Query: 317 SNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPVRESS--PKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKDENF-IAELGTSLFLETA-VNMSVGTVESILAGLGFGDASVRGM----------SQNTFIAFFPDIQNLDELDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSY 643
S T+Y++ F + + DLW L ++ TV D+ + K G R+GFV + +L+E +K+ I S+ L+ A+ +++ N + V++SS P++ + + QT + AS+ ++ TQ K + P V ++++L+ + I + +++ + VN+ + + ++L GF D VR + S +F++F + M F +K + T+ R + +E GLPL WT ++ + WG + + D + ++ ++TS I E + I T +R+ E +
Sbjct: 32 STTIYVSNFPNQMGTSDLWQLCKRHGTVTDVYIAHKLSKIGRRFGFVRFLKVKNNDLLLEDLNKEWIGSHHLYASMARFQRNQS----VQNQQTFVKQSSMGPELKNKPTSHAQTGRSY---ASMLNGNHNVSQYTQVKS---------DKSPTVTLMKKVKLDSSDLINIQNISSNVLAKVRDVNLIIN-IYNVLLKEGFSDFKVRYIGGLWIWIEFTSSESFVSFKEHKE---------MEWYFTHIKPISSTFTVDERMVWIEIVGLPLQAWTSNAFKKIASIWGEPV--FVDEDVNESMSVGRVCIKTSIKGTITEDCMVDINDATHTVRVKEFAGW 344
Query: 317 SNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQN--KKVDSINHSNVNTPPKVEQCRQLQLEKDENFI--AELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDELDLDFMSIG-FNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIR 636
S ++++T DS KDLW + + TV D +P K + RYGFV A L+ + + LH A+ ++ N +FS + +++QT K+ + S +GFA + + KK ++ V + P L DE+ + +++ T+L + S+ ++ +LA GF + ++ M + F I + ++ + + F+ +++ + I R I V G+PL W+ ++ +KWG ++ Y + ++ +I + T T I E I ++G+ + +R
Sbjct: 15 SISIFITNLPDSFNAKDLWRVSNQYGTVVDAFIPDKRSKANKRYGFVRFIKADNVERLVSNLCTIWVGNYRLHANIARFQRKPMNQYFS-----------------QTSKIQTNKQGKKDVSTMKAANGFAGSFAHAVKKGTKSHYEEVESQPA--------LVLDESCLNQSDMSTALMGKVKTFNSLSNLKPVLAKEGFDEIKLKYMGGLWVMIDFQTITSKEKFMANTSVVSWFSHLQQATHNVFIEERAIWVNIDGVPLKVWSKNTFKRIASKWGELI--YDDDQEEMYFHNKRICVLTKFTEPISETFKIIVQGRVFWVR 312
Query: 317 SNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKDENF-IAELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQ-NTFIAFFPDIQNLDELDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSY 643
S+T++++ F + KDLW L + V D+ + RK G R+GFV + LIE +K I ++ L A+ ++ PN N R P + + R+Q K ++NA +A+ N K ++ S++ + K ++ L+ + EL + ++ + + +L GF D R + +I F + N M+ F V+ + T+ + + +E GLPL WT ++ + WG + + D++ ++ ++T + I EV S+ I+ T ++ + E +
Sbjct: 17 SSTIFVSNFPKTTITKDLWQLCNRHGVVTDVYIARKLSKFGQRFGFVRFIKIKDLKTLIEDLNKIWIGNHHLFASKARFDRTHPN-----NTRQP---------NSQDQRMQEKKPLNNNAYQTRTSRSYAE-MLNGKANAKKESSIQSIMK-----KVTLDNSDLMDCFELNHVVLVKVRDAHLIPNINHVLKKEGFVDCKCRYVGGLWIWIEFNNPLSNHLFKQNKEMAWYFTQVRSITKSFTVDEKLVWLEITGLPLHAWTTNAFKKIASVWGEPM--FVDEDTNENMATGRVCIKTKVSGAISEVCSVVIKDITHQVHVKEFAGW 323
Query: 317 SNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKV--DSINHS-NVNTPPKVEQCRQLQLEKDENFIAELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQN-TFIAFF--PDIQNLDELDLDFMSIG--FNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSYNCTSLQDDEEQTESEEGEVVSPNPYDTVWELEVNEHVGKK----------EEATDIRGEEMVQPKQDHVVQEEKAHESVEKVEEVPEKGDLPSRLSKNPSMEDNTPN---QNEAQSENRSAQKKVLDKSIPEHK 764
