title: Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea.
abstract: In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)(Val) genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNA(Val) genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNA(Val) marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNA(Val) gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNA(Val) region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNA(Val) marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation.
authors.affiliation: Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Campus Universitario Norte, E-27002 Lugo, Spain.
authors.forename: Pilar
authors.initials: P
authors.lastname: Calo-Mata
authors.forename: Ananias
authors.initials: A
authors.lastname: Pascoal
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Fernández-No
authors.forename: Karola
authors.initials: K
authors.lastname: Böhme
authors.forename: José M
authors.initials: JM
authors.lastname: Gallardo
authors.forename: Jorge
authors.initials: J
authors.lastname: Barros-Velázquez
mesh_terms: D000818:Animals; D008928:Mitochondria / Q000235:genetics*; D033561:Penaeidae / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000235:genetics; D012366:RNA, Transfer, Val / Q000032:analysis* / Q000235:genetics; D013045:Species Specificity
chemical_list: D012336:RNA, Ribosomal, 16S; D012366:RNA, Transfer, Val