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AR TICLE Nine Draft Genome Sequences of Claviceps Purpurea S doi:10.5598/imafungus.2018.09.02.10 IMA FUNGUS · 9(2): 401–418 (2018) IMA Genome-F 10 ARTICLE Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans 1 A3B4, Miao Liu D3EF1%#4GB>4, Lieschen De Vos4I> 1 B4E34J4,5>I!K4, Kasia Dadej OB3A4B%1, >D$4,5>$PT=J4>K2PF4U$I1I$G1, Quentin C. Santana4PG1, Nicole Soal4[EG4!EE4>$F4, and Michael JB4 1U\]3$!^%!'*<!$UUP&<!*! 2>\3$!^%!&<&\&<<>>\*>&_! =#%4>@>G!K\`&<+=&q;;< Iq!K\ 43A4>A4>%A@%A@?$I I$A";<DI<<;+Gv^xABz%A@K 53!$[[G?$I$A{&>|*<;G Abstract: EClaviceps purpurea s.lat., including C. Key words: arundinis, C. humidiphila and C. cf. spartinae.E Davidsoniella eucalypti, Quambalaria eucalypti and Teratosphaeria destructans, . The insect associate Grosmannia galeiformis E Fusarium Eucalyptus circinatum } Fusarium fujikuroi"EF. Poaceae circinatum$&;F. circinatumE%%G! ". Article info: Gx;&F$;<&+vx;*F$;<&+vIx&q3;<&+. IMA Genome-F 10A ! Nine draft genome sequences of " Claviceps purpurea s.lat., including # et al. 1986, Miles et al. 1996, Scott 2009). These $[ C. arundinis, C. humidiphila and C. %&'*+! cf. spartinae 1976, Miles et al. &''*34et al. &''+;<<= $ conditions 34et al. &''+!;<<*>et INTRODUCTION al. 2006) ? $ "[ Claviceps purpurea (Clavicipitaceae, Hypocreales) is a plant \ (Poaceae \ @$ $$" © 2018 International Mycological Association You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: [ Non-commercial: No derivative works: For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. VOLUME 9 · NO. 2 401 [et al. $IK$et al. 2000) in C. purpurea NUCLEOTIDE SEQUENCE ACCESSION s. latE[ NUMBERS ^ C. arundinis, C. humidiphila, and C. spartinae E (Douhan et al. ;<<+I$et al. ;<&_ 33AJ[>A#4AAII\JFqq'=*&E ARTICLE G $$[\3<&<<<<<< "`#et al. 2016). In Canada, [B<&<<<<<< [{<&<<<<<< [<&<<<<<< G [O<&<<<<<< [\<&<<<<<< [\A<&<<<<<< > ;<<; >K ] [\!<&<<<<<< [\[<&<<<<<< \ E;<&q3$ F!A@ G\ x$ ! $ G\I&='*&< x C. spartinae 4= !. humidiphila, and the C. purpurea MATERIALS AND METHODS s. lat."%&D$ $ } % I 3"I3vA33TM I $&< at 20 °!>&M;$ }F23F" SEQUENCED STRAINS [!EA 3 ] 3 &'+| E [ Claviceps purpurea s.str. $ \F " \F Canada: Saskatchewanx [$ GP& q'&q F &<;'' B x & K Triticum aestivum, 2000, R. Clear |<<);{!EA&q<)\F!TM J4>K#>;+3U>!;_<*q|Czech Republic: [K>"q"$x;_)_<) AKDq'+=F&q<=[Secale cereale, v @$ E % G ;+ ) ;<<=GI$#>_+;3U>!;_&|;= \FG[q"$x&)&<<) !!!||&"^ *M| ; &< ) I P _< ))# v % Claviceps purpurea s.lat. G E % G Canada: AlbertaxFG_+_=F&&+&;B ;__°!=A3F Bromus inermis|G&'_*BI! =_ \F ! #>|+ 3U>! ;_<_|+v > _;q& F &&<*= B $" Elymus albicans|G&'_*B q_ M & I!