Metavirome survey
In this study, metagenomics data of eight ray-finned fish species were investigated for their virome. Overall, 2228888 sequence reads were assigned to the virus kingdom. Pooled genome assay revealed a high abundance of Pandoravirus (31%), Herepesvirales (23%), and Bamfordvirae (10%) of all kingdom of viruses. In the following virome of each ray-finned fish will be presented. The presented study results are taxonomically assigned, and as some groups of viruses may not have some supper group classifications like class, order, or family, we defined them in their related sections. Accordingly, the genus of Pandoravirus, the order of Herpesvirales, the family of Polydnavirus, and the kingdom of Bamfordvirae are the roots of their clades, as shown in Fig. 1.
Diversity of viral species in Acipenser schrenckii
According to the viral taxonomy, Acipenser schrenckii metagenomics data was comprised of 464,973 classified and 91,977 reads. A. schrenckii comprised three main clades of Pandoravirus, the order of Herpesvirales, and the kingdom of Bamfordvirae (5%). As illustrated in Fig. 1, the genus Pandoravirus encompassed 34% of all viruses, followed by Herpesvirales with 28%. The most prevalence Pandoraviral species were P. malecodensis (28%), P. dulcis (24%), P. neocaledonia (10%), P. salinus (9%), P. quercus (4%) and P. inopinatum (2%). Other unclassified Pandoravirus species were composed of 24% of this lineage (Fig. 1A).
The order of Herpesvirales with 131,119 reads composed 28% of all the virome of A.schrenckii. In addition to Alloherpesviridae, the Herpesviridae family was contained in some members of human herpesviruses. Accordingly, the subfamily of Betaherpesvirinae (3% of all viruses) was comprised of Roseolovirus (41% of Betaherpesvirinae) and Cytomegalovirus (22% of Betaherpesvirinae), which was responsible for known human-associated viral pathogens. Accordingly, Human alphaherpesvirus 2 (1%) within the subfamily of Alphaherpesvirinae, Human betaherpesvirus 7 (5%), Human betaherpesvirus 6B (1%), and Human betaherpesvirus 6A (0.1%) within Betaherpesvirinae and Human gammaherpesvirus 8 (0.4%) belong to the Gammaherpesvirinae subfamily were constituted the human-associated viruses of the family of Herpesviridae.
The kingdom of Bamfordvirae and its order, Nucleocytoviricota, contained two major clades of large viral families Megaviricetes (65%) and Poxviridae (26%). The class of Megaviricetes has contained three families, including Phycodnaviridae (71%), Mimiviridae (20%), and Pimascovirales (9%). The Mimiviridae family was comprised of two genera of Mimivirus (24%) and Cafeteriavirus (11%) and five different species named Moumouvirus (58%), Megavirus chiliensis (22%), Acanthamoeba polyphaga mimivirus (2%), Cafeteria roenbergensis virus (11%), and Yellowstone lake mimivirus (5%).
Viral population of Odontobutis haifengensis
Herpesvirales (19%), Pandoravirus (17%), Orthornavirae (10%), and Bafordvirae (10%) were the most abundant orders of the viruses in the virome of O. haifengnis. Family Herpesviridae (14%) comprised 74% of the order of Herpesvirales. Alphaherpesvirinae subfamily consisted of Human alphaherpesvirus 2 (0.05% of viruses). The subfamily of Betaherpesvirinae was comprised of Human betaherpesvirus 6b (0.6% of viruses) and Human betaherpesvirus 7 (0.1% of viruses).
As shown in Fig. 1B, the giant Pandoravirus was made by P. salinus (37%), P. macleodensis (22%), P. dulcis (12%), P. inopinatum (6%), P. neocaledonia (5%), and P. quercus (3%). Furthermore, 1773 unassigned reads were also formed by other Pandoravirus species (16%).
The order of Orthornavirae with 6542 reads comprised two main sub-order of Kitrinoviricota (40%) and Pisuviricota (38%). The majority of viral species in these two sub-orders were those associated with vegetable and marine viral species. However, the Flaviviridae family (45%) within the Kitrinoviricota sub-order consisted of major human viral pathogens, namely Hepacivrus (63%) and Tick-borne encephalitis virus (19%).
