Open AccessCharacterization of Penaeus vannamei mitogenome focusing on genetic diversity
Author(s) -
Paulo Eduardo Soares,
Márcia Danielle A. Dantas,
Rita de Cássia Barreto Silva-Portela,
Lucymara Fassarella Agnez-Lima,
Daniel Carlos Ferreira Lanza
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0255291
Subject(s) - heteroplasmy , mitochondrial dna , biology , indel , genetics , mtdna control region , hypervariable region , genome , evolutionary biology , genetic diversity , population , computational biology , gene , single nucleotide polymorphism , allele , haplotype , genotype , demography , sociology
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. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P . vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.