BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A371E3H2 ((Cysteine-rich receptor-like protein kinase 3 {ECO:0000313|EMBL:RDX60591.1}) (Fragment))
Query: 41 YEVRSFFTEIELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTA 192
YE FF + L +S +C N+T AF A Q+L DL ATPKI FF A K QV GG +YA+AQC TV++ C CL GY+NI CL + GS+ GCF+RYS T FF+DN +I PYL++G SSKK A
Sbjct: 129 YESNGFFDQTTLPGNSMICG-NQTAVGATAFNATAQQVLMDLQIATPKINGFFAATKTQVAGGG-------AIYAIAQCAETVTESGCLDCLNVGYNNIHICLPNTDGSA-----YDAGCFMRYSETAFFADNQTIDITPYLKQGGSSKKGA 267
Query: 101 FDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFS 171
F K V Y + QC +S+ DC C + I+ C ++ G CFLRY F+S
Sbjct: 673 FATASETKGDVLTYTMFQCRKYLSKIDCLNCFNTAFVQIRNC----SAAASGARVIYDDCFLRYESGEFYS 739
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A438DKY5 ((Cysteine-rich receptor-like protein kinase 3 {ECO:0000313|EMBL:RVW36088.1}))
Query: 37 ESSGYEVRSFFTEIELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAIIAGGVG 199
+SS YE SF+ E ++ +C N+T AF LL DL ATP+ + + A K++V GG TVY VAQC+ S C +CL NI++CL S G + GCFLRYS TPFF+DN T+I+P+L+KG S+KK AII G VG
Sbjct: 2 DSSPYESSSFYDETTGSGNTAICG-NQTAAQATAFQEAVNGLLSDLETATPRTNDSYAAYKKEVVGGG-----GATVYGVAQCVERASASACKECLKVADGNIKSCLP-----STDGRAVDAGCFLRYSNTPFFADNQTTDILPFLEKGGSTKKKAIIGGVVG 153
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AW Y N H +L+DE++D EY E KK+IEIAL CTQS VS+RPTMSEVV +L
Sbjct: 422 AWTLYENDKHLELVDESLDPEEYKAEEVKKIIEIALMCTQSSVSMRPTMSEVVFLL 477
Query: 41 YEVRSFFTEIELGTSSEVCAD-NKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAIIAGGVG 199
YE F+ E + E C + N ++ AAF A LL+DL ATP I FF A+KR + ++ +VY +AQC+ T+ C C+ Y+NIQ CL + G + GCF+RYS PFF+DN N+ P+L+ GSSSKKTA+IAG G
Sbjct: 9 YETTYFYGETTQEPNGEYCENQNTSLALGAAFRTTADSLLRDLQIATPGINGFFTASKRDIV-----GVSNASVYGIAQCVQTIDMSGCLACMQVAYTNIQRCLPATDGRA-----VDSGCFMRYSNKPFFADNQTINLDPFLKTGSSSKKTALIAGVAG 158
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVMLVNDASPEPK 265
AWK Y NGTH +L+DE++ EY E KK+IEIAL CTQ+ +LRPTMSEVVV+L + S E +
Sbjct: 405 AWKLYENGTHLELVDESLGPDEYEAEEVKKIIEIALMCTQASHALRPTMSEVVVLLKSTGSMEHR 469
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2I4FR69 ((cold-responsive protein kinase 1-like {ECO:0000313|RefSeq:XP_018834145.2}))
Query: 202 WKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVMLVNDASPE 263
W + +G H DL+D+T+D ++Y VE KK+IEIAL CTQ+ RP+MSE+VV+L + S E
Sbjct: 548 WNLHESGKHLDLVDDTLDPNDYTVEEVKKIIEIALMCTQASAIQRPSMSEIVVLLKSKGSTE 609
Query: 99 QVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFF 170
+ F S YA+ QC +S DC C S I+ C ++ G GCFLRY F+
