BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: Q2VER7 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A5N6QZE1 (Amino_oxidase domain-containing protein {ECO:0000259|Pfam:PF01593})
Query: 51 TKFTRTRPRSHPLLKVSCVDYPRPDIDNTLPFLEAAYLSSFFSTASRPNKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKVKFALGLLPAIIGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFVAMSKSLNFINPDELSMQCVLIALNRFLQDPNKSMLELVFAPAEEWISRSDSDIIDATMTEL---ARLFPDEIAADQSKAKIL--KYHVVKTPRSVYKTIPDCEPCRPLQKSPIEGFYLAGDYTKQRYLASMEGAVLSGKLCAQAILQDHESLLSRRKQVLAEAT 431
+ +RTR PL +V C+D+PRP+++NT+ FLEAAYLSS F T+ RP KPL VVIAGAGLAGLSTAKYLADAGHKP+LLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMP+KPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEK+KFA+GLLPA++GGQ+YVEAQDG +V+DWMRKQGIPDRVT EVF+AMSK+LNFINPDELSMQC+LIALNRFLQ+ + S + + E + D I + E+ +R+ E+ D + L +V++ V+ T AGDYTKQ+YLASMEGAVLSGK CAQAI+QD+E L++ ++ LA A+
Sbjct: 61 SNISRTRKGVSPL-QVVCMDFPRPELENTVNFLEAAYLSSSFRTSPRPTKPLKVVIAGAGLAGLSTAKYLADAGHKPVLLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPSKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKIKFAIGLLPAMLGGQSYVEAQDGFTVKDWMRKQGIPDRVTDEVFIAMSKALNFINPDELSMQCILIALNRFLQEKHGSKMAFLDGNPPERLCLPIVDHIQSLGGEVRLNSRIQNIELNHDGTVKSFLLTNGNVIEGDAYVFATP-------------------AGDYTKQKYLASMEGAVLSGKFCAQAIVQDYELLIAGGQRRLAPAS 426
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6H2AC76 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: Q2HXJ7 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
Query: 301 DPNKSMLELVFAPAEEWISRSDSDIIDATMTELARLFPDEIAADQSKAKILKYHVVKTPRSVYKTIPDCEPCRPLQKSPIEGFYLAGDYTKQRYLASMEGAVLSGKLCAQAILQDHESLLSRRKQVLAEATAV 433
DPN+SMLELVFAPAEEWISRSDSDIIDATM+EL+RLFPDEIAADQSKAKILKYHVVKTPRSVYKT+PDCEPCRPLQ+SPIEGFYLAGDYTKQ+YLASMEGAVLS K CAQAI+QD++ LL+ R +V+AEA+ V
Sbjct: 441 DPNRSMLELVFAPAEEWISRSDSDIIDATMSELSRLFPDEIAADQSKAKILKYHVVKTPRSVYKTVPDCEPCRPLQRSPIEGFYLAGDYTKQKYLASMEGAVLSEKFCAQAIVQDYD-LLAARGEVIAEASLV 572
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: V5K782 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}) (Fragment))
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2D3C328 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
Query: 23 DKFPLSFSATLSTTLKQQQQQQH----PLSRSTKFTRTRPRSHPLLKVSCVDYPRPDIDNTLPFLEAAYLSSFFSTASRPNKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKVKFALGLLPAIIGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFVAMSKSLNFINPDELSMQCVLIALNRFLQDPNKSMLELV 310
D F ++ T + Q H P +RS TRT+ PL KV C+DYPRP++DNT FLEAAYLSS F T+ RP KPL +VIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFP+VLPAPLNGIWAIL+NNEMLTWPEKVKFA+GLLPA++GGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVF+AMSK+LNFINPDELSMQC+LIALNRFLQ+ + S + +
Sbjct: 30 DSFNITSGKTDVLSFGQSDTMGHRLQFPGARSF-ITRTKKNVCPL-KVVCIDYPRPELDNTSNFLEAAYLSSVFRTSPRPAKPLKIVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPDVLPAPLNGIWAILRNNEMLTWPEKVKFAIGLLPAMLGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFIAMSKALNFINPDELSMQCILIALNRFLQEKHGSKMAFL 319
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2J6L7G7 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
Query: 44 QHPLSRSTKFTRTRPRSHPLLKVSCVDYPRPDIDNTLPFLEAAYLSSFFSTASRPNKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKVKFALGLLPAIIGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFVAMSKSLNFINPDELSMQCVLIALNRFLQDPNKSMLELVFAPAEEWISRSDSDIIDA 328