Virome of Odontobutis yaluensis
The virome of O. yaluensis consisted of three main orders of Herpesvirales (24%), Bamfordvirae (15%), and Pandoravirus (8%). Further orders were including, Baculoviridae (6%) and Orthornavirae (5%). Three major prevalent families of Herpesvirales were Herpesviridae (79%), Alloherpesviridae (15%) and Malacoherpesviridae (5%). The Herpesviridae viruses comprised Human alphaherpesvirus 3 and Human betaherpesvirus 6B in alpha- and Betaherpesvirinae sub-families, respectively (Fig. 1C).
Sub-order of Nucleocytoviricota within Bamfordvirae was comprised of two prominent families of avian Poxviridae and giantviruses of Megaviricetes. Mimiviridae family was encompassed 5% of Bamfordvirae, and it has consisted of Mimivirus (59%), Moumouvirus (35%), and Cafeteriavirus (5%). Megavirus chiliensis was the only member of the genus Mimivirus.
Further giantviruses were investigated in the Pandoravirus taxonomy. P. macleodensis (30%), P. salinus (27%), P. dulcis (14%), P. inopinatum (5%), P. neocaledonia (5%), and P. quercus (3%) were the only recognized species, and 16% of the taxonomy were other Pandoraviruses (Fig. 1D).
Distribution of the viral population in Rhinogobius giurinus
59% of the metagenomics data of R. giurinus was comprised of three major orders of Pandoravirus (24%), Herpesvirales (20%), and Bamfordvirae (15%). Other viral taxa were including, Polydnaviridae (5%), Baculoviridae (3%), and Caudovirales (3%). Further virus-associated sequence reads can be found in Fig. 1D.
The order of Pandoravirus consisted of P. dulcis (38%), P. macleodensis (20%), P. salinus (9%), P. quercus (9%), P. neocaledonia (7%), and P. inopinatum (3%). Further, Pandoraviruses formed 15% of this giantvirus category.
Herpesviridae was comprised 79% of the Herpesvirales order, of which Alphaherpesvirinae was composed of Human alphaherpesvirus 2 and Human alphaherpesvirus 3. Roseolovirus within Betaherpesvirinae was contained Human betaherpesvirus 6B, Human betaherpesvirus 6A and Human betaherpesvirus 7. Reads associated with Human gammaherpesvirus 4 and Human gammaherpesvirus 8 were observed in the Gammaherpesvirinea subfamily.
Bamfordvirae was contained two main supper-orders, namely Nucleocytoviricota (85%) and Preplasmiviricota (15%). Similar to Preplasmiviricota, Poxviridae within Nucleocytoviricota was composed of avian viruses. In addition, Megaviricetes within Nucleocytoviricota consisted of three major groups of giantviruses, including, Phycodnaviridae (89%), Mimiviridae (5%), and Pimascovirales (5%). Phycodnaviridae was comprised of several species including, Phaeovirus (23%), Prymnesiovirus (19%), Prasinovirus (9%), Raphidovirus (7%), Chlorovirus (1%), Chrysochromulina ericina virus (0.7%), Aureococcus anophagefferens virus (0.7%) and Orpheovirus IHUMI-LCC2 (0.3%). The species of the Mimiviridae family were as follows; Moumouvirus (53%), M. chiliensis (24%), Cafeteria roenbergensis virus (21%), and Yellowstone lake mimivirus (1%). The order of Pimascovirales has included Iridoviridae (65%) and Ascovirus (35%) families.
Diversity of virome of Hiodon tergisus
Virome analysis of H. tergisus showed an almost different distribution of viral taxonomic among the ray-finned fishes. However, the sequence reads rate was significantly different from others as Pandoravirus with 142901 sequence reads comprised 41% of viruses in H. tergisus. Herpesvirales with 18%, Polydnaviridae with 11%, and Bamfordvirae with 4% were the other prevalent viral clades in the taxonomy assignments (Fig. 1E).
Pandoravirus was composed of P. macleodensis (30%), P. salinus (18%), P. dulcis (16%), P. neocaledonia (13%), P. quercus (2%), and P. inopinatum (2%). Other Pandoraviruses formed the last 20% of this taxonomy. Herpesvirales was composed of three main families including, Herpesviridae (48%), Alloherpesviridae (48%), and Malacoherpesviridae (2%). Alphaherpesvirinae contained half of the Herpesvirales while Beta- and Gammaherpesvirinae had 20% and 28% of other viruses of this family, respectively. Human alphaherpesvirus 2 (3%), Human betaherpesvirus 6B (4%), Human betaherpesvirus 7 (2%), Human betaherpesvirus 6A (0.3%), Human gammaherpesvirus 8 (0.4%) were the human-associated viruses of Herpesviridae family.