S ++++T F + +DLW + + V D +P + +G+R+GFV + L+ + LH A+ + R+P+ S K + +K S K E G N+ V ++NH V+ P + L+ D + ++ +G L + NM++ ILA GF +++ M I FF P ++ + +G F+S++ I R V+ G+PL WT ++ +KWG L + + + ++ ++T + I E V I + GK IR EV+ + ++D+E + ES+E D+V E N ++ K+ E I G++ V PK+ ++ H + E P + P ++ +T + N + EN S QK +KSIPE K
Sbjct: 27 STSIFITNFPEQFSFRDLWKVCQDYGRVIDAYIPNRRSKTGSRFGFVRFIHIKDVDRLVRNLCTIWVGRLRLHANVARFQ------------RSPLNNSKYK------NHINAEQKSFVGESSKVNESGVRHNSYAGAVKQKAMNHGVEVDNKPSLVLDDSCILQCDFS-LSLMGKVLDFGSLSNMNI-----ILAKEGFDKLTLKYMGGFWVLIEFFSKPVLEKFKP----HVGVGSWFSSLQYASNSFMIDERVAWVDIEGVPLKVWTKNTFTKISSKWGEFL--FEEDKENLCLNSKRVCIKTKLENNIFESVKIIVHGKIHWIRAKEVSDWVPDFMEDEEGKDESDE----ETEDADSVKE---NSNLNKRINPEGDSDSEEVPETIFGDDHVTPKKGDAKKDGAEHGTNNVTEASDATLKYPPGFT--PVVDADTKSDDVDNLLREENASNQKVFEEKSIPEVK 456
BLAST of DCAR_000311 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A445IID4 ((Transcription factor PIF1 isoform C {ECO:0000313|EMBL:RZB85642.1}))
Query: 301 RKKSTRQNGMRRPTPKSNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAK--RKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKD------ENFIAELGT---------SLFLETAVNMS---VGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDELDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVE 639
R K T R ++Y + F + + KDLW F++ VR+I +P++ ++G RYGFV + Q L++K I L + K R+K R ++ P R Q + R+ NA + D +NT +++ D + N Q+QLE + E ++A L L ET ++ +G + +L GL DA+ TF+ F+S++R + + R ++ G+P+ W PK+ +Q++A G ++ ++ ++ + T I V + I+G + + I E
Sbjct: 931 RAKLTHSGSNWRDNKDITSLYFSRFAEDITEKDLWYHFKRWGDVREIFIPKRRNLAGRRYGFVRFKGVQDIPFLVKKLDSIVIGGLKLFVNLPKYGREKGRET-------RGNIQAKLP------MDRKQGGEFRNRNAPPISYADALRRNT-SREGDQKSVFIPNNQHTSLSVAQIQLEPEDTLWLKEAWVAHLKNPAMYDRVEEELMWETGKDIRTTFMGDDQVLLLGLSEYDANQLINGDRTFL--------------------FSSIERWHPNMRVDYRLTWIQCWGIPVQAWNPKHFNQIIAPMGEVVDIDDAVEEKRRVDKARLLIRTQWRPSIQHTVEVMIDGAKFMVHINE 1255
BLAST of DCAR_000311 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A445IHP3 ((Transcription factor PIF1 isoform A {ECO:0000313|EMBL:RZB85640.1}))
Query: 301 RKKSTRQNGMRRPTPKSNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAK--RKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKD------ENFIAELGT---------SLFLETAVNMS---VGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDELDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVE 639
R K T R ++Y + F + + KDLW F++ VR+I +P++ ++G RYGFV + Q L++K I L + K R+K R ++ P R Q + R+ NA + D +NT +++ D + N Q+QLE + E ++A L L ET ++ +G + +L GL DA+ TF+ F+S++R + + R ++ G+P+ W PK+ +Q++A G ++ ++ ++ + T I V + I+G + + I E
