| 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 | |
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. View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/ Data from this analysis can be viewed in JBrowse here. |
ATGTCTATTCAACATGCAAAGTCTTTTATGCCCTTATCACTCGTTCAAAA
ACTCACACGTTTTGCTCTCTTCCCCCAAAAGGCCCTCTGCTTAGAATTTG
TAAAGCCACACACTCACACACTCAACTCCTCTCTCCCTGTGTAAATCTCT
CTCTCTCTGTTTTTATAATTTTATACACGACCCTTTTTTGTCCTTATCAT
TTCTGACAACCCCTTCACCTGAATCCACACATACAAACACACACACAAAT
ATTATTTTAGTGGGTTGAAAATTCAAGAACTGGGTCAAAACCCTAGGGTT
ATGAAGCAATATCCACCCAGTTGGTGATTATTCTGTCTCTGAATGGAGGG
AGGCATTTTCTGATGGATTATGATGACAAAATTTCTGAAGGCCATAAGTC
AGCTAATGCAGAGAATTCCAAGTCATCACCCGTGGTGCCTCCATTTGCTC
TTCCCAAGTATGATTTTGATGATAGCCTACAGGGTGACCTAAGATTTGAA
GGATTGGTCGAAAATGAAGTTTTTCTTGGCATTTCGAGTCAAGAAGACAG
CCAGTGGATTGAGGACTTTTCTAGAGGAAATAATGGTATAGAATTTAGTT
CATCTGCGACAGAGCCTTGTTCCATTTCAAGGCATAACAATGTTTGGTCA
GAGGCAACATCTTCAGAGTCTGTTGCGATGCTTCTGAAGTCCGTTGGACA
GGAGGAAAGGATTCAGGGAGAAACTTTGATTCAGGAGTTGGACACTGGCA
ATGAATTAGGCAATTTAGCTACAGAAATGGAGCCTAACTTGAAGAAGGAC
GATAAGGTGGAGTCTATAACTACCTCACAACCTACTGCGACTCCTGATTC
TTTTCTGGATCGGAGGAATGTGAATGCTGTAGAATCAAAAAAGGATAATG
TTCCTGTTGATGGAAGTTCTGGCGTTGTTTCAATTGTTTCCAGTGTAATT
CTAAGCGAGGCAGATGAGGGACCAGATGATAAATGTGATGATACTACACA
TTTGAAAGTTAATATTATAGACCAGCCCGTTGACAATTTAGAAGGCTGCA
ACATTGACCAAGGTTCTGCAGTGACTTCTCAGCTGGGTAATGTTGAAGTC
GGGGCCTGCAACAAAGGTGAAAAGACTAGTGAGCCAATTCAAAATCCTCT
GGGTGACACCTCATCTGTGGCTTGTGTAGATGCTCATACCTTTGAGGTTG
TGAATAAAGATGCCGAGTATTCTGCCTGTACTGGGGTCGAAGTCAGTATT
GTTGAATTAAAGGAGAACTCTTTCGGCAACCAACCAAACAGTCTGGAAAG
ACAGAATGTTGAGGCCGTTGACATTAAGACAGTAAATTCTTCCTGTCCAG
AGCATGATATGGACTCGGTGGTTGAGAATGAGAATTCTGAAAACTGTAGT
GGGGGAGTGGCTGTTGCTGAAGCTTCTTCGTTGCTTGCTGCAGACCATAA
ATTTACTGAACAGGTGGAAGGAAGTGGCATTGAATATGCTGAGAATCCGG
ATACATCTGTATCTTGCATTGTCTCTGGATCACAATGTGGAATACAGTTG
TCTTCTAAGGATTCAAGTGATCTCAGAACATCTGGAGTCCTTGAGGATAA
TAATTCTCCTGAAGCACAAACATCCTCTTTCGTAGTTGGTGGACATGTGC
AGATGAGCAAAAGTCATATTTCCTCTGGGCAGGAAGATGTCCACCTTTTT
