| 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. |
TGTCTATTCAACATGCAAAGTCTTTTATGCCCTTATCACTCGTTCAAAAA
CTCACACGTTTTGCTCTCTTCCCCCAAAAGGCCCTCTGCTTAGAATTTGT
AAAGCCACACACTCACACACTCAACTCCTCTCTCCCTGTGTAAATCTCTC
TCTCTCTGTTTTTATAATTTTATACACGACCCTTTTTTGTCCTTATCATT
TCTGACAACCCCTTCACCTGAATCCACACATACAAACACACACACAAATA
TTATTTTAGTGGGTTGAAAATTCAAGAACTGGGTCAAAACCCTAGGGTTA
TGAAGCAATATCCACCCAGTTGGTGATTATTCTGTCTCTGAATGGAGGGA
GGCATTTTCTGATGGATTATGATGACAAAATTTCTGAAGGCCATAAGTCA
GCTAATGCAGAGAATTCCAAGTCATCACCCGTGGTGCCTCCATTTGCTCT
TCCCAAGTATGATTTTGATGATAGCCTACAGGGTGACCTAAGATTTGAAG
GATTGGTCGAAAATGAAGTTTTTCTTGGCATTTCGAGTCAAGAAGACAGC
CAGTGGATTGAGGACTTTTCTAGAGGAAATAATGGTATAGAATTTAGTTC
ATCTGCGACAGAGCCTTGTTCCATTTCAAGGCATAACAATGTTTGGTCAG
AGGCAACATCTTCAGAGTCTGTTGCGATGCTTCTGAAGTCCGTTGGACAG
GAGGAAAGGATTCAGGGAGAAACTTTGATTCAGGAGTTGGACACTGGCAA
TGAATTAGGCAATTTAGCTACAGAAATGGAGCCTAACTTGAAGAAGGACG
ATAAGGTGGAGTCTATAACTACCTCACAACCTACTGCGACTCCTGATTCT
TTTCTGGATCGGAGGAATGTGAATGCTGTAGAATCAAAAAAGGATAATGT
TCCTGTTGATGGAAGTTCTGGCGTTGTTTCAATTGTTTCCAGTGTAATTC
TAAGCGAGGCAGATGAGGGACCAGATGATAAATGTGATGATACTACACAT
TTGAAAGTTAATATTATAGACCAGCCCGTTGACAATTTAGAAGGCTGCAA
CATTGACCAAGGTTCTGCAGTGACTTCTCAGCTGGGTAATGTTGAAGTCG
GGGCCTGCAACAAAGGTGAAAAGACTAGTGAGCCAATTCAAAATCCTCTG
GGTGACACCTCATCTGTGGCTTGTGTAGATGCTCATACCTTTGAGGTTGT
GAATAAAGATGCCGAGTATTCTGCCTGTACTGGGGTCGAAGTCAGTATTG
TTGAATTAAAGGAGAACTCTTTCGGCAACCAACCAAACAGTCTGGAAAGA
CAGAATGTTGAGGCCGTTGACATTAAGACAGTAAATTCTTCCTGTCCAGA
GCATGATATGGACTCGGTGGTTGAGAATGAGAATTCTGAAAACTGTAGTG
GGGGAGTGGCTGTTGCTGAAGCTTCTTCGTTGCTTGCTGCAGACCATAAA
TTTACTGAACAGGTGGAAGGAAGTGGCATTGAATATGCTGAGAATCCGGA
TACATCTGTATCTTGCATTGTCTCTGGATCACAATGTGGAATACAGTTGT
CTTCTAAGGATTCAAGTGATCTCAGAACATCTGGAGTCCTTGAGGATAAT
AATTCTCCTGAAGCACAAACATCCTCTTTCGTAGTTGGTGGACATGTGCA
GATGAGCAAAAGTCATATTTCCTCTGGGCAGGAAGATGTCCACCTTTTTG
ACAAAGATGTATCTTCTCTTGGGACAGAAGATGCAAAGTCACTCACAACA
TCCCTGCCTCCTGATGAATCTAATAAAGCAAACATAGTTCAAGGAGCAGA
ACTCCTTAATTCTGCGAGTAATGAGCGAGGATCAGAAGTTACAGACGAAA
TGAACTTATCATCGTGTGGCATGCCGATTGATCCTCCATTGCTTCACGGG
AGCAAGACTACTGCTGATGGAGCTACTTTTGGTGAGCAAGAGCATAAGTC
ACAGGTTGCTAATTTATTAGGCACAGAGAGTTCACCACAAGTGTCAGCTG
ATCTAGAGCCTTTTAGTTTTCCTGAATCTGGACAAGCAAGTCGGATAAAT
CAAGAAGCAGGTCCGGAGGGTTCCAAAAAGGTGGAAGCATGTCCATCTCT
AATTAGTTCAGAAATAAAGCTGGTTGACGATGCTGCACTAGCAGCACATA
AAAGCAATGAAGAAATATATTTGGAAAGAAGTGCTGAATTGGCATCGTCT
GAAGTTGCAGATGCGGTGTTACCATCAAGCCAAACTCTTGTTCCTGTAGA
ATCTGTTCCAGTCTCCATGCTAGAATCCTCTACTATTTCCCAAAAGAATG
ACGATGTTACAGCAACTTCCGGAACAGAATTAACAGAAAATCCTAGCACT
AAAGTTGATTCACCTGAGAAGAATGAAGATTCTGTTTCTCTTGCTTGCCC
