Table 1.
Genome sequences included in the comparative analysis.
| Isolate | Contigsa | Kbpb | Countryc | Fish hostd | Tissue | Year | Publicatione | Accession Number |
|---|---|---|---|---|---|---|---|---|
| JIP 02/86 | 1 | 2,860 | France | O. mykiss | Kidney | 1986 | Duchaud et al., 2007 | AM398681.2 |
| CSF259-93 | 1 | 2,901 | ID, USA | O. mykiss | Spleen | 1993 | Wiens et al., 2014 | CP007627 |
| NCIMB 1947T | 1 | 2,716 | WA, USA | O. kisutch | Kidney | n.a.i | Wu et al., 2015 | CP007207 |
| DIFR 950106-1/1 | 1 | 2,736 | Denmark | O. mykissg | Spleen | 1995 | Castillo et al., 2016 | SAMN02903962 |
| FPG101 | 1 | 2,835 | Canada | O. mykiss | n.a. | 2008 | Castillo et al., 2016 | SAMN03290989 |
| MH1 | 1 | 2,848 | Chile | Salmo salar | Skin | 2008 | Castillo et al., 2016 | SAMN02941921 |
| PG2 | 1 | 2,851 | Chile | O. mykiss | Skin | 2009 | Castillo et al., 2016 | SAMN02941922 |
| 5 | 1 | 2,848 | Chile | Fish farm freshwater | 2013 | Castillo et al., 2016 | SAMN02941920 | |
| 3 | 1 | 2,805 | Chile | Fish farm freshwater | 2013 | Castillo et al., 2016 | SAMN02941918 | |
| VQ50 | 1 | 2,807 | Chile | O. mykiss | Skin | 2006j | Castillo et al., 2016 | SAMN02941923 |
| OSU THCO2-90f | 1 | 2,784 | OR, USA | O. kisutch | Kidney | 1990 | Rochat et al., 2017a | LT670843 |
| KU 051128-10 | 179 | 2,572 | Japan | River water | 2005 | This study (EFN) | GCA_900186555 | |
| KU 060626-4 | 182 | 2,527 | Japan | P. altivelis | Kidney | 2006 | This study (EFN) | GCA_900186475 |
| KU 060626-59 | 204 | 2,518 | Japan | P. altivelis | Skin lesion | 2006 | This study (EFN) | GCA_900186495 |
| KU 061128-1 | 202 | 2,515 | Japan | River water | 2006 | This study (EFN) | GCA_900186605 | |
| IT02 | 43 | 2,648 | Italy | O. mykiss | Spleen | 2011 | This study (GC) | GCA_900186545 |
| IT09 | 46 | 2,716 | Italy | O. mykiss | Spleen | 2012 | This study (GC) | GCA_900186525 |
| NO004 | 58 | 2,774 | Norway | Salmo trutta | Fin | 1998 | This study (HN) | GCA_900186755 |
| NO014 | 66 | 2,682 | Norway | O. mykiss | Spleen | 2008 | This study (HN) | GCA_900186785 |
| NO042 | 73 | 2,583 | Norway | Salmo salar | Spleen | 2008 | This study (HN) | GCA_900186825 |
| NO083 | 42 | 2,690 | Norway | O. mykiss | Kidney | 2011 | This study (HN) | GCA_900186805 |
| NO098 | 52 | 2,617 | Norway | Salmo salar | Ovarian fluid | 2011 | This study (HN) | GCA_900186815 |
| DK002 | 40 | 2,686 | Denmark | O. mykiss | kidney | 1990 | This study (ID) | GCA_900186425 |
| DK150 | 66 | 2,775 | Denmark | O. mykiss | Kidney | 1995 | This study (ID) | GCA_900186365 |
| DK095 | 66 | 2,816 | Denmark | G. aculeatus | Skin | 2000 | This study (ID) | GCA_900186385 |
| DK001 | 48 | 2,704 | Denmark | O. mykiss | Spleen | 2009 | This study (ID) | GCA_900186405 |
| FPC 840 | 274 | 2,516 | Japan | P. altivelis | Kidney | 1987 | This study (J-FB) | GCA_900186575 |
| FPC 831 | 226 | 2,600 | Japan | O. kisutch | Peduncle lesion | 1990 | This study (J-FB) | GCA_900186485 |
| LVDJ XP189 | 258 | 2,685 | France | Tinca tinca | Kidney | 1992 | This study (J-FB) | GCA_900186645 |
| JIP 08/99 | 261 | 2,549 | France | O. mykiss | Kidney | 1999 | This study (J-FB) | GCA_900186595 |
| JIP 16/00 | 368 | 2,503 | France | O. mykiss | n.a. | 2000 | This study (J-FB) | GCA_900186515 |
| FRGDSA 1882/11 | 74 | 2,687 | France | O. mykiss | n.a. | 2011 | This study (J-FB) | GCA_900186415 |
| CH8 | 58 | 2,699 | Switzerland | O. mykiss | Spleen | 2009 | This study (NS) | GCA_900186345 |
| CH1895 | 65 | 2,748 | Switzerland | Salmo truttah | Skin | 2011 | This study (NS) | GCA_900186435 |
| LM-01-Fp | 46 | 2,753 | Chile | O. mykiss | Kidney | 2006 | This study (RA-H) | GCA_900186685 |
| LM-02-Fp | 43 | 2,685 | Chile | O. mykiss | Kidney | 2006 | This study (RA-H) | GCA_900186665 |
| FI055 | 78 | 2,732 | Finland | O. mykiss | Inner organs | 1996 | This study (TW) | GCA_900186395 |
| FI056 | 41 | 2,694 | Finland | O. mykiss | inner organs | 1996 | This study (TW) | GCA_900186375 |
| FI146 | 99 | 2,838 | Finland | Pond water | 2000 | This study (TW) | GCA_900186455 | |
| FI070 | 52 | 2,715 | Finland | P. fluviatilis | Mouth | 2006 | This study (TW) | GCA_900186445 |
| FI166 | 62 | 2,732 | Scotland | Salmo salar | n.a. | 2007 | This study (TW) | GCA_900186565 |
Number of contigs (≥ 1 Kbp, plasmids excluded).
Cumulated contig length.
The names of USA states are abbreviated.
Abbreviated species names for Gasterosteus aculeatus, Oncorhynchus mykiss, Oncorhynchus kisutch, Perca fluviatilis, Plecoglossus altivelis.
Initials of contact name for newly sequenced isolates; Erina Fujiwara-Nagata, Greta Caburlotto, Hanne Nilsen, Inger Daslgaard, Jean-François Bernardet, Nicole Strepparava, Ruben Avendaño-Herrera, Tom Wiklund. n.a., no data available.
The spelling OSU THC02-90 has been used in several publications (e.g., Nicolas et al., 2008) but the original name of this strain is OSU THCO2-90 (Bertolini et al., 1994).
Information on host fish for DIFR 950106-1/1 can be found in Madsen and Dalsgaard (1999).
S. trutta lacustris.
The exact date of isolation of the type strain NCIMB 1947T is unknown; it was most likely isolated by E.J. Ordal sometime between 1945 and 1960.
VQ50 was isolated by R. Avendaño-Herrera in 2006 in Veterquímica (VQ).