GACAAAGATGTATCTTCTCTTGGGACAGAAGATGCAAAGTCACTCACAAC
ATCCCTGCCTCCTGATGAATCTAATAAAGCAAACATAGTTCAAGGAGCAG
AACTCCTTAATTCTGCGAGTAATGAGCGAGGATCAGAAGTTACAGACGAA
ATGAACTTATCATCGTGTGGCATGCCGATTGATCCTCCATTGCTTCACGG
GAGCAAGACTACTGCTGATGGAGCTACTTTTGGTGAGCAAGAGCATAAGT
CACAGGTTGCTAATTTATTAGGCACAGAGAGTTCACCACAAGTGTCAGCT
GATCTAGAGCCTTTTAGTTTTCCTGAATCTGGACAAGCAAGTCGGATAAA
TCAAGAAGCAGGTCCGGAGGGTTCCAAAAAGGTGGAAGCATGTCCATCTC
TAATTAGTTCAGAAATAAAGCTGGTTGACGATGCTGCACTAGCAGCACAT
AAAAGCAATGAAGAAATATATTTGGAAAGAAGTGCTGAATTGGCATCGTC
TGAAGTTGCAGATGCGGTGTTACCATCAAGCCAAACTCTTGTTCCTGTAG
AATCTGTTCCAGTCTCCATGCTAGAATCCTCTACTATTTCCCAAAAGAAT
GACGATGTTACAGCAACTTCCGGAACAGAATTAACAGAAAATCCTAGCAC
TAAAGTTGATTCACCTGAGAAGAATGAAGATTCTGTTTCTCTTGCTTGCC
CGTCAAAATGCATTTCAGATATTGGGAACATGGATGGAGATGCCTCTGCT
AATTCATTTGAAGAAAATGTGTATACTCCTGCTATCATCAGTTGTGCAAA
GGCTCCGCTAAGTGAAAAGGAACAGAAAACAAGAACTATAGAGGTCTCAA
TTGGTGATGTCCAGCATCCTGAGGCAACAGATGGTGCTGCTGAAATGGTT
CAATCTGTTCCATTGGATGCTACTTTCAACAATGGGGAAATCAGTACTTC
TCAGGTTAACATGTCAACTGGTTTAACAGAGGGAAAAATCATGAAGGATA
TGCAATTAAATCCTGTTCAGGTTCACGAAAGATCAACAGATGTCAAGGAG
TATCCATCTGATGGTAATATGGGACCTCCCTCTGTTGTCAGTTGTGTAAA
GATTCCGATAAGTGAAACTGGACAGACGTCGAGAGGCAAAGATGCCTCAG
TCTCCACTGTCCATCATTCTGAAGGAACAGCTGGTGCTGGTGAAAATGTT
CAATCTGCTGCATTGCATATGGAACATGATAATTCCAATGAAGGGACAAA
CATCAGTATGGAGGTCAGTTCATCTACTGGTTTATCTGAAAGCGAAATCA
TCAAGGGTTCACCATCATATCCGAGCATCCCAGTCAACAAAATATCAACT
GATGTTGAGGGATATCCTTTAGCAGCTGATTGCTCTCGGATAGATCTTAC
AATGCCTGAACATTCTCTTGAAAATTCTGAAGGACCTGGACCTATGTCAG
GTAAGAAACGTGCAGGTGCCAGAGGGACCTCTGAGCGGAAAACAAGACTA
GGTTCTGTTAAGACAACAGCTAGAACAAATAGTAGGAAAAGAGGTATGCA
GGAAACACCTTCGAAACAGTTTGACGAAGATAAATCAATGATGATCTCAA
GTTTACCTGGGAATAGCAATGCTGAACTAAGTGGTATAAAAGTTTGTGGC
GCCCTTCCTACTCCCATGTCTACTATTCCAGATTTAAACACTTCAGTTAC
TCCCGCATATTATCAACAACCTTTCACTGATACCCAACAAGTGCAATTGC
GAGCACAGATACTTGTATATGGATCACTAATGCAAAATTCCGTACCTGAC
GAGGCTTGTATGATTGCAGCATTTGGGCCATCTGATGGTAGTGGTGGATG
TCTTTGGGAGTGTGCATGGCGTGCTTGTAGTGAAAGGATACAAACTCAGA
