MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSIPDTQLLVAQIADACKNW
GFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTE
HTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLREL
CEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCP
SPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYII
NVGDIIQMDRKFIELLAYFCDHF*
| Relationships |
|---|
| The polypeptide, DCAR_001615, derives from mRNA, DCAR_001615. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A068TMF8 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 381.719 bits (979), Expect = 4.255e-131
Identity = 187/267 (70.04%), Postives = 217/267 (81.27%), Query Frame = 0
Query: 1 MGE--VDVSFIQAIEHRPKPTVTEAQGIPLIDLSI-------PDTQLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGE VD +F+Q IEHRPKPT EA+GIPLIDLS D LV++I DA + WGFFQVINHGVP + REK+ AS+ FF+ KEEKL+V RDE NP GYYDTEHTKNVRDWKEVFDF+V++P +P S +P D+EV++ INQWP+NP LRE+CEEYA EV+KL+FKL+ LIALSLGL +RF+ FED T+FIRLN+YPPCPSP LALGVGRHKDAGALT+L QDDVGGLEVK KTDGEWI VKPTPNAYIINVGDIIQ+
Sbjct: 1 MGEAAVDPAFVQDIEHRPKPTRIEAEGIPLIDLSALNSPHSDADLARLVSEIGDASQKWGFFQVINHGVPLECREKMELASRKFFALPKEEKLKVGRDEANPYGYYDTEHTKNVRDWKEVFDFSVKNPTFIPASHEPDDQEVRELINQWPQNPPELREVCEEYAHEVEKLAFKLLELIALSLGLPKNRFNGFFEDETTFIRLNHYPPCPSPHLALGVGRHKDAGALTILAQDDVGGLEVKSKTDGEWILVKPTPNAYIINVGDIIQV 267
Match: A0A2R6RH86 ((Protein DMR6-LIKE OXYGENASE 2 like {ECO:0000313|EMBL:PSS29371.1}))
HSP 1 Score: 381.719 bits (979), Expect = 5.062e-131
Identity = 185/264 (70.08%), Postives = 214/264 (81.06%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSIPDTQ------LLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQAIEHRPK VTEA GIPLIDLS ++ LVA+I DACKNWGFFQVINHGVP REK+ SAS++FF+Q+ EEK +VRR E +P+GYYD EHTKNVRDWKEVFDF VE P ++P S +P D+E+K NQWP P N RE CE+Y +E +KLS+KL+ LI+LSLGL A RF++ F+D TSF+RLNYYP CP P LALGVGRHKDAGALTVL QDDVGGLEVK KTDGEWIRVKPTPNAYI+NVGDIIQ+
Sbjct: 1 MGEVDSAFIQAIEHRPKLAVTEADGIPLIDLSPLNSSDSKAIARLVAEIGDACKNWGFFQVINHGVPLDCREKIESASRTFFTQSLEEKSKVRRGELSPMGYYDGEHTKNVRDWKEVFDFVVEVPTLIPASHEPDDKELKMLHNQWPLYPPNFREACEDYTRETEKLSYKLLELISLSLGLPAKRFNEFFKDKTSFLRLNYYPRCPVPHLALGVGRHKDAGALTVLAQDDVGGLEVKRKTDGEWIRVKPTPNAYIVNVGDIIQV 264
Match: A0A6I9U3B5 ((protein DMR6-LIKE OXYGENASE 1 {ECO:0000313|RefSeq:XP_011088308.1}))
HSP 1 Score: 380.948 bits (977), Expect = 7.742e-131
Identity = 185/266 (69.55%), Postives = 210/266 (78.95%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSIPDT--------QLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQA+EHRPKP EAQGIPLIDLS ++ L A+I DAC+ WGFFQVINHGVP +REK+ S+ FF+ KEEK +V RDE NP GYYDTEHTKNVRDWKEVFDFTV PMVMP S +P D E+K+ INQWP NP +RE+CEEY E++KL KL+ LIALSLGLA DRF+ F+D T+FIRLNYY PCP PDLALGVGRHKD GALT+L QDDVGGLEVK KTDGEWI VKPTP+AYIINVGDIIQ+
