An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome
Abstract
:1. Introduction
2. Materials and Methods
2.1. Specimen Collection
2.2. Metavirome Preparation
2.3. Viral Metagenome Library Analyses
2.4. Viral Genome Architecture and Phylogeny
2.5. Eukaryotic 18S and 28S rRNA Analyses
3. Results and Discussion
3.1. Flavivirus-Like Genome Fragment
3.2. Picornavirales-Like Genome Fragments
3.3. Totivirus-Like Genome Fragments
3.4. Viral Diseases in Holothurians
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Family | Sample Location | Latitude | Longitude | Collection Date | Sequence Library Size (reads) | # Contigs | N50 Contigs | Contigs Matching Viral Genomes E < 10−20 | Reads Mapped to Viral Contigs |
---|---|---|---|---|---|---|---|---|---|---|
Cucumaria miniata | Cucumariidae | Salish Sea | 48.2333 N | 122.7917 W | 7 January 2016 | 1,686,849 | 5394 | 811 | 3 | 247,494 |
Apostichopus californicus * | Stichopodidae | Ketchikan | 55.4351 N | 131.9481 W | 26 October 2016 | 897,618 | 3431 | 804 | 11 | 195,230 |
Apostichopus californicus | Stichopodidae | Ketchikan | 55.4351 N | 131.9481 W | 26 October 2016 | 1,019,071 | 3900 | 880 | 2 | 179,175 |
Holothuria scabra | Holothuridae | Amity Banks | 27.4115 S | 153.4344 E | 10 December 2015 | 822,244 | 21,777 | 838 | 1 | 368 |
Synaptula recta | Synaptidae | Dunwich | 27.4952 S | 153.3985 E | 10 December 2015 | 983,151 | 19,760 | 847 | 0 | 299 |
Holothuria difficilis | Holothuridae | Amity Banks | 27.4115 S | 153.4344 E | 10 December 2015 | 794,579 | 5803 | 846 | 1 | 301 |
Stichopus horrens | Stichopodidae | Amity Banks | 27.4115 S | 153.4346 E | 10 December 2015 | 1,577,532 | 21,194 | 817 | 2 | 423 |
Holothuria atra | Holothuridae | Heron Island | 23.4441 S | 151.9113 E | 19 December 2015 | 875,840 | 18,866 | 793 | 1 | 345 |
Holothuria pardalis | Holothuridae | Dunwich | 27.4952 S | 153.3985 E | 10 December 2015 | 1,467,795 | 7424 | 896 | 0 | 306 |
Species of Metagenome | Contig # | Viral Order | Contig Length (nt) | Holothurian Species Recruited | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sh | Ha | Hs | Hp | Hd | Sr | Cm | Ac | Ac * | ||||
Stichopus horrens | 17,482 | Ghabrivirales | 1070 | + | ||||||||
Stichopus horrens | 5835 | Ghabrivirales | 2224 | + | + | + | + | + | + | + | ||
Stichopus horrens | 10,295 | Ghabrivirales | 796 | + | + | + | + | + | ||||
Holothuria atra | 17,799 | Picornavirales | 793 | + | ||||||||
Holothuria scabra | 11,085 | Ghabrivirales | 679 | + | ||||||||
Holothuria difficilis | 4411 | Ghabrivirales | 688 | + | + | + | + | |||||
Cucumaria miniata | 4304 | Picornavirales | 636 | + | ||||||||
Cucumaria miniata | 1913 | Picornavirales | 1826 | + | ||||||||
Cucumaria miniata | 1781 | Picornavirales | 782 | + | ||||||||
Apostichopus californicus | 91 | Amarillovirales | 8883 | + | + | + | ||||||
Apostichopus californicus | 3426 | Picornavirales | 1158 | + | + | |||||||
Apostichopus californicus * | 942 | Picornavirales | 1156 | + | + | + | ||||||
Apostichopus californicus * | 792 | Picornavirales | 767 | + | + | |||||||
Apostichopus californicus * | 791 | Picornavirales | 1491 | + | + | |||||||
Apostichopus californicus * | 708 | Picornavirales | 1241 | + | + | + | + | + | + | + | + | + |
Apostichopus californicus * | 557 | Picornavirales | 789 | + | + | |||||||
Apostichopus californicus * | 45 | Picornavirales | 1368 | + | + | |||||||
Apostichopus californicus * | 1580 | Picornavirales | 854 | + | + | |||||||
Apostichopus californicus * | 1446 | Picornavirales | 597 | + | + | |||||||
Apostichopus californicus * | 1223 | Picornavirales | 810 | + | ||||||||
Apostichopus californicus * | 1120 | Picornavirales | 1132 | + | + | |||||||
Apostichopus californicus * | 1020 | Picornavirales | 934 | + | + |
Group | Taxonomic Assignment | Holothurian Species | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Holothuria pardalis | Holothuria difficilis | Holothuria scabra | Holothuria atra | Synaptula recta | Stichopus horrens | Cucumaria miniata | Apostichopus californicus | Apostichopus californicus * | ||
Unicellular Eukaryotes | Alveolata | 1 | 2 | 6 | 8 | |||||
Apusozoa | 2 | |||||||||
Amoebozoa | 2 | |||||||||
Cryptomonada | 1 | 9 | ||||||||
Heterokonta | 1 | |||||||||
Metamonada | 1 | |||||||||
Viridiplantae | 2 | 2 | 2 | 63 | 11 | 18 | 6 | 1 | ||
Fungi | Ascomycota | 17 | 14 | 6 | 7 | 8 | 17 | 14 | 2 | 21 |
Basidiomycota | 11 | 8 | 6 | 9 | 8 | 13 | 14 | 12 | 16 | |
Fungi intercae sedis | 1 | 1 | 2 | 2 | ||||||
Metazoa | Annelida | 1 | ||||||||
Arthropoda | 4 | 2 | 4 | 1 | 3 | 4 | 3 | 5 | 5 | |
Asteroidea | 2 | |||||||||
Chordata | 3 | 1 | 2 | 2 | 4 | 14 | 3 | 3 | ||
Cnidaria | 1 | 1 | 1 | 2 | ||||||
Echinoidea | 1 | |||||||||
Holothuria | 1 | 1 | 1 | 3 | 1 | 1 | ||||
Mollusca | 1 | 2 | 1 | 1 | ||||||
Nematoda | 3 | |||||||||
Phoronida | 1 | |||||||||
Platyhelminthes | 1 |
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Hewson, I.; Johnson, M.R.; Tibbetts, I.R. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020, 12, 1057. https://doi.org/10.3390/v12091057
Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses. 2020; 12(9):1057. https://doi.org/10.3390/v12091057
Chicago/Turabian StyleHewson, Ian, Mitchell R. Johnson, and Ian R. Tibbetts. 2020. "An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome" Viruses 12, no. 9: 1057. https://doi.org/10.3390/v12091057