Supplementary material Table 2. Novel non-LTR retrotransposons from Fungi detected in this study and their accession numbers in databases

Species / element / database: genomic scaffold/protein
and/or
database: contig [location of HMM signal]

Fusarium verticillioides

/ FvNLR1 / Broad Institute:Supercontig 22 [241250..242662]
FvNLR2 / Broad Institute:Supercontig 22 [163676..164860]
FvNLR3 / Broad Institute:Supercontig 19 [420956..422368]
FvNLR4 / Broad Institute:Supercontig 19 [911832..912965]

Fusarium oxysporum

/ FoNLR1 / Broad Institute:Supercontig 24 [421797..423134]
FoNLR2 / Broad Institute:Supercontig 9 [2049193..2050533]
FoNLR3 / Broad Institute: Supercontig 19 [305335..306777]
FoNLR4 / Broad Institute:Supercontig 4 [805363..806694]
FoNLR5 / Broad Institute:Supercontig 25 [281050..282345]
FoNLR6 / Broad Institute:Supercontig 9 [783652..784944]
FoNLR7 / Broad Institute:Supercontig 36 [323171..324304]
FoNLR8 / Broad Institute:Supercontig 9 [1590722..1592017]
FoNLR9 / Broad Institute:Supercontig 3[3302..4471]

Podospora anserina

/ PaNLR1 / CNRS: chrm6_SC2 [2929241..2927760]

Trichoderma virens

/ TvNLR1 / JGI:scaffold_8 [352172..353371]
TvNLR2 / JGI:scaffold_32 [39640..40920]

Chaetomium globosum

/ CgNLR1 / GenBank: CH408031/EAQ90184
CgNLR2 / GenBank: CH408029/EAQ91984
CgNLR3 / GenBank: CH408031/EAQ90175
CgNLR4 / GenBank: CH408036/EAQ83156
CgNLR5 / GenBank: CH408034/EAQ84580
CgNLR6 / GenBank: CH408033/EAQ87030

Aspergillus clavatus

/ AcNLR1 / Broad Institute:Supercontig 84 [5589..6716]
AcNLR2 / Broad Institute:Supercontig 76 [1716065..1717399]

Aspergillus flavus

/ AflaNLR1 / Broad Institute:Supercontig 16 [4683..6101]

Aspergillus fumigatus

/ AfNLR1 / Sanger:Contig6 [3520..4872]
AfNLR2 / Sanger: Contig1375.1 [196474..197775]
AfNLR3 / Sanger: Contig1375.1 [177889..176519]
AfNLR4 / Sanger: Contig40 [435138..433948]

Aspergillus terreus

/ AtNLR1 / GenBank: NT_165938/XP_001218108

Aspergillus nidulans

/ AnNLR1 / GenBank: EAA60682/AACD01000158
AnNLR2 / GenBank: EAA63063/AACD01000046
AnNLR3 / Broad Institute: Contig 46 [70703..75742]

Aspergillus niger

/ AniNLR1 / GenBank: AM270275/--
AniNLR2 / GenBank: AM270184/CAK45822
AniNLR3 / GenBank: AM270084/--
AniNLR4 / GenBank: AM270275/--

Aspergillus oryzae

/ AorNLR1 / Broad Institute:Supercontig 23[333851..335269]
AorNLR2 / Broad Institute:Supercontig 21 [275127..276422]
AorNLR3 / Broad Institute:Supercontig 20 [11773..13074]
AorNLR4 / Broad Institute:Supercontig 21[265152..266447]

Histoplasma capsulatum

/ HcNLR1 / GenBank: CH476657/EDN07034
HcNLR2 / Broad Institute: Supercontig 3 [1247388..1248473]
HcNLR3 / GenBank: CH476664/EDN04466
HcNLR4 / GenBank: CH476660/EDN09606
HcNLR5 / GenBank: CH476656/EDN06465
HcNLR6 / GenBank: CH476667/EDN05263

Supplementary material Table 2 (continued). Novel non-LTR retrotransposons from Fungi detected in this study and their accession numbers

Species / element / database: genomic scaffold/protein
and/or
database: contig [location of HMM signal]

Ascosphaera apis

/ AaNLR1 / BaylorCollege of Medicine: Scaffold232 [14232..12940]
AaNLR2 / BaylorCollege of Medicine: Scaffold 451 [6254..7018]

Coccidioides immitis

/ CiNLR1 / Broad Institute: Supercontig 2 [7402333..7403562]
CiNLR2 / Broad Institute:Supercontig 1 [5254742..5256064]
CiNLR3 / GenBank: CH476726/EAS37393
Broad Institute:Supercontig 1 [7400295..7401614]

Coccidioides posadasii

/ CpNLR1 / Broad Institute:Supercontig 19 [116956..118263]
CpNLR2 / Broad Institute:Supercontig 38 [47715..49040]

Paracoccidioides brasiliensis

/ PbNLR1 / Broad Institute: Supercontig 13 [971351..972706]
PbNLR2 / Broad Institute: Supercontig 7 [361047..362336]
PbNLR3 / Broad Institute:Supercontig 19[599663..601000]

Uncinocarpus reesii

/ UrNLR1 / Broad Institute:Supercontig 5 [2238844..2240145]
UrNLR2 / Broad Institute:Supercontig 2 [219318..220613]

Botrytis cinerea

/ BcNLR1 / Broad Institute: Supercontig 72 [115530..116762]

Mycosphaerella fijiensis

/ MfNLR1 / JGI: scaffold_48 [104874..106178]
MfNLR2 / JGI:scaffold_50 [169798..171063]
MfNLR3 / JGI:scaffold_3 [1699761..1700951]
MfNLR4 / JGI:scaffold_1 [3872529..3873806]
MfNLR5 / JGI:scaffold_8 [452062..453552]
MfNLR6 / JGI:scaffold_7 [1155417..1156895]
MfNLR7 / JGI:scaffold_11 [652743..654101]
MfNLR8 / JGI:scaffold_2 [2464004..2465389]

Pyrenophora tritici-repentis

/ PtNLR1 / Broad Institute: Supercontig 2[2445825..2447192]
PtNLR2 / Broad Institute: Supercontig 4[1005957..1007270]
PtNLR3 / Broad Institute: Supercontig 30[25811..27103]
PtNLR4 / Broad Institute: Supercontig 19 [312577..313842]
PtNLR5 / Broad Institute: Supercontig 4[943429..944715]
PtNLR6 / Broad Institute: Supercontig 19 [271816..273240]
PtNLR7 / Broad Institute: Supercontig 7[23389..24918]
PtNLR8 / Broad Institute: Supercontig 12 [735973..737256]
PtNLR9 / Broad Institute: Supercontig 6[39229..40596]
PtNLR10 / Broad Institute: Supercontig 28[11427..12803]

Sclerotinia sclerotiorum

/ SsNLR1 / GenBank: CH476626/EDO03066
Broad Institute: Supercontig 8 [836..2164]
SsNLR2 / GenBank: CH476639/EDN95917
Broad Institute: Supercontig 8 [241766..243064]
SsNLR3 / GenBank: CH476641/EDN97563
Broad Institute: Supercontig 19 [190946..192238]
SsNLR4 / GenBank: CH476626/EDO02464
Broad Institute: Supercontig 13 [971783..973129]
SsNLR5 / Broad Institute: Supercontig 3 [2370410..2371762]
SsNLR6 / Broad Institute: Supercontig 8 [12937..14271]

Stagonospora nodorum

/ SnNLR1 / GenBank: CH445366/EAT76579
SnNLR2 / Broad Institute: Supercontig 51 [16199..17539]

Pichia stipitis

/ PsNLR1 / JGI:chr_5.1 [552858..554144]
PsNLR2 / JGI:chr_1.2 [894912..896198]
PsNLR3 / JGI:chr_8.1 [257751..261973]
PsNLR4 / JGI:chr_1.1 [1784580..1785854]

Supplementary material Table 2 (continued). Novel non-LTR retrotransposons from Fungi detected in this study and their accession numbers

Species / element / database: genomic scaffold/protein
and/or
database: contig [location of HMM signal]

Coprinus cinereus

/ CcNLR1 / GenBank: AACS01000058/EAU90697
Broad Institute: Contig 58 [108634..110007]
CcNLR2 / GenBank: AACS01000157/EAU86818
Broad Institute: Contig 157 [11030..12397]
CcNLR3 / GenBank:AACS01000159/EAU86808
Broad Institute: Contig 159 [113379..114833]
CcNLR4 / GenBank:AACS01000220/EAU83689
Broad Institute: Contig 220 [127599..128909]
CcNLR5 / GenBank:AACS01000313/EAU81240
Broad Institute: Contig 313 [99351..100655]
CcNLR6 / GenBank: AACS01000351/EAU80354
Broad Institute: Contig 351 [19519..20856]
CcNLR7 / Broad Institute: Contig 377 [7198..7875]

Phanerochaete chrysosporium

/ PcNLR1 / JGI:scaffold_6 [1668557..1669951]
PcNLR2 / JGI:scaffold_19 [341598..342986]
PcNLR3 / JGI:scaffold_20 [345770..347209]
PcNLR4 / JGI:scaffold_48 [5402..6841]
PcNLR5 / JGI:scaffold_132 [ 56..1495]
PcNLR6 / GenBank: DQ097836/AAZ28934
PcNLR7 / JGI:scaffold_12 [432983..439266]

Postia placenta

/ PpNLR1 / JGI:scaffold_262 [23251..24615]
PpNLR2 / JGI: scaffold_254 [25804..27120]
PpNLR3 / JGI: scaffold_262 [33881..35254]
PpNLR4 / JGI: scaffold_30 [354784..356127]
PpNLR5 / JGI: scaffold_28 [422209..423531]
PpNLR6 / JGI: scaffold_89 [282868..284160]

Sporobolomyces roseus

/ SrNLR1 / JGI:scaffold_1 [ 277739..279046]

Puccinia graminis f. sp. tritici

/ PgtNLR1 / Broad Institute: Supercontig 35 [339618..340895]
PgtNLR2 / Broad Institute: Supercontig 11 [1259007..1259819]
PgtNLR3 / Broad Institute: Supercontig 68[371108..372394]
PgtNLR4 / Broad Institute: Supercontig 23 [488682..489971]
PgtNLR5 / Broad Institute: Supercontig 12 [1317699..1318988]
PgtNLR6 / Broad Institute: Supercontig 23 [331196..332479]
PgtNLR7 / Broad Institute: Supercontig 33 [16818..17915]

Laccaria bicolor

/ LbNLR1 / JGI: scaffold_32 [338695..340053]
LbNLR2 / JGI: scaffold_19 [328819..330829]
LbNLR3 / JGI:scaffold_14 [1048457..1049803]
LbNLR4 / JGI:scaffold_67 [ 23520..24863]
LbNLR5 / JGI:scaffold_6 [87916..89262]
LbNLR6 / JGI:scaffold_19 [328819..329889]
LbNLR7 / JGI:scaffold_19 [328822..330165]
LbNLR8 / JGI:scaffold_6 [32601..33896]
LbNLR9 / JGI:scaffold_45 [169809..171140]

Ustilago maydis

/ UmNLR1 / GenBank: AACP01000238/EAK82814