Sbjct: 957 RAKLTHSGSNWRDNKDITSLYFSRFAEDITEKDLWYHFKRWGDVREIFIPKRRNLAGRRYGFVRFKGVQDIPFLVKKLDSIVIGGLKLFVNLPKYGREKGRET-------RGNIQAKLP------MDRKQGGEFRNRNAPPISYADALRRNT-SREGDQKSVFIPNNQHTSLSVAQIQLEPEDTLWLKEAWVAHLKNPAMYDRVEEELMWETGKDIRTTFMGDDQVLLLGLSEYDANQLINGDRTFL--------------------FSSIERWHPNMRVDYRLTWIQCWGIPVQAWNPKHFNQIIAPMGEVVDIDDAVEEKRRVDKARLLIRTQWRPSIQHTVEVMIDGAKFMVHINE 1281
BLAST of DCAR_000311 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A445IHT8 ((Transcription factor PIF1 isoform B {ECO:0000313|EMBL:RZB85641.1}))
Query: 301 RKKSTRQNGMRRPTPKSNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAK--RKKSMPNHHFSPNPRAPVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKD------ENFIAELGT---------SLFLETAVNMS---VGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDELDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVE 639
R K T R ++Y + F + + KDLW F++ VR+I +P++ ++G RYGFV + Q L++K I L + K R+K R ++ P R Q + R+ NA + D +NT +++ D + N Q+QLE + E ++A L L ET ++ +G + +L GL DA+ TF+ F+S++R + + R ++ G+P+ W PK+ +Q++A G ++ ++ ++ + T I V + I+G + + I E
Sbjct: 940 RAKLTHSGSNWRDNKDITSLYFSRFAEDITEKDLWYHFKRWGDVREIFIPKRRNLAGRRYGFVRFKGVQDIPFLVKKLDSIVIGGLKLFVNLPKYGREKGRET-------RGNIQAKLP------MDRKQGGEFRNRNAPPISYADALRRNT-SREGDQKSVFIPNNQHTSLSVAQIQLEPEDTLWLKEAWVAHLKNPAMYDRVEEELMWETGKDIRTTFMGDDQVLLLGLSEYDANQLINGDRTFL--------------------FSSIERWHPNMRVDYRLTWIQCWGIPVQAWNPKHFNQIIAPMGEVVDIDDAVEEKRRVDKARLLIRTQWRPSIQHTVEVMIDGAKFMVHINE 1264
BLAST of DCAR_000311 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6L2KII8 ((RNA-directed DNA polymerase, eukaryota, reverse transcriptase zinc-binding domain protein {ECO:0000313|EMBL:GEU47694.1}) (Fragment))
Query: 304 STRQNGMRRPTPKSNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPV-RESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQN--KKVDSINHSNVNTPPKV--EQCRQLQLEKDENFIAELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDEL-DLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSYNCTSLQDDEEQTESEEG 660
S++++G+ R S +++++ F DS KDL++ ++ V D +P K G R+GFV I F+ ++ +N+ + + K F RAP+ +++ P + G+ R ++++ + + G K+ N K + + H+ +TP V E+C L+ +L SL S+ ++++L GF D +VR + + + F ++ + D + F +++ D R + VE G+PL W+ ++ KWG ++ Y ++ + + +I + T +S I E I GK + IR EV + L+D E + S +G
Sbjct: 114 SSKEDGVNRI---STSIFVSNFPDSFSAKDLFLSCKQYGHVVDSFIPLKRTKEGKRFGFV---------RFINVFNVDHLVNNLCTIWVGRSKLHANIARFQ---RAPLNKKNFPVMSKGEVKR-----GANNSSRLNGRVMGNGKSYVNVVKACNIVGHT--DTPAIVLDEECVNLK---------DLSDSLMGRVKEFASLTNLKTVLLNEGFVDLTVRYLGELWVLLEFSSSKSKEAFRDNVGVCSWFLEIRQTSLDINHDGRIVWVEVEGIPLKLWSLNTFRRIAKKWGDLI--YVDDMNENCFHSKRICLYTKSSSNIFETFKIIFHGKVFWIRAKEVLGWVPELLEDSEYEEHSVDG 443
