Zhao Mingli

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  • Dataset
    Nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) from coastal waters and estuaries in North and South America, including the Caribbean and Gulf of Mexico from 2006 to 2020
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2023-03-02) Schott, Eric ; Plough, Louis V. ; Zhao, Mingli
    This record contains nucleotide sequences of CsRV1 virus amplified from blue crabs (Callinectes sapidus) across the study region. RNA from crabs identified as infected using a sensitive Rt-qPCR assay was amplified using primers specific to segment and segment 9 of the virus genome. A subset of CsRV1-positive RNA preparations were amplified using a full-genome amplification set of primers to amplify the entire CsRV1 genome. (http://primal.zibraproject.org; Quick et al. 2017). The segment-specific data: seg9 (960 nt amplicon) and seg8 (807 nt amplicon) were trimmed and used to create maximum likelihood trees. Similarly, the full genome sequences were used for a maximum likelihood tree. In total, 22 complete or near-complete genomes, 42 seg8 ORF sequences, and 96 seg9 ORF sequences of CsRV1 were collected from 15 geographic locations along the US Atlantic coast, Gulf of Mexico, Caribbean Sea and S. America between 2006 – 2021. Sequence generation and tree building was accomplished by Mingli Zhao with input from coauthors Plough and Kough. Pairwise analyses and ML trees can be found in the Supplemental Materials of results publication Zhao et al. (2023). The sequences generated in this study are deposited in NCBI GenBank, with accession numbers OP067244-OP067635 and are accessible under BioProject PRJNA939818. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/890835