de Souza, J. E. S. | Search bioRxiv

bioRxiv2020

Assessing the sex-related genomic composition difference using a K-mer-based approach: a case of study in Arapaima gigas (Pirarucu).

Arapaima gigas is one of the largest freshwater bony fish in the world, in which adults could weigh 200 kilograms and measure 3 meters in length. Due to its large size and its low-fat meat, Arapaima gigas has quickly become a species of special interest in fish-farming. One challenge faced during their production is the lack of an efficient sexing methodology, since their sexual maturation occurs late (around the third to the fifth year) and the genetic mechanisms linked to their sex determination system are not known yet. For a more sustainable management, it is of paramount importance to seek an effective and non-invasive method to differentiate sexually juvenile individuals of Arapaima gigas. For this, the establishment of genetic markers associated with sexual differentiation would be an advantageous tool. In this study, we proposed a k-mer based approach to identify genome features with sex-determining properties. For this purpose, we used genomic data from four adult representatives of Arapaima gigas, two males and two females, and counted the k-mers comprising them. As result, we found k-mers from repetitive regions with high difference and disproportion in the count among individuals of the opposite sex. These differences in the k-mer-based genomic composition indicate the existence of genetic factors involved in the sexing of individuals in Arapaima gigas.

genomics↗

bioRxiv2019

Novel Variants in COL4A3 and COL4A4 are Causes of Alport Syndrome in Rio Grande do Norte, Brazil

BackgroundAlport syndrome is a progressive and hereditary nephropathy, characterized by hematuria and proteinuria, and extrarenal manifestations as hearing loss and eye abnormalities. The disease can be expressed as autosomal recessive or dominant, caused by variants in COL4A3 and COL4A4 loci, respectively, or X-linked caused by variants in COL4A5 locus. MethodsTwo unrelated families with Alport Syndrome from northeast of Brazil were studied and whole exome sequencing were performed. DNA sequences were mapped against the human genome (GRCh38/hg38 build) to identify associated mutations. ResultsVariant analysis showed deleterious variants in COL4A3 and COL4A4 loci in chromosome 2. Two variants were detected with alternative alleles in a homozygous state in the probands. One novel premature stop codon at position 481 of COL4A3 protein is present in one family and one frameshift mutation leading to a premature stop codon at position 786 of COL4A4 protein in the other family. Both Alport cases presented their variants surrounded by a broad runs of homozygosity (ROH). ConclusionsThe autosome recessive inheritance coupled with the runs of homozygosity in both families suggest inbreeding.

genomics↗