AATCAGATGCCAGCAACCTGGAAACCCCTGTGCGATCATTCTCTGCAGGT
AGCAAAGGTTCGGATCAACCAGTTAAAAAAAGTAAAAGTTCACGTCAGAG
TAAATCTACTTTACCTGCAGATAGAGCTAGCAGTAAGGATATCCCATCGC
CAGTTGTTAATCCTATTATACCCCTATCATCACCTCTTTGGAACGTATCT
ACCCCCTCTGGTGTTGGTTTGCAGTCCAGTGGCACATATGTTGATTATCA
TCAGCCATTTGGTCCCTTGCAGCCTTGTCAGCCCCAAGGTACAAAAGGTT
TTGGTGAACAGAACCCCTCTTGGCTTTCTCAGATTAACTTTCCTGGTCAG
TGGGTTGCTACTCCACAAACTTCATCCCTTGATGTCAATGCATCTGTATC
TTCAAAGTTTTGTACTGAACCAGTAAAACTAACCCCATCCAAAGTTTCAT
CTGTGCCAAGTGACCCTGCCAGAAAGCAAACCCAATTTTCTGTTTCCACT
GGTGGGAGTGCTGGGCTGTCTTCAGGGATTCATTTTCAGACTGATGTAAC
AAAGACTTCTGTTCTGCCTGGTCAGATTTGTGATAATACTAAACATAAGA
AGAGGAAGAAGGTTTCTGTCAGCAAGAGCCCAGGGCAAATCCCGTCACTA
ACTTTAGATCAGGCAGCATCTTTAAGTGATACAAGTAATCATATCTCTAA
AAAAGGAACTGCTCCCCAGGCTATTTTCCAGAATTCTTTGCTCGCTCCAA
GTCTGCCAGAAATGAGATCCCCTGCTGTCAATAATGCATCATCTATGCCA
AATGCAGCCACAGCTACTTTTTTGGGATCAACAGGCCGTTCCAGCAACAA
TCTACCAGCTGTCTATCCATTAGTTTCGAGTGATCAACCTACGAGAGTGG
ATCAGATTGTGGATAAGAATAGTATAATGTCAGAGGAATCACTGAATGCA
GTCGAGGCAGCTAGGTTACAAGCAGAAGGTGCTGCTGCACATGCTGCTGC
TGCAGTCGGAAACTGCAATGGTGTTTGGAGCCAGCTGAGTAAGCTGAAGA
ATTCTGGTTTAAGATTTGATGATGAGACAAAACTTTCTTCTGCAGCTATG
GCAATAGCTGCAGCTGCTTCTGTTGCAAAGGCTGCAGCTGCAGCAGCCAA
ACTTGCATCGAATATTGCAATTGGAGCAAAACTAATGGCGGATGAGGTAT
CAACCGCAAGTGTAACCAGAAAAGATCCCCATAGCACTGGAATGTCTATG
GCCTGTTCTTCAAATAGTTCTCTGTTGGCTGGAGAAGGAAATGTCTCCAC
TAGTTCAATTATTACTGCTGCGAAAGAGACAGTTAAGAAGAGAGTCGAAG
CTGCCACAGCTGCCTCAAAGCATGCTGAAAACTTGGATGCTATGGTTAAA
GCTGCTGAACTGGCAGCAGAGGCCGTTTCACAAGCCGGAAAAATTGTTTC
TATTGGCGATCCCTTGCCTTTGAGTGAGTTGTTAGGCTCTGGTCCTATGG
ACTACTGGAGAACTCCCCAGGTATTTCCTGAACAAGGGGTGATAGCAGGC
ATTGACCAACGGAAAACATTTGTTCCTGAAAAGCTTGTTCCTGCTCAACC
ACCAAAAGATGGAGCAATTGTTACGGGAGAAGCAGTGGATCGTGGTACTA
TTGCAAGTGTTGGAAAGAACTCATTGTCTACTCAAAGAGGCCACCGTGCA
TCTGACCCTGCTCTTGATTCATATGGGGGAACAAACTCTGAAATTGTTAA
ATCTCGTGATGCCCAAAGAATTTCACCACTTACATCTCTTGAGAATGTAA
TGGTGGAAGGTTGCTTTGTCGAGGTCTTCAAAGAAGGGGGTAAATATAAG
GCAGCATGGTATCCAGCCAAGATTTTGAATTCGGATGACGAGAAAGCTTT
TGTCTGTTACACTGAACTCCAAGCAGATGATGGGTCAGGGAAACTAAAGG
