During the first four months of 2015, Dr. Parente and his team continued to work on the transcriptome of Pterigoplichthys anitisiti
, drafted a section of a paper on these results, assembled the transcriptome of Ancistrus spp
. and Corydoras nattereri
, began their analysis, assembled the mitogenomes of these three species, and sequenced the transcriptome of 12 other species. As noted in their previous quarterly report, more than 57 million nucleotides were assembled to construct the transcriptome of P. anitisiti
. In this transcriptome, 51,530 components were detected. BLAST searches against the UniProt database for Human and Zebrafish found that around 33,000 of those had positive hits with known gene sequences. Similar results were found for Ancistrus spp
. and C. nattereri
. The defensome genes of P. anitisiti
were studied in detail, and Dr. Parente and his team have begun analyzing defensome genes in the two other species, but the results are still very preliminary.
The team encountered some difficulties in mid-January 2015 when the next-generation sequencing equipment they are using at the Brazilian National Institute of Cancer (INCA) broke down while running their samples. No samples were lost, but the breakdown cost them a significant quantity of expensive NGS reagents. Fortunately, INCA is covering the cost of sequencing of their samples, but this unexpected problem delayed the project schedule by four to six weeks. Part of their samples (12 of 36) had already been sequenced, and another sequencing run was scheduled for early May.
|The research team at the Andorinhas waterfall on the Roncador river in the district of Santo Alexio. Pictured are Paolo Buckup (top), Emmanuel Neuhaus (center), Thiago Parente (left foreground), and Jose Gomes (right foreground). (Photo: Carla Quijada).||Labwork to obtain sequencing of genes (Photo: Dr. Parente).|
The PI attended the international meeting PRiMO 18 (Pollutant Responses in Marine Organisms) in Trondheim, Norway, May 24-27, 2015, where he met with U.S. collaborators on the project. Dr. Parente, accompanied by the two undergraduate students and the computational biology specialist on the project, also attended the international meeting Evolution 2015, held in Guarujá, Brazil, June 26-30, 2015. Dr. Parente and his colleagues are now working to finish sequencing the transcriptomes from the previously sampled species and analyze the evolution of at least CYP1A and a receptor gene. Two more field trips are planned, one to Manaus and one to Guyana. The excursion to Manaus is aimed at exposing two selected species (most probably Pterygoplichthys pardalis
and Dekeyseria amazonica
) to water enriched with humic acids (from the Rio Negro) and to crude oil. The excursion to Guyana will provide an opportunity to sample two particular species, Lithogenes sp
. and Corymbophanes sp
. For this excursion, the team is applying for a licence to collect biological samples in Guyana. In order to increase the chances to collect those species, and also for safety reasons, the excursion must happen in one of the few dry months in Guyana, which are September-October or February-March. A no-cost extension on this project has been issued through June 2016 to allow for more time to complete the field work and subsequent analyses.
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