Sbjct: 1 MGEVDPAFIQALEHRPKPHSVEAQGIPLIDLSPANSPDPDPGSLSALAAEIGDACEKWGFFQVINHGVPLHVREKIDLVSRKFFALPKEEKKKVSRDEVNPSGYYDTEHTKNVRDWKEVFDFTVGEPMVMPASHEPDDRELKEVINQWPENPSEMREVCEEYGAEMQKLGHKLLELIALSLGLARDRFNGFFKDQTTFIRLNYYAPCPIPDLALGVGRHKDGGALTILAQDDVGGLEVKRKTDGEWILVKPTPDAYIINVGDIIQV 266
Match: V4UAQ0 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 380.948 bits (977), Expect = 1.665e-130
Identity = 182/270 (67.41%), Postives = 216/270 (80.00%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSI----------PDTQL--LVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +F+QA+EHRPK +VTEA+GIPLIDLS PD+ + LV +I +ACKNWGFFQVINHGVP+ R + + ++ FF Q EEK +VRRDE+ +GYYDTEHTKNVRDWKEVFDF VESP +MP SPDP D+E+ + NQWP P RE CEEYAKEV+KL++KLM LIALSLGL D F+ F+D T+F+RLN+YPPCP+P LALGVGRHKDAGALTVL QDDVGGLEVK K+DGEW+RVKPTP+AYIINVGDIIQ+
Sbjct: 1 MGEVDEAFVQALEHRPKLSVTEAEGIPLIDLSALSATNTSIKNPDSTIRDLVVEIGNACKNWGFFQVINHGVPTDKRRSIENMARKFFEQPLEEKRKVRRDEKKVVGYYDTEHTKNVRDWKEVFDFVVESPCLMPTSPDPEDKEIAETYNQWPDYPPEFREACEEYAKEVEKLAYKLMELIALSLGLPPDSFNGFFKDQTTFVRLNHYPPCPAPHLALGVGRHKDAGALTVLAQDDVGGLEVKRKSDGEWVRVKPTPDAYIINVGDIIQV 270
Match: A0A5J5BVT7 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 380.178 bits (975), Expect = 1.902e-130
Identity = 185/267 (69.29%), Postives = 216/267 (80.90%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSI---PDTQ------LLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQAIEHRPK + EA+GIPLIDLS PD+ LVA+I +ACKNWGFFQVINHGVP + R+ + AS+ FF+Q+ EEK +VRRDE NP+GYYDTEHTKNVRDWKEVFDF VE+PMVMP S +P D+E+ K+INQWP P LRE E YA+E+KKLS+KL+ LI+LSLGL A R + F+D TS IRLN+YPPCP P LALGVGRHKD GALT+L QDDVGGLEVK KTDGEWIRV+PTP+AYIINVGDIIQ+
Sbjct: 1 MGEVDSAFIQAIEHRPKLAIVEAEGIPLIDLSALNSPDSSNPSAISRLVAEIGEACKNWGFFQVINHGVPFERRQNMELASRKFFAQSTEEKRKVRRDEMNPMGYYDTEHTKNVRDWKEVFDFAVENPMVMPASHEPDDKELTKWINQWPDYPSELREASEAYAEELKKLSYKLVELISLSLGLPAKRLNAFFKDQTSSIRLNHYPPCPIPHLALGVGRHKDPGALTILGQDDVGGLEVKRKTDGEWIRVRPTPDAYIINVGDIIQV 267
Match: A0A5B7AJN6 ((Putative 2-oxoglutarate and Fe(II)-dependent oxygenase superfamily protein {ECO:0000313|EMBL:MPA56970.1}) (1.14.11.- {ECO:0000313|EMBL:MPA56970.1}) (Fragment))
HSP 1 Score: 380.178 bits (975), Expect = 3.226e-130
Identity = 183/268 (68.28%), Postives = 217/268 (80.97%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSIPDT----------QLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQAIEHRPK + EAQGIP IDLS+ ++ LVA+I DACKNWGFFQVINHGVP + R+K+ AS+ F Q+ EEK +VRRDE NP+GYYDTEHTKNVRDWKEVFD TVE+P V+P S +P D+E+K++INQWP+ P LRE EEYA+E+K LS+KL+ LI+LSLGL A R + F+D TSFIRLN+YPPCP P LALGVGRHKDAGALT+L QDDVGGLEVK KTDGEWIRV+PTP+A+IINVGDIIQ+
Sbjct: 12 MGEVDSAFIQAIEHRPKLAIIEAQGIPAIDLSVLNSADHYSNASAKSRLVAEIGDACKNWGFFQVINHGVPLERRQKLELASRKLFDQSTEEKRKVRRDEVNPMGYYDTEHTKNVRDWKEVFDLTVENPTVVPASHEPDDKELKEWINQWPQYPPELREAFEEYAQEMKNLSYKLLELISLSLGLPAKRLNDFFKDQTSFIRLNHYPPCPIPHLALGVGRHKDAGALTILAQDDVGGLEVKRKTDGEWIRVRPTPDAFIINVGDIIQV 279