AATGGGTTCCACTTAAAGGGGATAACTCCAAGGCACCTATAATACGTATT
CCACATCCTGCAACTAGCATGTGCTTTGAAAGAAGTAGGAAGAGACGGAG
AGCGGCAGTGATGGACTATACTTGGTGTGTTGGAGACAGAGTTGACGCGT
GGATGCAAGATTGCTGGCTTGAGGGAGTTGTGTCTGAGAAGAAAAATGAT
GAAACAACATTTAAAATATCTATTCCAGCTCTTGGAGGCACTTCAGCTGT
TAAAACATGGAATCTTCGCCCAACCGTAACTTGGCAGGATGGAAAGTGGA
TAGAGTGCCCCTCTGCAGTTCAGCAGTCCCCTACTCAGGGTGATACACCA
CAGGAGAAGCGTGTGAAGTTGGGACATCCCGCTGTAGAGGCTGCTAAGGT
GGACAAGAGTTTAAGAGGCAATGATCTCATGGAATCAAAGGAGCATGATG
AATCAAGACAACTTCCTTTACTAGCTAGTGAAAAAGAATTTAACATTGGG
AATAATACTGGAGATATTAAACTTGATGCTCCAAGAATTGCAAGGACTGG
ATTGCAGAAAGAAGGCTCAAGGGTGGTTTTTGGTGTTCCTAAGCCAGGAA
AGAAGCGTAAATTCATGGATGTAAGCAAACATCTTGACTCTGACCAATGC
AATAAAAATGCAAAAACAAGCGATTTAGTCAAAACTGCAAGATACTTGCC
TCAAGGAAGAGGGGGTGGTCGTGGTTGGAATAACAATACTAAAGATGATA
TCAAAGAAAAGCAAGCTAAAGAAGACAAGGTCAAAGTTATCAGGTCTGGA
GTGGCACAGAAGACTAATGCTTTGCTATCTGCCAAATCTATGGGGAAAAC
TGTCAGCAAGGAACAGAACAATCCAGCTCTGCGGGACCTTATGGAATTTG
GCTCCGTCTCTAATTCCCCTTCTGAAGGTCCAACTTCTTCAAAAGGTCCT
AGAGTTCCAAATAAAAGAGTACCCTCTTCAAGTACCAAAACCGTCCTTCT
GAATAAAGGAAAGCATGCAGCTGGTGGAGAGGTTGATAAGAAAGTTGATC
CGCATGTTACTGAGATTCGAAGATCAAACCGGAAGATTCAACCAACATCA
CGGCTATTGGAAGGATTGCAGAGCTCTCTAATCGGTTCAAAGATGCCCTC
TGTCCCGCATGAAAAAGTTCAAAAAAACCTGAACAGAGGTGACAGTAGCA
GCCATGGCTGAGCTTCTATGGATGAGGAAAGGTCTAGATTGGCACATCTG
AAGTTCACTGGATTCCGAAGGCAATGATTTCATGTCTGGAGGATAGAATT
GAGACCGTGCTCTGCTGCTTCAGCTGTAGAATCTAGACCGTAGATATTTA
TAAGTTATCATAATTTGATTCCTTACAGATCTTCAAGACTTTACTCCGTT
AGCCTGTACTGTATATGGAATCATGGATAATCACCCTTGATGGATGAAGA
TGGAGACTTGTATGCAGTCCTTAATTTAGTATTCTTTTTTCCTAATATCT
TATTTGCTGCCCA
MDYDDKISEGHKSANAENSKSSPVVPPFALPKYDFDDSLQGDLRFEGLVE
NEVFLGISSQEDSQWIEDFSRGNNGIEFSSSATEPCSISRHNNVWSEATS
SESVAMLLKSVGQEERIQGETLIQELDTGNELGNLATEMEPNLKKDDKVE
SITTSQPTATPDSFLDRRNVNAVESKKDNVPVDGSSGVVSIVSSVILSEA
DEGPDDKCDDTTHLKVNIIDQPVDNLEGCNIDQGSAVTSQLGNVEVGACN
KGEKTSEPIQNPLGDTSSVACVDAHTFEVVNKDAEYSACTGVEVSIVELK
ENSFGNQPNSLERQNVEAVDIKTVNSSCPEHDMDSVVENENSENCSGGVA
VAEASSLLAADHKFTEQVEGSGIEYAENPDTSVSCIVSGSQCGIQLSSKD
