Adiditional file 1.
List of begomovirus genome sequences (acronym, complete name, available information and accession numbers) used for sequence comparison (Table 1) and phylogenetic analysis (Figure 1).
AbMV-[US:Haw] [Abutilon mosaic virus-[United States of America:Hawaii]-DNA-A (U51137) and DNA-B (U51138);
BCaMV-[MX:Son:86] [Bean calico mosaic virus-[Mexico:Sonora:1986]-DNA-A (AF110189) and DNA-B (AF110190);
BDMV-[CO:87] [Bean dwarf mosaic virus-[Colombia:1987]-DNA-A (M88179) and DNA-B (M88180);
BGMV-[BR:Cam1:78] [Bean golden mosaic virus-[Brazil:Campinas1:1978]-DNA-A (M88686) and DNA-B (M88687);
BGYMV-[DO:87] [Bean golden yellow mosaic virus-[Dominican Republican:1987]-DNA-A (L01635) and DNA-B (L01636);
BlYSV-[BR:Coi25:07] [Blainvillea yellow spot virus-[Brazil:Coimbra25:2007]- DNA-A (NC010837) and DNA-B (NC010838);
CabLCJV-[JM:CUc32:05] [Cabbage leaf curl Jamaica virus-[Jamaica:CUc32:2005]-DNA-A (DQ178610) and DNA-B (DQ178611);
CabLCuV-[US:Flo:96] [Cabbage leaf curl virus-[United States of America:Florida:1996]-DNA-A (U65529) and DNA-B (U65530);
CdTV-[MX:SinIC:83] [Chino del tomate virus-Tomato[Mexico:Sinaloa IC:1983]-DNA-A (AF101476) and DNA-B (AF101478);
CLCrV-AZ[US:Cal:91] [Cotton leaf crumple virus-Arizona[United States of America:California:1991]-DNA-A (AY742220) and DNA-B (AY742221);
CoYSV-[MX:Yuc:05] [Corchorus yellow spot virus-[Mexico:Yucatan:2005]-DNA-A (DQ875868) and DNA-B (DQ875869);
CuLCrV-[US:Ari:91] [Cucurbit leaf crumple virus-[United States of America:Arizona:1991]-DNA-A (AF256200) and DNA-B (AF327559);
DesLDV-[MX:Yuc:05] [Desmodium leaf distortion virus-[Mexico: Yucatan:2005]-DNA-A (DQ875870) and DNA-B (DQ875871);
DiYMoV-[US:Flo:98] [Dicliptera yellow mottle virus-[United States of America:Florida:98]-DNA-A (AF139168) and DNA-B (AF170101);
EuMPV [Euphorbia mosaic Peru virus]-DNA-A (AM886131);
EuMV-A[MX:Yuc:04] [Euphorbia mosaic virus-A [Mexico:Yucatan:2004]-DNA-A (DQ318937) and DNA-B (DQ318938);
EuYMV-[BR] [Euphorbia yellow mosaic virus-[Brazil]-DNA-A (FJ619507) and DNA-B (FJ619508)
MaMPRV-[PR:90] [Macroptilium mosaic Puerto Rico virus-[Puerto Rico:1990]-DNA-A (AY044133) and DNA-B (AY044134);
MaYMFV-[US:Flo:85] [Macroptilium yellow mosaic Florida virus-[United States of America:Florida:1985]-DNA-A (AY044135) and DNA-B (AY044136);
MCLCuV-CR[CR:Gua:98] [Melon chlorotic leaf curl virus-Costa Rica [Costa Rica:Guanacaste:1998]-DNA-A (AY064391) and DNA-B (AY440790);
MeMV-PR[PR:] [Merremia mosaic virus-Puerto Rico [Puerto Rico:]-DNA-A (AF068636) and DNA-B (AY965899);
OMoV6319-[BR:NV] [Okra mottle virus-Brazil [Brazil:Nova Veneza:2008]-DNA-A (EU914817) and DNA-B (EU914818)
OMoV-soy[BR:Sag8:08] [Okra mottle virus-soybean[Brazil:Sag8:08]-DNA-A (FJ686695) and DNA-B (FJ686696)
