Publications by authors named "Walter J Siqueira"

3 Publications

  • Page 1 of 1

Isolation and characteristics of eight novel polymorphic microsatellite loci in Lippia alba (Verbenaceae).

Am J Bot 2012 Aug 26;99(8):e301-3. Epub 2012 Jul 26.

Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil.

Premise Of The Study: A set of eight microsatellite (simple sequence repeat [SSR]) markers for Lippia alba, an important medicinal and cosmetic plant, was developed to aid studies of genetic diversity and to define efficient strategies for breeding programs.

Methods And Results: Using a (CT)(8)- and (GT)(8)-enriched library, a total of 11 SSR loci were developed and optimized in L. alba. Of the 11 loci, eight were found to be polymorphic after screening 61 accessions from two populations. The parameters used to characterize loci were expected heterozygosity (H(e)) and number of alleles. A total of 44 alleles were identified, with an average of 5.5 alleles per loci, which were moderately to highly informative according to H(e).

Conclusions: These new SSR markers have potential for informing genetic diversity, allele mining, and mapping studies and will be used to generate information for breeding programs of L. alba.
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http://dx.doi.org/10.3732/ajb.1100578DOI Listing
August 2012

Evaluation of monocot and eudicot divergence using the sugarcane transcriptome.

Plant Physiol 2004 Mar;134(3):951-9

Centro de Biologia Molecular e Engenharia Genética, Universidade de Campinas, Caixa Postal 6010, 13083-970, Campinas SP, Brazil.

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
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http://dx.doi.org/10.1104/pp.103.033878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC389918PMC
March 2004

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.

Genome Res 2003 Dec 12;13(12):2725-35. Epub 2003 Nov 12.

Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970 Campinas-SP, Brazil.

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
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http://dx.doi.org/10.1101/gr.1532103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403815PMC
December 2003