SSDLRTSGVLEDNNSPEAQTSSFVVGGHVQMSKSHISSGQEDVHLFDKDV
SSLGTEDAKSLTTSLPPDESNKANIVQGAELLNSASNERGSEVTDEMNLS
SCGMPIDPPLLHGSKTTADGATFGEQEHKSQVANLLGTESSPQVSADLEP
FSFPESGQASRINQEAGPEGSKKVEACPSLISSEIKLVDDAALAAHKSNE
EIYLERSAELASSEVADAVLPSSQTLVPVESVPVSMLESSTISQKNDDVT
ATSGTELTENPSTKVDSPEKNEDSVSLACPSKCISDIGNMDGDASANSFE
ENVYTPAIISCAKAPLSEKEQKTRTIEVSIGDVQHPEATDGAAEMVQSVP
LDATFNNGEISTSQVNMSTGLTEGKIMKDMQLNPVQVHERSTDVKEYPSD
GNMGPPSVVSCVKIPISETGQTSRGKDASVSTVHHSEGTAGAGENVQSAA
LHMEHDNSNEGTNISMEVSSSTGLSESEIIKGSPSYPSIPVNKISTDVEG
YPLAADCSRIDLTMPEHSLENSEGPGPMSGKKRAGARGTSERKTRLGSVK
TTARTNSRKRGMQETPSKQFDEDKSMMISSLPGNSNAELSGIKVCGALPT
PMSTIPDLNTSVTPAYYQQPFTDTQQVQLRAQILVYGSLMQNSVPDEACM
IAAFGPSDGSGGCLWECAWRACSERIQTQKSDASNLETPVRSFSAGSKGS
DQPVKKSKSSRQSKSTLPADRASSKDIPSPVVNPIIPLSSPLWNVSTPSG
VGLQSSGTYVDYHQPFGPLQPCQPQGTKGFGEQNPSWLSQINFPGQWVAT
PQTSSLDVNASVSSKFCTEPVKLTPSKVSSVPSDPARKQTQFSVSTGGSA
GLSSGIHFQTDVTKTSVLPGQICDNTKHKKRKKVSVSKSPGQIPSLTLDQ
AASLSDTSNHISKKGTAPQAIFQNSLLAPSLPEMRSPAVNNASSMPNAAT
ATFLGSTGRSSNNLPAVYPLVSSDQPTRVDQIVDKNSIMSEESLNAVEAA
RLQAEGAAAHAAAAVGNCNGVWSQLSKLKNSGLRFDDETKLSSAAMAIAA
AASVAKAAAAAAKLASNIAIGAKLMADEVSTASVTRKDPHSTGMSMACSS
NSSLLAGEGNVSTSSIITAAKETVKKRVEAATAASKHAENLDAMVKAAEL
AAEAVSQAGKIVSIGDPLPLSELLGSGPMDYWRTPQVFPEQGVIAGIDQR
KTFVPEKLVPAQPPKDGAIVTGEAVDRGTIASVGKNSLSTQRGHRASDPA
LDSYGGTNSEIVKSRDAQRISPLTSLENVMVEGCFVEVFKEGGKYKAAWY
PAKILNSDDEKAFVCYTELQADDGSGKLKEWVPLKGDNSKAPIIRIPHPA
TSMCFERSRKRRRAAVMDYTWCVGDRVDAWMQDCWLEGVVSEKKNDETTF
KISIPALGGTSAVKTWNLRPTVTWQDGKWIECPSAVQQSPTQGDTPQEKR
VKLGHPAVEAAKVDKSLRGNDLMESKEHDESRQLPLLASEKEFNIGNNTG
DIKLDAPRIARTGLQKEGSRVVFGVPKPGKKRKFMDVSKHLDSDQCNKNA
KTSDLVKTARYLPQGRGGGRGWNNNTKDDIKEKQAKEDKVKVIRSGVAQK
TNALLSAKSMGKTVSKEQNNPALRDLMEFGSVSNSPSEGPTSSKGPRVPN
KRVPSSSTKTVLLNKGKHAAGGEVDKKVDPHVTEIRRSNRKIQPTSRLLE
GLQSSLIGSKMPSVPHEKVQKNLNRGDSSSHG
| Relationships |
|---|
| The mRNA, XM_017366964.1, is a part of gene, LOC108199235. |
| The polypeptide, XM_017366964.1, derives from mRNA, XM_017366964.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |