PCR-Based Approach for Sequencing Mitochondrial Genomes of Decapod Crustaceans, with a Practical Example from Kuruma Prawn (Marsupenaeus japonicus)

Abstract

An approach for sequencing the entire mitochondrial genomes (mitogenomes) of decapod crustaceans using 79 newly designed and 7 published polymerase chain reaction (PCR) primers is described. The approach comprises the following steps: (1) the entire mitogenome is amplified in 2 or 3 long PCRs; (2) the 86 primers are used in different combinations to amplify contiguous, overlapping short segments of the entire mitogenome with the diluted long PCR products as templates; (3) direct cycle sequencing is conducted using the short PCR products. This strategy allows a more rapid determination of decapod mitogenomic sequences than a traditional method using cloned mitochondrial DNA and primer walking strategy. As a practical example, the mitogenomic sequence for a kuruma prawn Marsupenaeus japonicus (Crustacea: Decapoda), was determined using the PCR-based approach.

The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations

“…2; Table 1). The overall A + T content of L. vannamei and F. chinensis (67.8% and 68.9% respectively) is higher than the average among the other malacostracan mitochondrial genomes (Hickerson and Cunningham, 2000;Wilson et al, 2000;Yamauchi et al, 2002Yamauchi et al, , 2003Yamauchi et al, , 2004Miller et al, 2004Miller et al, , 2005Place et al, 2005;Segawa and Aotsuka, 2005;Sun et al, 2005;Miller and Austin, 2006) (Table 1). The two sequences were deposited in GenBank (L. vannamei: DQ534543 and F. chinensis: DQ518969).…”

The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

“…In Decopoda, the situation is more complex: four penaeid shrimp species (Dendrobranchiata) share the pancrustacean ground pattern (Shen et al, 2007;Wilson et al, 2000;Yamauchi et al, 2004), but in the suborder Pleocyemata, members of Anomura, Astacidea and Brachyura show some rearrangements (Hickerson and Cunningham, 2000;Miller et al, 2005;Miller et al, 2004;Place et al, 2005;Segawa and Aotsuka, 2005;Sun et al, 2005;Yamauchi et al, 2003;Yang et al, 2008), while Japanese spiny lobster Panulirus japonicus (Palinura) maintains the pancrustacean ground pattern (Yamauchi et al, 2002).…”

Proteomics in Food Science

“…Among fishery products, Decapoda crustaceans are of major commercial value, especially those within the superfamily Penaeoidea (penaeid shrimps and prawns), which represent important resources for both fisheries and aquafarming facilities worldwide and account for more than 17% of the global consumption of seafood products (Yamauchi et al, 2004;FAO, 2009). Due to phenotypic similarities among penaeid species, differentiation between them is difficult even when there is no processing and the external features remain intact.…”