Sbjct: 73 KYFATAQQVSGSSRAYAMVQCRNYLSTADCIACFTAAESQIRNC-----SAANGARVIYDGCFLRYESAIFY 139
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2K3NIJ4 ((Cysteine-rich receptor-like protein kinase 2-like protein {ECO:0000313|EMBL:PNY02866.1}) (Fragment))
Query: 41 YEVRSFFTEIELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAIIAGGVG 199
YE FF + L +S +C K A+ A QLL DL ATPKI FF A K + A +YA+AQC TV+ G C CL G++NIQ C + G + GCF+RYS PFF+DN +I P+L++GSSS K AII G VG
Sbjct: 1 YESNGFFDQTTLPGNSVLCG-TKKANGTTAYNATAQQLLLDLKTATPKIPGFFAATKTPI--------AGNAIYAIAQCAETVTDGGCLACLKVGFNNIQGCFPNTDGIA-----FDAGCFMRYSEIPFFADNQTIDITPFLKQGSSSNKGAIIVGAVG 145
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AWK Y H +LID+T++ S+Y+ E KK I IAL CTQ+ + RPTMSE+VV+L
Sbjct: 414 AWKLYEVDRHLELIDKTLNPSDYDAEEVKKFIAIALLCTQATAATRPTMSEIVVLL 469
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A0B2QUD6 ((Cysteine-rich receptor-like protein kinase 2 {ECO:0000313|EMBL:KHN25160.1}) (2.7.10.1 {ECO:0000313|EMBL:KHN25160.1}))
Query: 41 YEVRSFFTEI-ELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAII 194
YE F+ + E+G V NK+ A F V Q L DL ATPKIK F+ A K QV A S +YA+AQC+ T S C C+ GY+N+Q+CL S GS+ GCF+R+S TPFF+DN NI PYL++G SSKK AII
Sbjct: 131 YESERFYQQTNEIGGG--VTCGNKSTNA-TGFRAVGQQALLDLQKATPKIKGFYAATKTQV------AGGSANIYAIAQCVETASPQKCLDCMQVGYNNLQSCLP-----STDGSAYDAGCFMRFSTTPFFADNQTINIRPYLKEGGSSKKWAII 271
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AWK Y G +L+D+ ID +EY+ E AKK+IEIAL CTQ+ + RPTMSE++V+L
Sbjct: 542 AWKLYERGMQLELVDKDIDPNEYDAEEAKKIIEIALLCTQASAAARPTMSELIVLL 597
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A0B2QAK0 ((Cysteine-rich receptor-like protein kinase 2 {ECO:0000313|EMBL:KHN18255.1}) (2.7.10.1 {ECO:0000313|EMBL:KHN18255.1}))
Query: 41 YEVRSFFTEI-ELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAII 194
YE F+ + E+G V NK+ A F V Q L DL ATPKIK F+ A K QV A S +YA+AQC+ T S C C+ GY+N+Q+CL S GS+ GCF+R+S TPFF+DN NI PYL++G SSKK AII
Sbjct: 131 YESERFYQQTNEIGGG--VTCGNKSTNA-TGFRAVGQQALLDLQKATPKIKGFYAATKTQV------AGGSANIYAIAQCVETASPQKCLDCMQVGYNNLQSCLP-----STDGSAYDAGCFMRFSTTPFFADNQTINIRPYLKEGGSSKKWAII 271
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AWK Y G +L+D+ ID +EY+ E KK+IEIAL CTQ+ + RPTMSE+VV+L
Sbjct: 542 AWKLYERGMQLELVDKDIDPNEYDAEEVKKIIEIALLCTQASAATRPTMSELVVLL 597
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A3Q0FF32 ((cysteine-rich receptor-like protein kinase 2 {ECO:0000313|RefSeq:XP_022642675.1}))
Query: 41 YEVRSFFTEIELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKK 190
YE FF + L +S +C N+T + F A Q+LKDL ATPKI FF A K QV + +YA+AQC TVS+ C CL GY+NI+ CL + G + GCF+RYS T FF+DN +I P+LQ+GSSSKK
