FULL GENOME RESOURCES for Apis mellifera, its pathosphere and microbiota.

Table S1.  Full genome resources¹ for Apis mellifera, its pathosphere and microbiota.

(modified from Schwarz RS, Huang Q, and Evans JE. 2015. Hologenome theory and the honey bee pathosphere.  Current Opinion in Insect Science. doi:10.1016/j.cois.2015.04.006)

Taxon and isolate	GenBank accession	Location	Reference
PATHOSPHERE
Viruses
Iflaviridae
DWV IT DWV PA DWV Ox DWV Korea-1 DWV Korea-2 DWV DJE202 DWV Warwick-2009	NC_004830 AY292384 KC786223 JX878304 JX878305 KJ437447 GU109335	Italy USA UK S Korea S Korea UK UK	[1] [1] [2] [3] [3] [4] [4]
DWV Kakugo DWV KV-like Ox	NC_005876 KC786224	Japan UK	[5] [2]
SBPV Rothamsted SBPV Harpenden	NC_014137 GU938761	UK UK	[6] [6]
SBV Rothamsted SBV CSBV-GZ SBV CSBV-LN SBV Kor19 SBV Kor21 SBV Oksapmin SBV AmSBV-Viet4 SBV AmSBV-Viet6	NC_002066 AF469603 HM237361 JQ390592 JQ390591 KJ629183 KM884993 KM884995	UK China China S Korea S Korea PNG Vietnam Vietnam	[7] [8] [9] [10] [10] [11] unpublished unpublished
VDV-12,3 VDV-1 Zriffin VDV-1 Ox	NC_006494 JF440525 KC786222	Netherlands Israel UK	[12] [13] [2]
Dicistroviridae
ABPV Rothamsted ABPV Poland 1 ABPV Hungary 1	NC_002548 AF486073 AF486072	UK Poland Hungary	[14] [15] [15]
BQCV SA BQCV Poland-4 BQCV Poland-5 BQCV Poland-6 BQCV Hungary-10 BQCV AY BQCV JL1	NC_003784 EF517519 EF517520 EF517521 EF517515 JX149531 KP119603	S Africa Poland Poland Poland Hungary S Korea China	[16] [17] [17] [17] [17] [18] unpublished
IAPV IAPV CA IAPV MD IAPV PA IAPV DVE31-OP3-PA-USA-2007 IAPV IS1-ISRAEL-2007 IAPV OZ6-AUSTRALIA-2007 IAPV Wus-China-2008 IAPV Korea1 IAPV Korea2 IAPV Korea3 IAPV 4782IAPV	NC_009025 EU218534 EU224279 EU224280 EU436423 EU436455 EU436456 HQ897161 KC690268 KC690269 KC690270 JX045857	Israel USA USA USA USA Israel Australia China S Korea S Korea S Korea Spain	[19] [20] [20] [20] [21] [21] [21] unpublished [22] [22] [22] [23]
KBV PA KBV AY	NC_004807 KF956377	USA S Korea	[24] [25]
Unclassified
CBPV A-79P CBPV B-441	NC_010711 4 NC_010712 EU122231 4 EU122232	France France	[26] [26]
LSV-1 BruceSD_T17E02 LSV-2 BruceSD_T17E01	HQ871931 HQ888865	USA USA	[27] [27]
Bacteria
Firmicutes
Melissococcus plutonius ATCC 35311 Melissococcus plutonius DAT561	APO12200 (chr) AP012201 (pld) AP012282 (chr) AP012283 (pld)	UK Japan	[28] [29]
Paenibacillus larvae BRL-230010 Paenibacillus larvae DSM 25719 (ERIC I) Paenibacillus larvae DSM 25430 (ERIC II)	AARF00000000 (gen) ADFW00000000 (chr) ADFW01000008 (pld) CP003355 (chr) CP003356 (pld)	USA Germany Germany	[30] [31] [31]
Tenericutes
Spiroplasma apis B31T	CP006682	France	[32]
Spiroplasma melliferum KC3 Spiroplasma melliferum IPMB4A	AGBZ00000000 AMGI00000000	France Taiwan	[33] [34]
Fungi
Ascomycota
Ascosphaera apis USDA-ARSEF 7405	AARE00000000	USA	[30]
Aspergillus flavus NRRL33575	NZ_AAIH00000000	USA	[35]
Microsporidia
Nosema apis BRL01	ANPH00000000	Canada	[36]
Nosema ceranae BRL01	ACOL00000000	USA	[37]
Protists
Euglenozoa
Lotmaria passim SF6	AHIJ00000000	USA	[38]
Metazoa
Arthropoda
Varroa destructor Korean Varroa destructor Korean Varroa destructor Korean	ADDG00000000 (chr) AY163547 (mtd) NC_004454 (mtd)	USA USA France	[39] [40] [41]
MICROBIOTA
Actinobacteria
Bifidobacterium asteroides PRL2011 Bifidobacterium asteroides DSM20098 Bifidobacterium asteroides Bin2 Bifidobacterium asteroides Bin7	CP003325 (chr) JDTU00000000 (gen) NC_010908 (pld) JWME00000000 (gen) JWF00000000 (gen)	Italy Italy Italy Sweden Sweden	[42] [43] [44] unpublished unpublished
Firmicutes
Lactobacillus helsingborgensis wkB8 Lactobacillus helsingborgensis Bma5	CP009531 (chr) CP009532 (pld) PRJNA257138 7 (gen)	USA Sweden	[45] [46]
Lactobacillus kimbladii Hma2	PRJNA257141 7 (gen)	Sweden	[46]
Lactobacillus kullabergensis Biut2	JXBY00000000 (gen)	Sweden	[46]
Lactobacillus kunkeei MP2 Lactobacillus kunkeei EFB6 Lactobacillus kunkeei AR114	JPUI00000000 (gen) AZBY00000000 (gen) JPYX00000000 (gen)	Chile Germany Norway	[47] [48] [49]
Lactobacillus mellifer Bin4	PRJNA257185 7 (gen)	Sweden	[46]
Lactobacillus mellis Hon2	JXBZ00000000 (gen)	Sweden	[46]
Lactobacillus melliventris Hma8	PRJNA257139 7 (gen)	Sweden	[46]
Lactobacillus sp. wkB10	JRJB00000000 (gen)	USA	[45]
Proteobacteria
Frischella perrara PEB0191	CP009056 (gen)	USA	[50]
Gilliamella apicola wkB1T	CP007445 (chr)	USA	[51]
Snodgrassella alvi wkB2T	CP007446 (chr)	USA	[51]
HONEY BEE HOST
Apis mellifera ligustica DH4 hybrid	GCA_000002195 (chr)	USA	[52,53]

