General time reversible was selected by modelfinder and a tree was constructed using IQ-TREE with 1000 bootstrap replicates. Those samples unique to this study are bolded, with samples from the …
Bolded samples are unique to this study. Samples from the Northern Atlantic denoted with ♦, and the bootstrap values over 60 are listed at tree nodes. Linkages between symbionts and their hosts are …
SNPs phylogenies were analyzed for each species, and the scale for E. luxaltus was dissimilar to the E. ecacola; neither were statistically significant (p>0.5 for analysis of both species). The …
Modelfinder selected the general time reversible model and a tree was constructed using IQ-TREE with 1000 bootstrap replicates. Those samples from the Northern Atlantic denoted with ♦, and the …
Host identifications for each sample are listed in the right-hand column. Samples unique to this study are bolded and those from the Northern Atlantic are marked with a ♦.
Samples that are unique to this study are bolded. For binned genomes, the average nucleotide identity (ANI) of the genome compared to the reference sequence is shown. For E. luxaltus the reference …
Sample | FishID | Light organ | Accession # | E. escacola ANI | E. luxaltus ANI | Length (Mb) | GC content (%) | Complete (%) | Ave coverage |
---|---|---|---|---|---|---|---|---|---|
CC26E | Cryptopsaras couesii | esca | GCA002300443.1 | 73.7 | NA | 2.14 | 37.7 | 91.3 | 25 |
CC32E | Cryptopsaras couesii | esca | SRR8206628 | -- | -- | -- | -- | -- | 23 |
CC81C | Cryptopsaras couesii | caruncle | SRR8206630 | -- | -- | -- | -- | -- | 19 |
CCS1E ♦ | Cryptopsaras couesii | esca | RPOE00000000 | 73.6 | 99.9 | 2.14 | 37.7 | 90.8 | 567 |
CCS2C♦ | Cryptopsaras couesii | caruncle | RPOF00000000 | 73.7 | 99.9 | 2.20 | 37.6 | 90.3 | 313 |
CC62E | Cryptopsaras couesii | esca | SRR8206629 | -- | -- | -- | -- | -- | 19 |
Csp75C | Ceratias uranoscopus | caruncle | RPGC00000000 | 99.9 | 73.8 | 2.73 | 39.8 | 91.0 | 1600 |
CspS10C ♦ | Ceratias sp. | caruncle | RPGB00000000 | 99.2 | 73.6 | 2.72 | 39.8 | 91.1 | 99 |
CspS9C ♦ | Ceratias sp. | caruncle | RPGE00000000 | 99.1 | 73.8 | 2.69 | 39.8 | 89.3 | 26 |
CU44E | Ceratias uranoscopus | esca | RPGD00000000 | 99.1 | 74.0 | 3.04 | 39.8 | 88.3 | 15 |
CLS4E ♦ | Chaenophryne longceps | esca | RPGF00000000 | 99.9 | 73.7 | 2.73 | 39.8 | 90.4 | 330 |
CDS3E ♦ | Chaeonophryne sp. | esca | RPGG00000000 | 99.9 | 73.6 | 2.73 | 39.8 | 89.3 | 291 |
LMS8E ♦ | Linophryne maderensis | esca | RPGH00000000 | 99.8 | 73.8 | 3.40 | 40.0 | 88.8 | 1 |
MJ02E | Melanocetus johnsoni | esca | GCA002381345.1 | NA | 73.7 | 2.65 | 39.8 | 89.9 | 766 |
MJS5x ♦ | Melanocetus johnsoni | esca | RPGI00000000 | 99.9 | 73.8 | 3.09 | 39.8 | 91.1 | 321 |
DP02E | Oneirodes sp. | esca | RPGJ00000000 | 100.0 | 73.7 | 2.68 | 39.8 | 89.3 | 910 |
Transmission | Description | Symbiont and function | Host | Genome | References |
---|---|---|---|---|---|
Environmental | Acquired from free-living bacteria ![]() | Luminescence Aliivibrio fischeri Photobacterium leiognathi Photobacterium kishitanii Nutrition "Candidatus Endoriftia persephone" Various Gammaproteobacteria Burkholderia spp. | Fish and squid Fish Fish Tubeworms Mussels Insects | Comprable to free-living relatives ![]() | Dunlap and Urbanczyk, 2013; Gyllborg et al., 2012 Urbanczyk et al., 2011; Ast et al., 2007 Li et al., 2018; Kleiner et al., 2012 Ponnudurai et al., 2017 Kikuchi et al., 2005; Kikuchi et al., 2007 |
Proposed Environmental | Environmentally persistant cells ![]() | Luminescence "Candidatus Enterovibrio escacola" "Candidatus Enterovibrio luxaltus" | Anglerfish Anglerfish | Ongoing reduction | Hendry et al., 2018 Hendry et al., 2018 |
Mixed | Pseudovertical or surface transmission ![]() | Luminescence "Candidatus Photodesmus blepharus" "Candidatus Photodesmus katoptron" Nutrition Various Gammaproteobacteria “Candidatus Ishikawaella capsulata” | Flashlight fish Flashlight fish Clams Stink bug | Moderate toextreme reduction ![]() | Hendry et al., 2014; Hendry and Dunlap, 2014 Hendry et al., 2014; Hendry and Dunlap, 2014 Kuwahara et al., 2007 |
Inherited | Direct passage from parent to offspring on egg or sperm ![]() | Nutrition Buchnera aphidicola Carsonella ruddii Portiera aleyrodidarum Varied "Candidatus Synechococcus spongiarum" | Aphids Psyllids Whiteflies Sponges | Greatly reduced ![]() | Moran et al., 2008; Fisher et al., 2017 Moran et al., 2008; Fisher et al., 2017 Moran et al., 2008; Fisher et al., 2017 Gao et al., 2014; Burgsdorf et al., 2015 |
Collection data for anglerfish samples used in this study.
Gulf of Mexico samples were collected by the DEEPEND consortium at the given locations. Samples collected by S. Nyholm were collected by RRS Discovery expedition D243 east of the Cape Verde Islands at the given locations. A single sample (DP02E) was given a new taxonomic identification as a result of mitochondrial gene analysis.
Lophiiform mitochondrial sequences used in this study.
Genbank accession numbers and total sequence length are shown. Samples listed in bold were generated by this study or by Hendry et al. (2018).
Sequences from free-living Vibrionaceae species used to generate the housekeeping gene tree.
Genbank accession numbers of each gene are given.
Genomes from free-living Vibrionaceae species used for PhyloPhlan analysis.
Genbank accession numbers of each genome assembly are given.
The species-specific primers designed to amplify the chemotaxis protein cheA.
Species-specific primers designed to amplify the chemotaxis protein cheA.