#>+&3U>!;_<_+&Quebecx!F *_<3#!D!4 &=<<< >\! >I^I _<&= F *&<+ B &_ I \F 3F Ammophila sp., 8 Sep. 2015, J. Cayouette]Y. Dalpé & #>q_+3U>!;_&+'+ ;*<;+< F3 &<<< G$=+E%G Claviceps cf. spartinae \F3F}® 2 .0 Canada: Manitobax4R%Gq'<_F'+** %@$#E B Phalaris arudinacea, 2014, J. Menzies E " 3F K q<< > # #>;&+ 3U>! ;_&+q= Quebec: =<<!$#[;;< >^!I^E$ E #G^Jq+*|F|&+|BAmmophila I!\#F"G}%\[[#3F# breviligulata=&;<&qJ. Cayouette># # R #>q_q3U>!;_&+q_3U>__<;q*M @" $ } F"G} @v Claviceps humidiphila > E # U \ ] Germany: Bavariax I q++* F &=*+ [ 3$ ! ^% ! Dactylis sp., 1998 and #>_|* ;"&_<F"G}>U\P@ 3U>!;_&|&|!!!q=q"^ E%!$<&&_x } Claviceps arundinis }I}$E Czech RepublicxD$3$G`q'<& $<=* A et al. 2014) x F&qq=[Phragmites australis, 11 Jan. 2008, HEADCROP:20 SLIDINGWINDOW:4:20 MINLEN:36. The T#>_+=3U>!;_&|;q!!!'=="^ AD F et al. ;<&=. De novo 402 IMA FUNGUS IMA Genome – F10 (& ARTICLE !" !" %"# %"# $(%$ !$# !$# 99/100 !$# !$# 80/98 !$# !$# 100/100 60/85 "# $$ $$ $$ 97/100 $$ $$ $$ $$ ! $$ &$!%& &$!%& %#$ )&!&*# )&!&*# %& # # # 86/100 # # 90/100 # # # # 68/92 ))$# %&' ("%## Fig. 1. U>IClaviceps [%&^''$ =<;!@<*<*\@<+<|\!<q+'D@<='q4^^|_<+'`>IA@ GI$=&<&A$et al. ;<&; &<<<?GE$q_4$et ! al. ;<&=$! VOLUME 9 · NO. 2 403 [et al. A; $;<< # ] GK ;<&; A;G>$A> G>$<&&'#et al. ;<<' Complete (%) BUSCO’s $$;;4^ ARTICLE et al. ;<&; E $ ?$ G^! U A?G!U $; (Simão et al. ;<&_ (x) ' 4 4>^[G$q=+#Ket al. ;<<_OP E^D$ et al. ;<<+ $44D et al. ;<&q ; x$ ;;KE& E[3F} &^" Geneious 10.0.9 P N50 (bp) L50 GC (%) Coverage et al. ;<&;v$ } $ I$ et al. (2015) and Van # et al. ;<&* >%%E $ | https:// $) P ] G ;<&=. =<&''_<'28571566 ;||===<*'q'&= 21589 =;|=_+|__'q 46550 51,7 416=<_'+;_< 41916 190 51,4=<*';_+q 72 =''+q 189 51,5=<q++;q= 52 28795 229 51,9=<<__=+& =<_ =_&=' =<| 51,4 98,6 66 =''+' 257 51,4 '|= 214 96,9 51,5 219 126 51,4 98 *= 97,6 56 97,9 97,9 96,9 =<;_&|_' =;q'q 269 51,7 =' 97,9 =<'<&+|; 46498 197 51,6 =' 97,6 Total length Total (bp) >" I >I PAUPq<&<G;<<;;<< &<<< A@A@> A=;\}et al. 2012) &<<<<<<<<>!>! Number of protein coding gene models ;_^ RESULTS AND DISCUSSION 1442 ++;= contigs E } x Claviceps purpurea s.str. and C. cf. spartinae C. humidiphila and C. arundinisC. purpurea s.lat E& % & E &q;= ;=;& K =<+ > [\<&<<<<<< 2207 8777 [\A<&<<<<<<QEQZ01000000 &+=& &*&= 9040 8855 [<&<<<<<<[{<&<<<<<< ;=;&[B<&<<<<<< &q;=[\[<&<<<<<< 1698 8410 [\!<&<<<<<< &*=< 9008 2108 ';=< 8960 '<=+ [\3<&<<<<<< &'=< 8977 ;+*>=_'>E$4! a a a _&_EF_<;&*q**E A?G!U '*''+*v +q&<';=< The genome of Claviceps purpurea ;<& F!A@ . !4<<<<<<<<&$ G et al. ;<&= E ;<&= &qq; ++;= et al. K=<'>F_<q*_4!_&* D$ &'& } LM78 3U>!;_<_|+ LM458LM218 3U>!;_&+'+ LM454 3U>!;_&+q= LM576 3U>!;_&+q_ #>_+= 3U>!;_&|&|!!!q=q 3U>!;_&|;q!!!'== 20,1 LM28LM582 3U>!;_<*q| 3U>!;_&|;=!!!