Characterization of Penaeus vannamei mitogenome focusing on genetic diversity.

The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy.

Direct sequencing of the white spot syndrome virus from Brazil: Genome assembly and new insights on phylogeny.

White spot syndrome virus (WSSV) has been the cause of great economic losses in world shrimp farming. In this work the genome of a Brazilian WSSV isolate was determined from direct sequencing of total DNA extracted from an infected whiteleg shrimp, and assembled based on a chimera template approach. Comparisons between WSSV-BR and other isolates revealed that the Brazilian virus has a relatively small genome, and is very similar to isolates from Thailand and Mexico.

New insights about ORF1 coding regions support the proposition of a new genus comprising arthropod viruses in the family Totiviridae.

Analyzing the positions of 2A-like polypeptide cleavage sites in all available genomes of arthropod totiviruses we propose the limits of all ORF1 coding sequences and observed that two proteins previously predicted in infectious myonecrosis virus genome are unique in the arthropod totiviruses group. A putative protein cleavage site upstream the major capsid protein was also identified only in these genomes. In addition, protein models generated using ab initio and threading approaches revealed conserved structures possibly related to formation of viral protrusions and RNA packaging, clarifying the mechanisms involved in the extracellular transmission.

Analysis of new isolates reveals new genome organization and a hypervariable region in infectious myonecrosis virus (IMNV).

Infectious myonecrosis virus (IMNV) has been the cause of many losses in shrimp farming since 2002, when the first myonecrosis outbreak was reported at Brazilian's northeast coast. Two additional genomes of Brazilian IMNV isolates collected in 2009 and 2013 were sequenced and analyzed in the present study. The sequencing revealed extra 643 bp and 22 bp, at 5' and 3' ends of IMNV genome respectively, confirming that its actual size is at least 8226 bp long.