Polydnaviridae has only contained insect viruses. Additionally, the kingdom of Bamfordvirae has consisted of two main phyla of Nucleocytoviricota (89%) and Preplasmiviricota (11%). The class of Megaviricetes has contained two families and one order of giantviruses, including Phycodnaviridae (84%), Mimiviridae (4%), and Pimascovirales (12%). Phaeocystis globosa virus (56%), Ectocarpus siliculosus virus 1 (21%), Ostreococcus lucimarinus virus 2 (10%), Bathycoccus sp. RCC1105 virus BpV (0.8%), Micromonas sp. RCC1109 virus MpV1 (0.6%), Paramecium bursaria Chlorella virus A1 (1%), Heterosigma akashiwo virus 01 (2%), Aureococcus anophagefferens virus (0.9%), Orpheovirus IHUMI-LCC2 (0.7%), and Chrysochromulina ericina virus (0.7%) were the species within the Phycodnaviridae family. Four species, including Moumouvirus (51%), M. chiliensis (24%), Cafeteria roenbergensis virus (22%), and Yellowstone lake mimivirus (1%), were found in the Mimiviridae family. Pimascovirales was comprised of seven species including, Ranavirus (40%), Chloriridovirus (34%), Iridovirus (8%), Trichoplusia ni ascovirus 2c (7%), Spodoptera frugiperda ascovirus 1a (5%), Heliothis virescens ascovirus 3a (5%) and Lymphocystivirus (1%).
Metavirome assay of Polyodon spathula
The results revealed a similar distribution of viral populations in P. sapathula. Accordingly, genus Pandoravirus with 35% of all viruses was most prevalent, and the order of Herpesvirales followed it with 21% and Bamfordvirae with 6%. Other viral taxonomies are shown in Fig. 1F.
Pandoravirus was comprised of six species, including P. macleodensis (29%), P. dulcis (21%), P. salinus (13%), P. neocaledonia (9%), P. quercus (3%), and P. inopinatum (2%). Further, 25% of this genus consisted of other unassigned (19393 reads) Pandoravirus species.
The taxonomy of Herpesvirales was composed of two families of Herpesviridae (63%), Alloherpesviridae (31%), and one genus of Aurivirus (5%). Relatively similar to what was observed in other fishes, Alphaherpesvirinae consisted of Human alphaherpesvirus 2 (4%) and Human alphaherpesvirus 3 (2%). Human betaherpesvirus 6B (17%) and Human betaherpesvirus 7 (11%) were the human-associated Betaherpesvirinae. Additionally, no human virus was observed in the Gammaherpesvirinae subfamily.
The class of Megaviricetes was formed 67% of the phylum of Nucleocytoviricota and 53% of the kingdom of Bamfordvirae. Two families of Phycodnaviridae (59%) and Mimiviridae (29%) along with one order of Pimascovirales (11%) were formed viral taxonomy of Megaviricetes in P. spathula. Family Phycodnaviridae was comprised of a few genera including, Prymnesiovirus (51%), Prasinovirus (20%), Chlorovirus (10%), Phaeovirus (5%), and Raphidovirus (3%). Mimiviridae has also contained four species, including Moumouvirus (77%), M. chiliensis (14%), Cafeteria roenbergensis virus (5%), and Yellowstone lake mimivirus (1%). Pimascovirales was composed of four genera, namely Chloriridovirus (65%), Ascovirus (16%), Ranavirus (14%), and Lymphocystivirus (5%).
Analysis of viral species in Denticeps clupeoides
As shown in Fig. 1G, Pandoravirus with 32%, Herpesvirales with 29%, and Bamfordvirae with 8% were the most prevalent clades of the viral taxonomy of D. clupeoides. This result was relatively similar to those in other ray-finned fishes.
Six prevalent Pandoravirus species were P. macleodensis (34%), P. dulcis (16%), P. salinus (15%), P. neocaledonia (12%), P. quercus, and P. inopinatum (2%).