||& BA?G!U '|* U . LM81 3U>!;_<_+& } Claviceps Claviceps s.lat. s.lat s.lat. s.str. s.str. $$ [ spartinae spartinae cf. cf. Authors: H.D.T. Nguyen, W. Findlay, K. Dadej, Statistics of O. Pochopski, P. Shoukouhi, J.G. Menzies, * &'*+/36&7;T>;6?@ ["^x!!!||&"^!!!q=q"^!!!'=="^ E}G Claviceps purpurea Claviceps purpurea Claviceps purpurea Claviceps Claviceps Claviceps humidiphila Claviceps arundinis Claviceps purpurea Claviceps purpurea Claviceps purpurea Species Strain # Voucher # Version number of Table 1. Table a b *Contact: Miao Liu, z 404 IMA FUNGUS IMA Genome – F10 IMA Genome-F 10B $%%G! ARTICLE E $ $ Assembling pseudomolecules for F. circinatum the pitch canker pathogen, Fusarium %%G!%K circinatum, utilising additional } ^ genome sequence data and synteny } B " K within the Fusarium fujikuroi %%G! B et al. ;<&= complex De Vos et al. ;<&q $ @ INTRODUCTION complement of F. circinatum E $ ^} Fusarium $ [ $$ 4 et al. ;<&= > F. circinatum $ +<$$ associated Fusarium # ] G ;<<* %%G! B Fusarium fujikuroi " %%G! Fusarium. _< $ UR3 et al. 1998, 2000). Fusarium circinatum ^ SEQUENCED STRAIN OP Pinus USA: Californiax > Pinus radiata), 1996, spp. and Pseudotsuga menziesii 3 % @ T.R. Gordon, A.J. Storer & D. Okamoto%GI=q>\!|+|< [ !>B_&|_;I\[>*;&'|M 4et al. 2015). NUCLEOTIDE SEQUENCE ACCESSION E} NUMBER 4A J`<<<<<<<< $ J`<&<<<<<< B et al. 2012). The isolate E $ Fusarium circinatum, } %GI=q 4 et al. 1996), has a genetic 33AJ[>A# $3`et al. ;<<| 4A J`<<<<<<<< $ 3 ` et al. ;<&q J`<;<<<<<< K }$ E# } 3 ` et al. ;<&&`B et al. 2018). E'q+Bet al. MATERIALS AND METHODS ;<&|"q&q_ Bet al. 2012, De Vos et al. 2014) and this limits its Fusarium circinatum $ " ;< " $ E} ;_!&;< %%G!$ |3F" EFusarium verticillioides >et al&'';3F} }&&$ F3(G (Ma et al. 2010). This F. verticillioides" } F. circinatum " %GI=qPG&| %%G!E q&q_Bet al. ^ ;<&;@PG&| %%G!{et al. 1995, Ma et al. ;<&<Bet al. ;<&= P. radiataB! `Fet al. ;<&q@ G;<<_Get al. 2014). The genomes }$ of F. circinatum %GI=q PG&| } $ F. fujikuroi B et ^&K al. ;<&= E GU#3( `q A G} %%G!! D@+;q_&_='_^ them and F. temperatum$[$ $I} }$Bet ;< =* al. ;<&=3`et al. 2014). This highlights the fact that $ !#! 4 B $_&!#! $ VOLUME 9 · NO. 2 405 [et al. ARTICLE Fig. 2. >"}!^&^Get al. 2011, De Vos et al;<&qG}>%%E$|P]G;<&=E>E$;&|4] 4;<<=3et al.;<&;^E@>;@4 E$&'+*">#I>#$=&4et al;<&<` [$1+_EF. circinatum%GI=qbold. GGI![$;<AKet al. ;<&&K RESULTS AND DISCUSSION ^%GI=q4A J`<<<<<<<<Bet al. 2012), using E $ Fusarum circinatum, ^ 3 33AJ [>A#4A J`<<<<<<<< ;<<E$$ $ J`<;<<<<<< E F. circinatum #B} _+_$ "K q= '=; '&; 3F F_< =*= *== E E$;|=+;"4!q|q& && [ } &^&& F. verticillioides Fusarium%%G!>et al. ;<&<B E et al. 2012, Jeong et al;<&=Bet al.;<&=` A#GE et al. 1990) against a local Nest et al.;<&q!et al;<&_Bet al. 2015a, F.
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