Query: 300 ERKKSTRQNGMRRPTPKSN-TVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRAPVRE----SSPKVGDGKAARVQTPKKRDD-NASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKDENFIAELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDEL---DLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPKIYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSYNCTSLQDDEEQTESEEGEVVSPNPYDTVW 672
E + S R +G +S+ + ++T F D+ +++LW +F K + D+ +P K G ++ FV ++ VL + + S L + ++ ++ + V E ++ G K A +Q K++++ S K+KE +E+ Q+E D + EL +S + A+ + + +++IL G SV M ++ + F P + +++L D++ F V + R + V+ G+PL W+ + K+G L Y S +I + TS ID+ ++I G T+ +R+VE + Q D ++ E E+ VV P W
Sbjct: 10 EGEGSRRTHGYIHNVDQSSISFFVTNFPDNSTVEELWKVFAKYGRLGDVYIPSKVDKWGKKFAFVKFREVKEEGVLSQNLKDVWLGSFKLRINKSRFERKEDEKKKKELGSSNVLEDGGNNAQPGGSFKTALMQHSKRQEEVEKSKKSKE------------------------ALEEV--FQVEVDGRLLKELESSFVGKLALKVEIRRIKTILFMEGLSHISVTDMGRDLVLIFSPKVGEVEKLWNSKADWIRYYFKEVNPWLPSSFVDRRDLWVKVYGIPLHVWSENLFKVIRGKYGEFLDYDDCTASRAKLDIARIKISTSFRGFIDDPLNIMALGVTYSLRVVEEKNLENVFFQRDRDE-EHEQSWVVPPCSPKEAW 364
BLAST of DCAR_000311 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2U1NST0 ((Reverse transcriptase domain, Reverse transcriptase zinc-binding domain protein {ECO:0000313|EMBL:PWA76520.1}))
Query: 298 TAERKKSTRQNGMRRPTPK----------SNTVYLTGFKDSVQLKDLWILFRKSVTVRDIILPRKTGVSGNRYGFVITESAQQAMVLIEKFHKKNINSNVLHLEFAKRKKSMPNHHFSPNPRA-PVRESSPKVGDGKAARVQTPKKRDDNASVKTKEDGFAKNTQNKKVDSINHSNVNTPPKVEQCRQLQLEKDENF---IAELGTSLFLETAVNMSVGTVESILAGLGFGDASVRGMSQNTFIAFFPDIQNLDE-LDLDFMSIGFNSVKRVEWDHTIPSRRIDVEFRGLPLIGWTPKNCDQLVAKWGSILSYYTLIDSDGFYRAPK-IYMETSHTSCIDEVVSITIEGKTWEIRIVEVTSYNCTSLQDDEEQTE 656
+ +KK + + ++ P PK S+TVY++ F + +++LW + + T+ D+ + + G + F LI I LH A+ ++ + N P+ A V +S VG KA V K + S K +A ++ +N + K + L +D + +A LG S+ I GF + R + + F ++ D+ L ++ F+++K D + R I +E G+PL WT Q+ ++WG +L + D+DG R K + +++ H + + +++ T+ IR+ E+ S+ T + DD E E
Sbjct: 9 VSRKKKGSVFHRLQFPQPKASSVDDLAKISHTVYVSNFPSHLTMRELWNICGEKGTLVDVFIAKHKNKLGQMFAFCRFIKVVDMDTLINSLSNVWIGKLRLHANVARFERKVYN----PSQVAEKVFGNSSYVGT-KAENVPQVVKSNGTGSYSNKASSYANVAKSSTSGGGKATNSDQEVKGSIGTLITLSQDNSNDYPLALLGCYNDFR-----SIANTRFICQSEGFMEVEFRYLGGLWVLFEFTSLEAKDKFLKHKGIAAWFSTLKPWHDDFVVKERLIWLEIEGVPLRAWTDDTFKQICSQWGELL---FIDDTDGCNRLSKRLCIKSPHALLVFATIMVSLNDVTYAIRVRELCSWTPTFVDDDSESDE 370
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4.
There are a few different naming schemes for this assembly. First there is the Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.
LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926.
Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence.
RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records.
The NCBI Sequence report lists the correspondences between the various naming methods
This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove these same DCAR gene predictions.
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins.
