#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 19, 2025; 10:54 GMT TreeBASE (cc) 1994-2008 Study reference: Tripathi A.K., Singh K., Pareek A., & Singla-pareek S.L. 2015. Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biology, 15(42). TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16883] [ The following blocks are input data for analysis step 15350 ] BEGIN TAXA; TITLE TaxaForAnalysisStep15350; DIMENSIONS NTAX=22; TAXLABELS Arabidopsis_thaliana_ASF1L1 Arabidopsis_thaliana_ASF1L2 Chlamydomonas_reinhardtii_Cre08.g376350.t1.2 Chlamydomonas_reinhardtii_Cre08.g376350.t2.1 Homo_sapiens_CIAI Homo_sapiens_CIAII Oryza_sativa_ASF1L1 Oryza_sativa_ASF1L2 Physcomitrella_patens_Phpat.008G092000.1.p Physcomitrella_patens_Phpat.023G079900.1.p Physcomitrella_patens_Phpat.023G079900.2.p Physcomitrella_patens_Phpat.023G079900.3.p Physcomitrella_patens_Phpat.023G079900.4.p Physcomitrella_patens_Phpat.023G079900.5.p Physcomitrella_patens_Phpat.023G080100.1.p Physcomitrella_patens_Phpat.024G076800.1.p Picea_abies_MA_10428471g0010 Picea_abies_MA_10428471g0020 Picea_abies_MA_16730g0010 Picea_abies_MA_73031g0010 Saccharomyces_cerevisiae_ASF1 Selaginella_moellendorffii_90000 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25497] TITLE Histone_chaperone_ASF1_matrix; LINK TAXA = TaxaForAnalysisStep15350; DIMENSIONS NCHAR=481; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_ASF1L1 --------------------------------------------------------------------------MSSINITNVTVLDNPAPFVNPFQ------FEISYECLTSLKDDLE------------------------------------WKLIYVGSAEDETYDQVLESVLVGPVNVGNYRFVLQADSPDPLKIREEDIIGVTVLLLTCSYMDQEFIRVGYYVNNDYDDEQLREEPPTKVLIDKVQRNILTDKPRVTKFPINFHPEN------------------------------EQTLGD-----GPAPTEPFADSVVNGEAPVFLEQPQKLQEIEQFDDS--------------------------DVNGEAIALLDQ--PQNLQET------------------------------------------------------------------------------------ Arabidopsis_thaliana_ASF1L2 --------------------------------------------------------------------------MSAIKITNVAVLHNPAPFVSPFQ------FEISYECLNSLKDDLE------------------------------------WKLIYVGSAEDETYDQLLESVLVGPVNVGNYRFVFQADPPDPSKIQEEDIIGVTVLLLTCSYMGQEFLRVGYYVNNDYEDEQLKEEPPTKVLIDKVQRNILSDKPRVTKFPIDFHPEE------------------------------EQTAAT-----AAPPEQ--SDE----------QQP--------------------------------------NVNGEAQVLPDQSVEPKPEES------------------------------------------------------------------------------------ Chlamydomonas_reinhardtii_Cre08.g376350.t1.2 ---------------------------------------------------------------------------MAVSVVAVRALNNPALFTDPLA------FEIEYEALTALEQDLA------------------------------------WKLVYVGSADSDRYDQELENVEVGPVVQGNFKFVLEANPPKPELIPVDDLLGVTVILLTCSYRGREFIRVGYYVNNEYVDEELRENPPEQPRLDRLQRSILADHPRVTRYAIPFDDPEPADGVAP-------------------------MDEDGAMQAGVEMQQQAAAP------MAEVAAPAPPSSAVATGGFYG----------------------------AQPGPFDGMMPQQQLYEVPVQ-------------------------------------------------------------------------------- Chlamydomonas_reinhardtii_Cre08.g376350.t2.1 ---------------------------------------------------------------------------MAVSVVAVRALNNPALFTDPLA------FEIEYEALTALEQDLA------------------------------------WKLVYVGSADSDRYDQELENVEVGPVVQGNFKFVLEANPPKPELIPVDDLLGVTVILLTCSYRGREFIRVGYYVNNEYVDEELRENPPEQPRLDRLQRSILADHPRVTRYAIPFDDPEPADGVAP-------------------------MDEDGAMQAGVEMQQQAAAP------MAEVAAPAPPSSAVATGGFYG----------------------------AQPGPFDGMMPQQQLYEVPVQ-------------------------------------------------------------------------------- Homo_sapiens_CIAI --------------------------------------------------------------------------MAKVQVNNVVVLDNPSPFYNPFQ------FEITFECIEDLSEDLE------------------------------------WKIIYVGSAESEEYDQVLDSVLVGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQEFIRVGYYVNNEYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWED-----------------------------------NTEKLEDAESSNPNLQSLL-------STDALPSASKGWSTSEN------------------------------------SLNVMLESHMDCM----------------------------------------------------------------------------------- Homo_sapiens_CIAII --------------------------------------------------------------------------MAKVSVLNVAVLENPSPFHSPFR------FEISFECSEALADDLE------------------------------------WKIIYVGSAESEEFDQILDSVLVGPVPAGRHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLNPELRENPPMKPDFSQLQRNILASNPRVTRFHINWDN-----------------------------------NMDRLEAIETQDPSLGCGL-------PLNCTP--IKGLGLPGC------------------------------------IPGLLPENSMDCI----------------------------------------------------------------------------------- Oryza_sativa_ASF1L1 --------------------------------------------------------------------------MSAVNITNVAVLDNPTAFLNPFQ------FEISYECLIPLDDDLE------------------------------------WKLIYVGSAEDENYDQQLESVLVGPVNVGTYRFVLQADPPDPSKIREEDIIGVTVLLLTCSYMGQEFMRVGYYVNNDYDDEQLREEPPAKLLIDRVQRNILADKPRVTKFPINFHPEP-------------------------STSAGQ----------QQQEPQTASPE----------NHTGG-----------------------------------------------EGSKPAADQ------------------------------------------------------------------------------------- Oryza_sativa_ASF1L2 MSVIDILTRVDAICQKYGRYDAEKLHGSGVAGEDPFARLYASVDADLNECLEKAEAAKQEKNRATVVALNAEIRGTKAKLLEEDLPKLQRLALKKVKGLSKEELAIRGDLVTALPDRIQSIPDGSATSSKKTGLWGSSGSRAGTGIKFDSTYDLEWKLIYVGSAEDENYDQLLESVLVGPVNVGTYRFVLQADPPDPSKIRKEDIIGVIVLLLTCSYMGQEFIRVGYYVNNDNDDEQLREEPPAKLLIDRVQRNILADKPSVTKFPINFHPET--------------------------------SAGAGQEQ--QQQQQSGSPE----------NHPN------------------------------------------------QGSKPNPDQ------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.008G092000.1.p --------------------------------------------------------------------------MSAVNVTNVAVLDNPSMFQNPFQ------FEISYECLTALQDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNIGNYRFVLQADPPDVSRIPEEDVIGVTVLLLTCSYRGQEFIRVGYYVSNDYVDESLREEPPVRVLIDKVQRNILADKPRVTKFPILFNSPG-VIAP----------------------------EPQEVSDAFISPTTEFDMMNTNEKASGSH-TPAVVLDFTPTVEQ---DSDARASQPSLMFL----------MQNGAVRPVNLCAPQVLQEVC----------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G079900.1.p --------------------------------------------------------------------------MSAVNVTNVTVLDNPSMFQNPFQ------FEISYECLVPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPEPSKIPEEDIIGVTVLLLTCSYVGQEFLRVGYYVSNEYVDEPLREEPPAKVLIDRVQRNILADKPRVTKFPIVFNATP---------------------------------PSNQVTDNASANSYPMVYN---------APPPSQVT-------------DAELDDG--------------------VRPMEISSAYPQQD------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G079900.2.p --------------------------------------------------------------------------MSAVNVTNVTVLDNPSMFQNPFQ------FEISYECLVPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPEPSKIPEEDIIGVTVLLLTCSYVGQEFLRVGYYVSNEYVDEPLREEPPAKVLIDRVQRNILADKPRVTKFPIVFNATP---------------------------------PSNQVTDNASANSYPMVYN---------APPPSQVT-------------DAELDDG--------------------VRPMEISSAYPQQD------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G079900.3.p --------------------------------------------------------------------------MSAVNVTNVTVLDNPSMFQNPFQ------FEISYECLVPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPEPSKIPEEDIIGVTVLLLTCSYVGQEFLRVGYYVSNEYVDEPLREEPPAKVLIDRVQRNILADKPRVTKFPIVFNATP---------------------------------PSNQVTDNASANSYPMVYN---------APPPSQVT-------------DAELDDG--------------------VRPMEISSAYPQQD------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G079900.4.p --------------------------------------------------------------------------MSAVNVTNVTVLDNPSMFQNPFQ------FEISYECLVPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPEPSKIPEEDIIGVTVLLLTCSYVGQEFLRVGYYVSNEYVDEPLREEPPAKVLIDRVQRNILADKPRVTKFPIVFNATP---------------------------------PSNQVTDNASANSYPMVYN---------APPPSQVT-------------DAELDDG--------------------VRPMEISSAYPQQD------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G079900.5.p --------------------------------------------------------------------------MSAVNVTNVTVLDNPSMFQNPFQ------FEISYECLVPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPEPSKIPEEDIIGVTVLLLTCSYVGQEFLRVGYYVSNEYVDEPLREEPPAKVLIDRVQRNILADKPRVTKFPIVFNATP---------------------------------PSNQVTDNASANSYPMVYN---------APPPSQVT-------------DAELDDG--------------------VRPMEISSAYPQQD------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.023G080100.1.p --------------------------------------------------------------------------MAAVNVTNVSVLDNPSIFTNPFQ------FEISYECLLPLRDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGHYRFVFQADPPQLSRIPEKDIVGVTVLLLTCSYQGQEFIRVGYYVNNDYIEESLREEPPASVIIDKVQRNILADKPRVTKFPIVYHSSEPVMAPV---------------------------EPELVHSGCSSLPSAMDVS------SGCMPLPPTTSPMIN---------------------------------------CGMRP---LQEVC----------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.024G076800.1.p --------------------------------------------------------------------------MTAVNVTNVTVLDNPSMFMNPFQ------FEISYECLCPLQDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNIGNYRFVFQADPPELSKIPEEDTIGVTVLLLTCSYQGQEFIRVGYYVSNDYVEEALREEPPARVLIEKVQRNILADKPRVTKFPIVFNSPAPVLNHI---------------------------ESERITDSYISEPAAISTLHTYENVSDVHSTPPAAVDIMQTDEN---IVHAHASLDTPMDL----------APADEVRSVDLRTPQTLQEVC----------------------------------------------------------------------------------- Picea_abies_MA_10428471g0010 --------------------------------------------------------------------------MTSTHYLGFVIDIEVRVDLEKVE------IVLNCLVPKNLIELHSFL-------------------------------DLEWKLIYVGSAEDESYDQMLESVLVGPVNVGNYRFVFQADPPDPSKIRDEDIIGVTVLLLTCSYMGQEFIRVGYYVNNDYDDEQLREEPPPRVLIDRVQRNILADKPRVTKFPINFHPAT---------------------------------IG--------PPENPAPP-----------PDPM------------------------------------------------VEMRPDVQS------------------------------------------------------------------------------------- Picea_abies_MA_10428471g0020 --------------------------------------------------------------------------MLESVLVG-------PVNVGNYR------FVFQANLSHNLFLRIS-----------------------------------------------------ISSVLR--------RFCL-ADPPDPSKIRDEDIIGVTVLLLTCSYMGQEFIRVGYYVNNDYDDEQLREEPPPRVLIDRVQRNILADKPRVTKFPINFHPAT---------------------------------IG--------PPENPAPP-----------PDPM------------------------------------------------VEMRPDVQS------------------------------------------------------------------------------------- Picea_abies_MA_16730g0010 --------------------------------------------------------------------------MSAVNITNVTVLDNPAAFLNPFQ------FEISYECLTPLKDDLE------------------------------------WKLTYVGSAEDEKYDQVLESVLVGPVNVGNYRFVFQADPPDPSKIPDEDIIGVTVLLLTCSYQGQEFIRVGYYVNNDYADEQLREEPPQVVQLDKIQRNILADKPRVTKFPIAFHSTP---------------------------------DEQSVLSQLGSLPPNAGLL------------PSDAS-------------LLSADNS--------------------LSASDLMMDEVLLEGIAT--------------------------------------------------------------------------------- Picea_abies_MA_73031g0010 -------------------------------------------------------------------------MASCVSITNVTVLDNPAMFLNPFQ------LEISYESLIPLKYDLE------------------------------------WKLIYVGCAEDERYDQVLQTVHVGPVKVGNYRFVLQADPPEVELIRSEDLLGVAAIVLSCSYIGREFMRVGYYVSNQYVQQELIEEPPSTVAIDKIQRFVLASMPRVSRFPISFQICS----------------------------------AVQCDSNYSEGDRYEGED-------------------------------------------------------------DCGDVVDLLELFG---------------------------------------------------------------------------------- Saccharomyces_cerevisiae_ASF1 --------------------------------------------------------------------------MSIVSLLGIKVLNNPAKFTDPYE------FEITFECLESLKHDLE------------------------------------WKLTYVGSSRSLDHDQELDSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGVDDEEEE---------DDEEEDDDEDDEDDEDDDQEDGEGE-------AEEAAEEEEEEEEKTED------------------------------------NETNLEEEEEDIENSDGDEEEGEEEVGSVDKNEDGNDKKRRKIEGGSTDIESTPKDAARSTN---------------------------------- Selaginella_moellendorffii_90000 --------------------------------------------------------------------------MSAINITNVTVLDNPSMFLKPFQ------FEISYECLIPLKDDLE------------------------------------WKLIYVGSAEDEKYDQVLESVLVGPVNVGNYRFLFQADPPEWTKIPDEDILGVTVLLLTCSYLGQEFIRVGYYVSTEYADDSLNLEPPAKVLINQVRRTVLAEKPRVTKFPMAFNAPL---------------------------------ANEKVEEDANNTSN-----------------GSNLL------------------------------------------PVDAS-------------------------------------------------------------------------------------------- ; END; [ The following blocks are output data for analysis step 15350 ] BEGIN TREES; TITLE Histone_chaperone_ASF1_Result; LINK TAXA = TaxaForAnalysisStep15350; TREE ASF1_tree = [&R] (((((((Physcomitrella_patens_Phpat.023G079900.2.p:0.0,Physcomitrella_patens_Phpat.023G079900.1.p:0.0)0.1200:0.0,Physcomitrella_patens_Phpat.023G079900.3.p:0.0)0.0890:0.0,(Physcomitrella_patens_Phpat.023G079900.4.p:0.0,Physcomitrella_patens_Phpat.023G079900.5.p:0.0)0.1640:0.0)0.9990:0.06177011,Selaginella_moellendorffii_90000:0.19074696)0.6710:0.06108172,(Physcomitrella_patens_Phpat.024G076800.1.p:0.05453074,(Physcomitrella_patens_Phpat.023G080100.1.p:0.1315373,Physcomitrella_patens_Phpat.008G092000.1.p:0.08610819)0.4990:0.02517693)0.7090:0.04253176)0.6160:0.05811997,((Arabidopsis_thaliana_ASF1L1:0.05532341,Arabidopsis_thaliana_ASF1L2:0.10481879)0.7300:0.04913153,(Oryza_sativa_ASF1L1:0.05909811,(Oryza_sativa_ASF1L2:0.16710053,(Picea_abies_MA_10428471g0010:0.10661702,Picea_abies_MA_10428471g0020:0.19649401)1.0000:0.23588491)0.9900:0.18370404)0.8810:0.07130371)0.9370:0.06191623)0.4570:0.03229519,(Picea_abies_MA_16730g0010:0.05997896,(Picea_abies_MA_73031g0010:0.36586644,((Chlamydomonas_reinhardtii_Cre08.g376350.t1.2:0.0,Chlamydomonas_reinhardtii_Cre08.g376350.t2.1:0.0)1.0000:0.37296893,(Saccharomyces_cerevisiae_ASF1:0.39110213,(Homo_sapiens_CIAI:0.11146484,Homo_sapiens_CIAII:0.13143499)1.0000:0.30297244)0.4950:0.09618388)0.9070:0.1325273)0.7920:0.10850206)0.4570:0.00997744); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr80621] END;