Evaluation of variation within the barcode region of CytochromecOxidase I (COI) for the detection of commercialCallinectes sapidusRathbun, 1896 (blue crab) products of non-US origin

Abstract

Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as “blue crab” and “Product of the USA” may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as “Product of the USA” and “Product of Venezuela.” In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise Fst values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.

DNA barcoding allows identification of undescribed crab megalopas from the open sea

“… Megalopa ID Species identification 16S (%, mt, bp) References COI (%, mt, bp) References Megalopa sequences 16S COI MF10, MF20-23 Achelous floridanus DQ388058 (99, 2, 519) Mantelatto et al 90 * 1 ACC4724 (99, ?, ?) BOLD (Unpublished) MW264138 MW264439 ML30 Arenaeus mexicanus JX123471 (100, 0, 553) Zupolini et al (unpublished) JX123449 (99, 3, 665) Zupolini et al (unpublished) MW264139 MW264440 MF24-27 Callinectes amnicola No Seq MG462523 (99, 7, 658) Windsor et al 91 MW264140 MW264441 ML09 Callinectes arcuatus KY940141 (100, 0, 545) Lopes et al (unpublished) MG462537 (100, 0, 658) Windsor et al 91 MW264141 MW264442 ML20 Callinectes arcuatus KY940141 (99, 1, 545) Lopes et al (unpublished) MG462539 (99, 5, 658) Windsor et al 91 MW264142 MW264443 ML28 ...…”

Chromosome-level genome assembly of the blue crab,Callinectes sapidus

“…The lack of recombination-based linkage data or other cytogenetic information such as karyotypes for blue crab means that there is little outside reference data to guide the assembly. However, the chromosome level-genome assembly, together with that of P. trituberculatus , will permit genomic work assessing genetic diversity and species identification across the range ( Place and Plough 2017 ; Plough 2017 ; Windsor et al 2019 ; Lee et al 2020 ). Future work to advance blue crab aquaculture through selective breeding could make use of the genome through a genomic selection approach ( Meuwissen et al 2001 ; Heffner et al 2009 ), which has recently been applied to aquaculture species like shrimp and mollusks ( Hollenbeck and Johnston 2018 ; Zenger et al 2019 ; Houston et al 2020 ).…”

DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico

“…Although DNA barcoding procedures for identifying mislabeling may be costly and relatively time-consuming, technological breakthroughs are frequently introduced, and they may be used to streamline sample collection and identification that could support a successful traceability system [ 67 ]. New methodologies in development could help to genetically identify species originating from diverse regions and countries [ 68 ].…”