OYMoV-[MX:Igu] [Okra yellow mottle Iguala virus-[Mexico:Iguala]-DNA-A (AY751753);
PepGMV-CR[US:Ser:89] [Pepper golden mosaic virus-Costa Rica [United States of America:Serano:1989]-DNA-A (AY928516) and DNA-B (AY928517);
PHYVV-[MX:Sin:88] [Pepper hausteco yellow vein virus-[Mexico:Sinaloa:1988]-DNA-A (AY044162) and DNA-B (AY044163);
PYMPV-[PA:Div:Tom] [Potato yellow mosaic Panama virus-[Panama:Divisa:Tomato]-DNA-A (Y15034) and DNA-B (Y15033);
PYMV-Po[VE] [Potato yellow mosaic virus-Potato [Venezuela]-DNA-A (D00940) and DNA-B (D00941);
PYMV-TT[TT:Tom] [Potato yellow mosaic-Trinidad [Trinidad & Tobago:Tomato]-DNA-A (AF039031) and DNA-B (AF039032);
RhGMV-Sb[MX:Sin:05] [Rhynchosia golden mosaic virus-Soybean[Mexico:Sinaloa:2005]-DNA-A (DQ347950) and DNA-B (DQ356429);
RhGMYV-[MX:Yuc] [Rhynchosia golden mosaic Yucatan virus-[Mexico:Yucatan]-DNA-A (EU021216) and DNA-B (FJ792608)
RhMSV-[MX:Sin] [Rhynchosia mosaic Sinaloa virus-[Mexico:Sinaloa]-DNA-A (DQ406672) and DNA-B (DQ406673)
SbBMV-[AR:NOA:05] [Soybean blistering mosaic virus-[Argentina:NOA:2005]-DNA-A (EF016486);
SiCmMV-[BR:Coi4:07] [Sida common mosaic virus-[Brazil:Coimbra4:2007]-DNA-A (EU710751);
SiGMCRV-[CR] [Sida golden mosaic Costa Rica virus-[Costa Rica]-DNA-A (X99550) and DNA-B (X99551);
SiGMHV-[HN] [Sida golden mosaic Honduras virus-[Honduras]-DNA-A (Y11097) and DNA-B (Y11098);
SiGMV-[US:Flo] [Sida golden mosaic virus-[Unites States of America:Florida]-DNA-A (AF049336) and DNA-B (AF039841);
SiMMV-[BR:A2B2] [Sida micrantha mosaic virus-[Brazil:A2B2]-DNA-A (AJ557451) and DNA-B (AJ557453);
SiMMV-[BR:B1] [Sida micrantha mosaic virus-[Brazil:B1]-DNA-B (AJ557452);
SiMMVokra5157-[BR:Goi:07] [Sida micrantha mosaic virus-okra [Brazil:Goianapolis:2007]-DNA-A (EU908733) and DNA-B (EU908734)
SiMMVsoy-[BR:Sag:08] [Sida micrantha mosaic virus-soybean [Brazil:Sag3:08]-DNA-A (FJ686693) and DNA-B (FJ686694);
SiMoV-mic[BR:A1B3] [Sida mottle virus-Micrantha[Brazil:A1B3]-DNA-A (AJ557450) and DNA-B (AJ557454);
SiMoV-Rho[BR:Vic1:99] [Sida mottle virus-Rhombifolia[Brazil:Viçosa1:1999]-DNA-A (AY090555);
SiYLCV-[BR:Coi3:07] [Sida yellow leaf curl virus-[Brazil:Coimbra3:2007]- DNA-A (EU710751)
SiYMV-[BR:Vic2:99] [Sida yellow mosaic virus-[Brazil:Viçosa2:1999)-DNA-A (AY090658);
SiYMYuV-[MX:Yuc:05] [Sida yellow mosaic Yucatan virus-[Mexico:Yucatan:2005]-DNA-A (DQ875872) and DNA-B (DQ875873);
SLCV-[US:Imp:79] [Squash leaf curl virus-[United States of America:Imperial Valley:1979]-DNA-A (M38183) and DNA-B (M38182);
SMLCV-[US:Imp:79] [Squash mild leaf curl virus-[Unites States of America:Imperial Valley: 1979]-DNA-A (AF421552) and DNA-B (AF421553);