Match: M5VMX5 (Fe2OG dioxygenase domain-containing protein {ECO:0000259|PROSITE:PS51471})
HSP 1 Score: 379.407 bits (973), Expect = 4.685e-130
Identity = 186/271 (68.63%), Postives = 216/271 (79.70%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLS------IPDT-------QLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQ EHRPK ++TEA+GIPLIDLS PD+ + LV +I ACKNWGFFQVINHGV REK+ +A++ FF+Q EEK ++RRDE+ +GYYDTEHTKNVRDWKEVFDF VE P ++P S DP D+E ++INQWP NP LR +CEEYA+EV+KL+ KLMGLIALSLGL DRF+ F+D TSFIRLN+YPPCPSP LALGVGRHKD GALTVL QDDVGGLEVK KTDGEWIRVKPTPNAYIINVGD+IQ+
Sbjct: 1 MGEVDPAFIQDPEHRPKLSITEAEGIPLIDLSPINSILTPDSISELKAIEGLVREIGSACKNWGFFQVINHGVALDKREKIETAARKFFAQPLEEKRKIRRDEKIVVGYYDTEHTKNVRDWKEVFDFVVEEPTLVPASLDPEDKEETEWINQWPENPPELRLVCEEYAREVEKLALKLMGLIALSLGLPEDRFNSYFKDQTSFIRLNHYPPCPSPRLALGVGRHKDGGALTVLAQDDVGGLEVKRKTDGEWIRVKPTPNAYIINVGDVIQV 271
Match: A0A6P6WBM1 ((protein DMR6-LIKE OXYGENASE 2-like {ECO:0000313|RefSeq:XP_027112400.1}))
HSP 1 Score: 379.022 bits (972), Expect = 5.200e-130
Identity = 185/267 (69.29%), Postives = 216/267 (80.90%), Query Frame = 0
Query: 1 MGE--VDVSFIQAIEHRPKPTVTEAQGIPLIDLSI-------PDTQLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGE VD +F+Q IEHRPKPT EA+GIPLIDLS D LV++I DA + WGFFQVINHGVP + REK+ AS+ FF+ KEEKL+V RDE NP GYYDTEHTKNVRDWKEVFDF+V++P +P S +P D+EV++ NQWP+NP LRE+CE+YA EV+KL+FKL+ LIALSLGL +RF+ FED T+FIRLN+YPPCPSP LALGVGRHKDAGALT+L QDDVGGLEVK KTDGEWI VKPTPNAYIINVGDIIQ+
Sbjct: 1 MGEAAVDPAFVQDIEHRPKPTRIEAEGIPLIDLSALNSPHSDADLARLVSEIGDASQKWGFFQVINHGVPLECREKIELASRKFFALPKEEKLKVGRDEANPYGYYDTEHTKNVRDWKEVFDFSVKNPTFIPASHEPDDQEVRELTNQWPQNPPELREVCEDYAHEVEKLAFKLLELIALSLGLPKNRFNGFFEDETTFIRLNHYPPCPSPHLALGVGRHKDAGALTILAQDDVGGLEVKSKTDGEWILVKPTPNAYIINVGDIIQV 267
Match: A0A5J5B962 ((Uncharacterized protein {ECO:0000313|EMBL:KAA8538990.1}))
HSP 1 Score: 384.415 bits (986), Expect = 5.749e-130
Identity = 183/267 (68.54%), Postives = 216/267 (80.90%), Query Frame = 0
Query: 1 MGEVDVSFIQAIEHRPKPTVTEAQGIPLIDLSI---PDTQ------LLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGEVD +FIQAIEHRPK + EA+GIPLIDLS+ PD+ L A+I DACKNWGFFQVINHGVPS+ R+KV A + FF+Q+ EEK +V+RDE NP+GYYDTEHTKNVRDWKEVFD V+ P +MPVS DP D+E+ +IN+WP P LRE CEEYA+EV+KL FKL+ LI+LSLGLAA R F++ TSFIRLN+YP CP P LALGVGRHKDAGALTVL QD+VGGL+VK KTDGEWIR+KPTPNAYIIN+GDI+Q+
Sbjct: 1 MGEVDTAFIQAIEHRPKLAIIEAEGIPLIDLSVLNSPDSSNPSVISHLAAEIGDACKNWGFFQVINHGVPSERRQKVELAMRKFFAQSTEEKRKVKRDEMNPMGYYDTEHTKNVRDWKEVFDLAVQVPTLMPVSQDPNDKELMDYINRWPEYPPELREACEEYAEEVEKLCFKLLELISLSLGLAAKRLHGLFKEQTSFIRLNHYPACPIPQLALGVGRHKDAGALTVLAQDNVGGLQVKRKTDGEWIRIKPTPNAYIINIGDIMQV 267
HSP 2 Score: 159.073 bits (401), Expect = 1.036e-42
Identity = 73/101 (72.28%), Postives = 85/101 (84.16%), Query Frame = 0
Query: 158 VKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
