Repetitive Elements in Electric Knife Fish - A CodonCode Aligner User Showcase

Electric fish Eigenmannia
Electric Knife Fish

As a PhD student in the Department of Genetic and Evolutive Biology at the São Paulo University in Brazil, Felippe Lourenço Claro studies the dynamics, conservation, distribution and evolution of repetitive DNA elements in fish. He uses CodonCode Aligner to create a genomic library for repetitive DNA elements of six species of electric fish (genera Eigenmannia).

Besides constructing a genomic library, his research focuses on wheter the repetitive sequences are linked to sex chromosomes and heterochromatin regions, as part of which he looks at possible cytogenetic and molecular markers. To obtain a better understanding of the evolutionary dynamics of this multigene family in the genus Eigenmannia, Felippe will also analyze the association of SINE (Short INterspersed Elements) and 5S rDNA.

Felippe uses CodonCode Aligner for sequence editing, contig assembly, and to make multiple sequence alignments with Clustal. He also plans to use the restriction mapping feature of CodonCode Aligner to identify unique restriction sites to further analyze this genomic region.


The Electric Fish Eigenmannia, Repetitive Elements and Sex Chromosomes

Place where Eigenmannia can be found
One of the sampling locations for Eigenmannia
A research subject
A research subject

Repetitive DNA is a considerable fraction of the genome of many eukaryotic organisms. Composed of both functional sequences, such as ribosomal genes, and non-coding sequences, this part of the genome has been widely used as an object of study, since repetitive sequences may be associated with sex chromosomes and the heterochromatic blocks in general. These studies have helped in better understanding the dynamics of these chromosomal regions and the conservation and evolution of the repetitive portion of the genome.

The genus Eigenmannia (Gymnotiformes, Sternopygidae) consists of cryptic species in terms of morphological data, showing variation in chromosome number and possibly having sexual systems XY or ZW in which the sexual elements of the pair differ by the presence of heterochromatic blocks larger than those found in chromosomes autosomes, or multiple systems involving Y-autosome translocation.

Felippe's research aims to continue the studies on repetitive DNA in the genus Eigenmannia, focusing on possible cytogenetic and molecular markers, and whether or not they are linked to sex chromosomes and heterochromatin regions. The main goal is to obtain a better understanding of the dynamics of that part of the genome in this group of electric fish.

Also of interest for Felippe's research is the identification, localization, and sequencing of transposable elements. The goal is to obtain a better understanding of the distribution and conservation of these elements, and determine its relation to the differentiation of sex chromosomes and heterochromatin regions. The association of SINE type elements and the 5S rDNA will be analyzed to better understand the evolutionary dynamics of this multigene family in the genus Eigenmannia.


How CodonCode Aligner is used to study Eigenmannia

Sunset during a filed expedition at the Rio Grande
Sunset during a field trip at the Rio Grande river in Brazil

Felippe described how he uses CodonCode Aligner in his research to help him align and analyze his samples:

After importing his samples to CodonCode Aligner, he first aligns his samples to build contigs and find any possible sequencing errors or other issues with his sequences. As the next step, he uses CodonCode Aligner to generate a multiple sequence alignment of all his samples, using the Clustal algorithm, which he says fits best for fish and allows him afterwards for example to use PAUP to generate phylogenetic trees.

Felippe plans to use the restriction mapping feature in CodonCode Aligner to find unique restriction sites, which will help him to isolate specific regions from the genome using certain restriction enzymes. He will then use the isolated regions for southern blots to identify sequences of interest and compare the occurence of these sequences using the intensity of the bands.

"What makes CodonCode different from other programs is that you have all the features in one program with a totally user friendly environment.."
Felippe Lourenço Claro, São Paulo University, Brazil
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