Taxa are organized by Family (viruses) or Phylum.  ABPV: Acute bee paralysis virus, BQCV: Black queen cell virus, CBPV: Chronic bee paralysis virus, chr: chromosome, DWV: Deformed wing virus, gen: whole genome, KBV: Kashmir bee virus, KV: Kakugo virus, LSV: Lake Sinai virus, mtd: mitochondria, pld: plasmid, PNG: Papua New Guinea, SBPV: Slow bee paralysis virus, SBV: Sacbrood virus, UK: United Kingdom, USA: United States of America, VDV-1: Varroa destructor virus-1.

(1) As of 01 April 2015.

(2) Obtained from Varroa destructor mite but is also infectious to A. mellifera.

(3) Recombinant DWV/VDV genomes were not included.

(4) RNA 1 and RNA 2 genomes, respectively.

(5) Not a honey bee isolate, but present in A. mellifera per [54].

(6) Originally accessioned as Crithidia mellificae but renamed in [55].

(7) BioProject accession: at publication, only unassembled sequence reads were available. 

References

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28.      Okumura K, Arai R, Okura M, Kirikae T, Takamatsu D, Osaki M, Miyoshi-Akiyama T: Complete genome sequence of Melissococcus plutonius ATCC 35311. J Bacteriol 2011, 193:4029–4030.

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55.      Schwarz RS, Bauchan GR, Murphy CA, Ravoet J, de Graaf DC, Evans JD: Characterization of Two Species of Trypanosomatidae from the Honey Bee Apis mellifera: Crithidia mellificae Langridge and McGhee, and Lotmaria passim n. gen., n. sp. J Eukaryot Microbiol 2015, doi:10.1111/jeu.12209.