penaeid group. Therefore, we tested 32 EST-SSRs loci in PCR reactions. After establishing the best pattern of reaction and subsequent loci genotyping, nine SSRs-ESTs were polymorphic, with allele number ranging from two to 20, levels of observed heterozygosity from 0.32 to 0.86 and average PIC (Polymorphism Information Content) of 0.78. No pair of loci presented in linkage disequilibrium. However, after Bonferroni correction, we found that one of these showed a significant deficit of heterozygotes. The nine polymorphic loci from L.vannamei showed satisfactory amplification in at least one of the seven native species tested: the marine ones Xiphopenaeus kroyeri, Farfantepenaeus brasiliensis, Farfantepenaeus paulensis, Rimapenaeus constrictus and Litopenaeus schmitti and the freshwater ones Macrobrachium amazonicum and Macrobrachium jeskii, being useful also for genetic studies of these species. The genome annotation performed by access in ShEST website (Litopenaeus vannamei EST Genome Project) showed that only three of nine loci 4 have the gene and its protein product described. The other loci showed no matches with any other genomic database available for research. In this work, gene product could be elucidated for 99% of ESTs, being possible to establish 209 EC numbers, highlighting enzymes responsible for xenobiotics metabolism, immunity, energy production, reproduction, oxidative stress, among others. These codes were used for construction of some metabolic pathways present in the penaeid group, contributing for building a wide database of the genome of this important animal group. These data may be applied in genetic improvement programs as well as gene expression studies, such as realtime PCR and microarrays.