TbLRV-[CU] [Tobacco leaf rugose virus-[Cuba]-DNA-A (AJ488768);
TGMoV-[MX:RV:05] [Tomato golden mottle virus-[Mexico:RioVerde:2005]-DNA-A (DQ520943) and DNA-B (DQ406674)
TGMV-[BR:Com:84] [Tomato golden mosaic virus-[Brazil:Common:1984]- DNA-A (K02029) and DNA-B (K02030);
ToChLPV-A[MX:BLP:02] [Tomato chino La Paz virus A-[Mexico:Baja La Paz:2002]-DNA-A (AY3396180);
ToCmMV-[BR:Coi22:07] [Tomato common mosaic virus-[Brazil:Coimbra22:2007]-DNA-A (NC010835) and DNA-B (NC010836);
ToCMoV-BA[BR:Sea1:1996] [Tomato chlorotic mottle virus-Bahia[Brazil:Seabra:1996]-DNA-A (AF90004) and DNA-B (AF491306);
ToCMVCrumple-[BR:Betim1:1996] [Tomato chlorotic mottle virus-Betim1:1996]-DNA-A (AY090557);
ToCMV-MG[BR:Ig1:96] [Tomato chlorotic mottle virus-Minas Gerais[Brazil:Igarapé1:1996]-DNA-A (DQ336353) and DNA-B (DQ336354);
ToLCSinV-[NI:SL] [Tomato leaf curl Sinaloa virus-[Nicaragua:Santa Lucia]-DNA-A (AJ608286) and DNA-B (AJ508783);
ToLDV-[BR:Pda4:05] [Tomato leaf distortion virus-[Brazil:Paty do Alferes4:2005]-DNA-A (EU710749);
ToMHV-[CU:Qui] [Tomato mosaic Havana virus-[Cuba:Quivican]-DNA-A (Y14874) and DNA-B (Y14875);
ToMiLCV-[BR:Ube] [Tomato mild leaf curl virus-[Brazil:Uberlandia]-DNA-B (DQ336352);
ToMiMV-[BR:Pda58:05] [Tomato mild mosaic virus-[Brazil:Paty do Alferes58: 2005]-DNA-A (NC010833) and DNA-B (NC010834);
ToMLCV-[VE:Tru] [Tomato mosaic leaf curl vírus-[Venezuela:Trujillo]-DNA-A (AY508991) and DNA-B (AY508992)
ToMoTV-[CU] [Tomato mottle Taino virus-[Cuba]- DNA-A (AF012300) and DNA-B (AF012301);
ToMoV-[US:Flo:89] [Tomato mottle virus-[United States of America:Florida:1989]- DNA-A (L14460) and DNA-B (L14461);
ToMYLCAV-[VE:10][Tomato mild yellow leaf curl Aragua virus-[Venezuela:10]-DNA-A (AY927277) and DNA-B (EF547938)
ToRMV-[BR:Ube1:96] [Tomato rugose mosaic virus-[Brazil:Uberlandia1:1996]-DNA-A (AF291705) and DNA-B (AF291706);
ToSRV-[BR:PG1:Pep:03] [Tomato severe rugose virus-[Brazil:Petrolina de Goias1:Pepper:2003]- DNA-A (DQ207749) and DNA-B (EF534708);
ToYSV-[BR:Bic2:1999] [Tomato yellow spot virus-[Brazil:Bicas2:1999]- DNA-A (DQ336350) and DNA-B (336351);
ToYSV-bean[AR] [Tomato yellow spot virus-bean[Argentina]-DNA-A (FJ538207)
ToYVSV[Ba3] [Tomato yellow vein streak virus-[Ba3]-DNA-A (EF417915) and DNA-B (EF417916);
ToYVSV[G22] [Tomato yellow vein streak vírus-[G22]-DNA-A (EF459696);
TYCrV-[CU:Cap:07] [Tobacco yellow crinkle virus-[Cuba:Capsicum:2007]-DNA-A (FJ222587);
TYLCTHV [Tomato yellow leaf curl Thailand virus]-DNA-A (AF141922) and DNA-B (AF141897)
TYMLCV-[VE:Mer57] [Tomato yellow margin leaf curl virus-[Venezuela:Medida57]- DNA-A (AY508993) and DNA-B (AY508994);
WGMV-[JM:ST] [Wissadula golden mosaic-[Jamaica:St Thomas]-DNA-A (DQ395343) and DNA-B (EU151895)