Q P +RS FT ++ LKV CVDYPRPD+DNT FLEAAYLSS F T+ RP+KPL +VIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFP+VLPAPLNGI+AIL+NNEMLTWPEKVKFA+GLLPA++GGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVF+AMSK+LNFINPDELSMQC+LIALNRFLQ+ + S + + E + + D I++
Sbjct: 55 QFPSARS--FTPRSKKNVSPLKVVCVDYPRPDLDNTSNFLEAAYLSSTFRTSPRPSKPLKIVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPDVLPAPLNGIFAILRNNEMLTWPEKVKFAIGLLPAMLGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFIAMSKALNFINPDELSMQCILIALNRFLQEKHGSKMAFLDGSPPERLCKPIVDHIES 337
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A2Z6N503 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
Query: 1 MSHHVSAVITNNTYTNNLNHLLDKFPLSFSATLSTTLKQQQQQQHPLSRSTKFTRT-RPRSHPL-LKVSCVDYPRPDIDNTLPFLEAAYLSSFFSTASRPNKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKVKFALGLLPAIIGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFVAMSKSLNFINPDELSMQCVLIALNRFLQDPNKSMLELV 310
+S S++ +NNT + LSFS ++S L S ST+FT++ R R+H LKV C+DYPRP+IDNT+ F+EAAYLSS F RP KPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKD+DGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMP+KPGEFSRFDFPEVLP+P+NGIWAIL+NNEMLTWPEK+KFA+GLLPAI+GGQAYVEAQDGLSV++WMRKQGIP+RVT EVF+AMSK+LNFINPDELSMQC+LIALNRFLQ+ + S + +
Sbjct: 17 ISKFSSSINSNNTIS-----------LSFSGSVSMGLNLAS------SSSTRFTKSNRFRNHGSPLKVVCIDYPRPEIDNTVNFIEAAYLSSTFRANPRPTKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDEDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPSKPGEFSRFDFPEVLPSPINGIWAILRNNEMLTWPEKIKFAIGLLPAILGGQAYVEAQDGLSVKEWMRKQGIPERVTDEVFIAMSKALNFINPDELSMQCILIALNRFLQEKHGSKMAFL 311
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: V4U509 (Amino_oxidase domain-containing protein {ECO:0000259|Pfam:PF01593} (Fragment))
Query: 27 LSFSATLST-TLKQQQQQQHPLSRSTKF---TRTRPRSHPLLKVSCVDYPRPDIDNTLPFLEAAYLSSFFSTASRPNKPLNVVIAGAGLAGLSTAKYLADAGHKPILLEARDVLGGKVAAWKDDDGDWYETGLHIFFGAYPNVQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGIWAILKNNEMLTWPEKVKFALGLLPAIIGGQAYVEAQDGLSVQDWMRKQGIPDRVTTEVFVAMSKSLNFINPDELSMQCVLIALNRFLQ 300
L FS + S L+ + P+ +S K T TR P KV CVDYPRPDIDNT FLEAAYLSS F T+ RP+KPL VVIAGAGLAGLSTAKYLADAGHKP+LLEARDVLGGKVAAWKD DG+WYETGLHIFFGAYPN+QNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGI AIL+NNEMLTWPEKVKFA+GLLPAIIGGQAYVEAQDGL+VQ+WMRKQG+PDRVTTEVF+AMSK+LNFINPDELSMQC+LIALNRFLQ
Sbjct: 3 LCFSVSESAFNLRYGFRDSEPMGQSLKIRVKTGTRKGFCPS-KVVCVDYPRPDIDNTSNFLEAAYLSSSFRTSPRPSKPLKVVIAGAGLAGLSTAKYLADAGHKPLLLEARDVLGGKVAAWKDGDGNWYETGLHIFFGAYPNIQNLFGELGINDRLQWKEHSMIFAMPNKPGEFSRFDFPEVLPAPLNGILAILRNNEMLTWPEKVKFAIGLLPAIIGGQAYVEAQDGLTVQEWMRKQGVPDRVTTEVFIAMSKALNFINPDELSMQCILIALNRFLQ 279
BLAST of XM_017396654.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: V5RCN3 (Phytoene dehydrogenase {ECO:0000256|RuleBase:RU368016} (1.3.5.5 {ECO:0000256|RuleBase:RU368016}))
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
The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.
This analysis is a blastp search of all of the NCBI Daucus carota subsp. sativus Annotation Release 100 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 DCAR gene predictions from DCAR V1.0 Gene Prediction.
