SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.

Unlabelled: Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses.

Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families.

bettercallsal: better calling of serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Most current subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations.

Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus).

Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing ('genome skimming'). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species' native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data.

Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity.

Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry.

Validation of the ghost shrimp species Neocallichirus pinheiroi Hernáez, Windsor, Paula amp; Santana (Decapoda: Callianassidae) from the southwestern Atlantic.

Hernáez et al. (2020) described a new species of ghost shrimp, Neocallichirus pinheiroi, from northeastern coast of Brazil, Western Atlantic. Although the description and figures presented by Hernáez et al.

Evaluation of variation within the barcode region of Cytochrome Oxidase I (COI) for the detection of commercial Rathbun, 1896 (blue crab) products of non-US origin.

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 not harvested in the United States.

Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice .

L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses.

Resolution of the species complex: taxonomic status and identity of (Fabricius, 1798) and (Stimpson, 1858) (Brachyura, Decapoda, Portunidae).

The United States Food and Drug Administration (FDA) has recently adopted DNA barcoding for the purpose of determining the species identity of commercial seafood products. This effort has revealed instances of incongruence between current scientifically accepted taxon names and those utilized by the seafood industry in product labelling. One such case is that of "", a name utilized by the seafood industry to label commercial products under the market name "red swimming crab.

Three new species and a new genus of majoid crabs from the eastern Pacific (Decapoda, Brachyura).

Three new species and a new genus of majoid crabs from deep waters in the eastern Pacific are described and illustrated using morphological and molecular data. A new species of inachoidid, is described from Peru, which resembles Rathbun, 1893, in the general appearance of the carapace, but is distinguished by the details of tubercles on the carapace and thoracic sternum, proportions of the pereopod articles, and bathymetric distribution. A new epialtid, , is described from Ecuador; A Milne-Edwards, 1878 has, until now, been considered to be monotypic, occurring only in the western Atlantic.

The complete mitochondrial genome of (Gastropoda: Panpulmonata: Stylommatophora: Cerionidae).

We report the complete mitochondrial genome sequence of (Linnaeus 1758), the type species of the type genus of the family Cerionidae. The mitogenome is 15,043 bp in length, has a base composition of A (28.3%), T (34.