VKKL FKL+ L +LSLGLAA R + F++ TSFIRLN+YP CP P LALGVGRHKD GALTV QD+VGGL+VK KTD EWIR+KPTPNAYIIN+GDI+Q+
Sbjct: 362 VKKLCFKLLELTSLSLGLAAKRLNGLFKEQTSFIRLNHYPACPIPQLALGVGRHKDGGALTVFAQDNVGGLQVKRKTDAEWIRIKPTPNAYIINIGDIMQV 462
Match: A0A6P6VTQ8 ((protein DMR6-LIKE OXYGENASE 2-like {ECO:0000313|RefSeq:XP_027105875.1}))
HSP 1 Score: 378.637 bits (971), Expect = 8.411e-130
Identity = 186/267 (69.66%), Postives = 215/267 (80.52%), Query Frame = 0
Query: 1 MGE--VDVSFIQAIEHRPKPTVTEAQGIPLIDLSI-------PDTQLLVAQIADACKNWGFFQVINHGVPSQLREKVFSASKSFFSQAKEEKLRVRRDERNPLGYYDTEHTKNVRDWKEVFDFTVESPMVMPVSPDPRDEEVKKFINQWPRNPENLRELCEEYAKEVKKLSFKLMGLIALSLGLAADRFDKCFEDSTSFIRLNYYPPCPSPDLALGVGRHKDAGALTVLYQDDVGGLEVKPKTDGEWIRVKPTPNAYIINVGDIIQM 258
MGE VD +F+Q IEHRPKPT EA+GIPLIDLS D LV++I DA + WGFFQVINHGVP + REK+ AS+ FF+ KEEKL+V RDE NP GYYDTEHTKNVRDWKEVFDF+V++P +P S +P D+EV++ NQWP NP LRE+CEEYA EV+KL+FKL+ LIALSLGL +RF+ FED T+FIRLN+YPPCPSP LALGVGRHKDAGALT+L QDDVGGLEVK KTDGEWI VKPTPNAYIINVGDIIQ+
Sbjct: 1 MGEAAVDPAFVQDIEHRPKPTRIEAEGIPLIDLSALNSPHSDADLARLVSEIGDASQKWGFFQVINHGVPLECREKMELASRKFFALPKEEKLKVGRDEANPYGYYDTEHTKNVRDWKEVFDFSVKNPTFIPASHEPDDQEVRELTNQWPPNPPELREVCEEYAHEVEKLAFKLLELIALSLGLPKNRFNGFFEDETTFIRLNHYPPCPSPHLALGVGRHKDAGALTILAQDDVGGLEVKSKTDGEWILVKPTPNAYIINVGDIIQV 267
| Match Name | Stats | Description |
|---|---|---|
| A0A068TMF8 | E-Value: 4.255e-131, PID: 70.04 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A2R6RH86 | E-Value: 5.062e-131, PID: 70.08 | (Protein DMR6-LIKE OXYGENASE 2 like {ECO:0000313|E... [more] |
| A0A6I9U3B5 | E-Value: 7.742e-131, PID: 69.55 | (protein DMR6-LIKE OXYGENASE 1 {ECO:0000313|RefSeq... [more] |
| V4UAQ0 | E-Value: 1.665e-130, PID: 67.41 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A5J5BVT7 | E-Value: 1.902e-130, PID: 69.29 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A5B7AJN6 | E-Value: 3.226e-130, PID: 68.28 | (Putative 2-oxoglutarate and Fe(II)-dependent oxyg... [more] |
| M5VMX5 | E-Value: 4.685e-130, PID: 68.63 | Fe2OG dioxygenase domain-containing protein {ECO:0... [more] |
| A0A6P6WBM1 | E-Value: 5.200e-130, PID: 69.29 | (protein DMR6-LIKE OXYGENASE 2-like {ECO:0000313|R... [more] |
| A0A5J5B962 | E-Value: 5.749e-130, PID: 68.54 | (Uncharacterized protein {ECO:0000313|EMBL:KAA8538... [more] |
| A0A6P6VTQ8 | E-Value: 8.411e-130, PID: 69.66 | (protein DMR6-LIKE OXYGENASE 2-like {ECO:0000313|R... [more] |
Pages
back to top| Name | Description |
|---|---|
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 Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 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 Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
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. Data from this analysis can be viewed in JBrowse here. |