Sbjct: 127 YESAGFFDQTTLAGNSMICG-NQTAVVASDFNTSAQQVLKDLQIATPKISGFFAATKTQV--------SGAAIYAIAQCAETVSESGCLDCLTVGYNNIEVCLPNTEGRA-----FDAGCFMRYSETAFFADNQTIDITPFLQQGSSSKK 262
Query: 71 FTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAII 194
F + A +L +L ATPKIK F+ A K V G +YAV+QC+ T + C CL + N+Q CL + G++ GCF+RYS P F+DN +I P+L++G S+KK II
Sbjct: 763 FKVAAQPVLMELQQATPKIKGFYAATKTPVVGGS-------AIYAVSQCVETAMKTSCLNCLQVAHDNLQRCLPNTDGTA-----YDAGCFMRYSTIPLFADNQTIDIAPFLKQGGSTKKWGII 874
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVMLVNDASPE 263
+WK Y G H +L++E ID EY+ E K++IEI L CTQ+ + RPTMSEVVV+L + S E
Sbjct: 1146 SWKLYERGCHLELLEEGIDPDEYDGEEVKRIIEIGLLCTQATAAARPTMSEVVVLLKSRNSVE 1208
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AWK Y H +L+D+ +D EY+VE KK+IEIAL C Q+ RPTMSEVV L
Sbjct: 541 AWKLYEEDRHLELVDKKLDGKEYDVEEVKKVIEIALLCIQASAGARPTMSEVVASL 596
Query: 97 KRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDND 174
K + F A+ V YA+ QC +S+ +C C S I C ++ G CFLRY F+ + +
Sbjct: 673 KNKHFAIEDKARGEVITYAMFQCRNYLSKTECLSCFDTATSQILNC-----SAANGARIIYDSCFLRYESERFYDETN 745
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6P9EB68 ((cold-responsive protein kinase 1-like isoform X2 {ECO:0000313|RefSeq:XP_035544571.1}))
Query: 202 WKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVMLVNDASPE 263
W + +G H DL+D+T+D ++Y E KK+IEIAL CTQ+ RP+MSE+VV+L + S E
Sbjct: 549 WNLHESGKHLDLVDDTLDPNDYTAEEVKKIIEIALMCTQASAIQRPSMSEIVVLLKSKGSTE 610
Query: 114 YAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMP 180
YA+ QC +S DC C S I+ C ++ G GCFLRY F+ D IMP
Sbjct: 88 YAMVQCRNHLSTADCISCFTAAESQIRNC-----SAANGARVIYDGCFLRYESASFYYDEI---IMP 146
BLAST of DCAR_000702 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: I1LM48 ((Uncharacterized protein {ECO:0000313|EMBL:KRH30798.1, ECO:0000313|EnsemblPlants:KRH30798}))
Query: 41 YEVRSFFTEI-ELGTSSEVCADNKTVPAQAAFTLVAVQLLKDLADATPKIKNFFGAAKRQVFDGGPSAKASVTVYAVAQCLGTVSQGDCGKCLMGGYSNIQTCLSQSGGSSGGGSSASGGCFLRYSVTPFFSDNDITNIMPYLQKGSSSKKTAII 194
YE F+ + E+G V NK+ A F V Q L DL ATPKIK F+ A K QV A S +YA+AQC+ T S C C+ GY+N+Q+CL S GS+ GCF+R+S TPFF+DN NI PYL++G SSKK AII
Sbjct: 131 YESERFYQQTNEIGGG--VTCGNKSTNA-TGFREVGQQALLDLQKATPKIKGFYAATKTQV------AGGSANIYAIAQCVETASPQKCLDCMQVGYNNLQSCLP-----STDGSAYDAGCFMRFSTTPFFADNQTINIRPYLKEGGSSKKWAII 271
Query: 201 AWKSYNNGTHEDLIDETIDSSEYNVENAKKMIEIALKCTQSPVSLRPTMSEVVVML 256
AWK Y G +L+D+ ID +EY+ E AKK+IEIAL CTQ+ + RPTMSE++V+L
Sbjct: 543 AWKLYERGMQLELVDKDIDPNEYDAEEAKKIIEIALLCTQASAAARPTMSELIVLL 598
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.