Like what was observed in other ray-finned fishes, Herpesviridae had the most proportion (82%) of Herpesvirales order, and it was followed by Alloherpesviridae (18%) and Aurivirus (1%). As reported above, only Herpesviridae contained human-associated herpes viruses. Accordingly, Human alphaherpesvirus 2 (4%) in Alphaherpesvirinae subfamily, Human betaherpesvirus 6B (28%) in Betaherpesvirinae and Human gammaherpesvirus 8 (1%) in Gammaherpesvirinae have formed the human-associated herpes viral species.
The third prevalent viral taxonomy, the kingdom of Bamfordvirae, comprised two phyla of Nucleocytoviricota (90%) and Preplasmiviricota (10%). Megaviricetes was the main class of Nucleocytoviricota. It was also contained two main families, including Phycodnaviridae (90%) and Mimiviridae (4%) and one order, namely Pimascovirales (6%). Phycodnaviridae was contained six genera including, Prymnesiovirus (88%), Chlorovirus (4%), Phaeovirus (0.8%), Prasinovirus (0.8%), Raphidovirus (0.5%) and Coccolithovirus (0.08%). Pimascovirales has contained four genera and three species including, Ranavirus (73%), Chloriridovirus (16%), Ascovirus (10%) and Marseillevirus (0.1%) as genera and Heliothis virescens ascovirus 3a (4%), Trichoplusia ni ascovirus 2c (4%) and Spodoptera frugiperda ascovirus 1a (1%). Mimiviridae was comprised of two genera of Mimivirus (26%) and Cafeteriavirus (18%) and three species including, Moumouvirus (55%), Megavirus chiliensis (26%), and Cafeteria roenbergensis virus (18).
Virome structure of Rutilus rutilus
As one member of ray-finned fishes, the metagenomic data of R. rutilus were assessed for viral sequence reads. Pandoravirus (35%), Herpesvirales (25%), and Bamfordvirae (18%) were the dominant taxonomical groups of viruses in R. rutilus. Other viral members are shown in Fig. 1H.
Members of Pandoravirus were similar to other ray-finned fishes reported above. In this regard, P. macleodensis (34%), P. dulcis (18%), P. salinus (11%), P. neocaledonia (10%), P. quercus (7%), and P. inopinatum (2%) were the Pandoravirus species observed in the virome of R. rutilus.
Furthermore, Herpesviridae (63%), Alloherpesviridae (33%), and Malacoherpesviridae (2%) were established Herpesvirales taxonomy in R. rutilus. Human alphaherpesvirus 3 (0.7%) in the genus of Varicellovirus and Human alphaherpesvirus 2 (4%) in the genus Simplexvirus observed in Alphaherpesvirinae. Human betaherpesvirus 6B (23%) was the only human-associated herpesvirus in Betaherpesvirinae. Moreover, Human gammaherpesvirus 8 (5%) in the genus Rhadinovirus was observed in the Gammaherpesvirinae subfamily.
The Kingdom of Bamfordvirae was taxonomically comprised of two main phyla of Nucleocytoviricota (94%) and Preplasmiviricota (6%). Megaviricetes was made 36% of Nucleocytoviricota. Phycodnaviridae was the major family (93%) within the lineage of Megaviricetes, and it was followed by Pimascovirales (4%) and Mimiviridae (3%). Six genera found in the virome of R. rutilus were including, Prymnesiovirus (71%), Prasinovirus (11%), Chlorovirus (5%), Phaeovirus (5%), Raphidovirus (0.9%), and Coccolithovirus (0.007%). The giant viral species within the family were Phaeocystis globosa virus (71%), Ostreococcus lucimarinus virus 2 (11%), Aureococcus anophagefferens virus (6%), Ectocarpus siliculosus virus 1 (5%), Paramecium bursaria Chlorella virus A1 (4%), Heterosigma akashiwo virus 01 (0.9%), Chrysochromulina ericina virus (0.4%) and Orpheovirus IHUMI-LCC2 (0.1%). The order of Pimascovirales has contained five genera as follows; Chloriridovirus (43%), Ranavirus (35%), Ascovirus (11%), Iridovirus (10%), and Lymphocystivirus (0.5%). In addition, the family of Mimiviridae was composed of two genera, namely Cafeteriavirus (43%) and Mimivirus (28%). It was also observed five species within Mimiviridea including, Cafeteria roenbergensis virus (43%), Moumouvirus (28%), Acanthamoeba polyphaga mimivirus (15%), Megavirus chiliensis (14%), and Yellowstone lake mimivirus (0.9%).