GTCAAAATGCATTTCAGATATTGGGAACATGGATGGAGATGCCTCTGCTA
ATTCATTTGAAGAAAATGTGTATACTCCTGCTATCATCAGTTGTGCAAAG
GCTCCGCTAAGTGAAAAGGAACAGAAAACAAGAACTATAGAGGTCTCAAT
TGGTGATGTCCAGCATCCTGAGGCAACAGATGGTGCTGCTGAAATGGTTC
AATCTGTTCCATTGGATGCTACTTTCAACAATGGGGAAATCAGTACTTCT
CAGGTTAACATGTCAACTGGTTTAACAGAGGGAAAAATCATGAAGGATAT
GCAATTAAATCCTGTTCAGGTTCACGAAAGATCAACAGATGTCAAGGAGT
ATCCATCTGATGGTAATATGGGACCTCCCTCTGTTGTCAGTTGTGTAAAG
ATTCCGATAAGTGAAACTGGACAGACGTCGAGAGGCAAAGATGCCTCAGT
CTCCACTGTCCATCATTCTGAAGGAACAGCTGGTGCTGGTGAAAATGTTC
AATCTGCTGCATTGCATATGGAACATGATAATTCCAATGAAGGGACAAAC
ATCAGTATGGAGGTCAGTTCATCTACTGGTTTATCTGAAAGCGAAATCAT
CAAGGGTTCACCATCATATCCGAGCATCCCAGTCAACAAAATATCAACTG
ATGTTGAGGGATATCCTTTAGCAGCTGATTGCTCTCGGATAGATCTTACA
ATGCCTGAACATTCTCTTGAAAATTCTGAAGGACCTGGACCTATGTCAGG
TAAGAAACGTGCAGGTGCCAGAGGGACCTCTGAGCGGAAAACAAGACTAG
GTTCTGTTAAGACAACAGCTAGAACAAATAGTAGGAAAAGAGGTATGCAG
GAAACACCTTCGAAACAGTTTGACGAAGATAAATCAATGATGATCTCAAG
TTTACCTGGGAATAGCAATGCTGAACTAAGTGGTATAAAAGTTTGTGGCG
CCCTTCCTACTCCCATGTCTACTATTCCAGATTTAAACACTTCAGTTACT
CCCGCATATTATCAACAACCTTTCACTGATACCCAACAAGTGCAATTGCG
AGCACAGATACTTGTATATGGATCACTAATGCAAAATTCCGTACCTGACG
AGGCTTGTATGATTGCAGCATTTGGGCCATCTGATGGTAGTGGTGGATGT
CTTTGGGAGTGTGCATGGCGTGCTTGTAGTGAAAGGATACAAACTCAGAA
ATCAGATGCCAGCAACCTGGAAACCCCTGTGCGATCATTCTCTGGTAGCA
AAGGTTCGGATCAACCAGTTAAAAAAAGTAAAAGTTCACGTCAGAGTAAA
TCTACTTTACCTGCAGATAGAGCTAGCAGTAAGGATATCCCATCGCCAGT
TGTTAATCCTATTATACCCCTATCATCACCTCTTTGGAACGTATCTACCC
CCTCTGGTGTTGGTTTGCAGTCCAGTGGCACATATGTTGATTATCATCAG
CCATTTGGTCCCTTGCAGCCTTGTCAGCCCCAAGGTACAAAAGGTTTTGG
TGAACAGAACCCCTCTTGGCTTTCTCAGATTAACTTTCCTGGTCAGTGGG
TTGCTACTCCACAAACTTCATCCCTTGATGTCAATGCATCTGTATCTTCA
AAGTTTTGTACTGAACCAGTAAAACTAACCCCATCCAAAGTTTCATCTGT
GCCAAGTGACCCTGCCAGAAAGCAAACCCAATTTTCTGTTTCCACTGGTG
GGAGTGCTGGGCTGTCTTCAGGGATTCATTTTCAGACTGATGTAACAAAG
ACTTCTGTTCTGCCTGGTCAGATTTGTGATAATACTAAACATAAGAAGAG
GAAGAAGGTTTCTGTCAGCAAGAGCCCAGGGCAAATCCCGTCACTAACTT
TAGATCAGGCAGCATCTTTAAGTGATACAAGTAATCATATCTCTAAAAAA
GGAACTGCTCCCCAGGCTATTTTCCAGAATTCTTTGCTCGCTCCAAGTCT
GCCAGAAATGAGATCCCCTGCTGTCAATAATGCATCATCTATGCCAAATG
CAGCCACAGCTACTTTTTTGGGATCAACAGGCCGTTCCAGCAACAATCTA
CCAGCTGTCTATCCATTAGTTTCGAGTGATCAACCTACGAGAGTGGATCA
GATTGTGGATAAGAATAGTATAATGTCAGAGGAATCACTGAATGCAGTCG
AGGCAGCTAGGTTACAAGCAGAAGGTGCTGCTGCACATGCTGCTGCTGCA
GTCGGAAACTGCAATGGTGTTTGGAGCCAGCTGAGTAAGCTGAAGAATTC
TGGTTTAAGATTTGATGATGAGACAAAACTTTCTTCTGCAGCTATGGCAA
TAGCTGCAGCTGCTTCTGTTGCAAAGGCTGCAGCTGCAGCAGCCAAACTT
GCATCGAATATTGCAATTGGAGCAAAACTAATGGCGGATGAGGTATCAAC
CGCAAGTGTAACCAGAAAAGATCCCCATAGCACTGGAATGTCTATGGCCT
GTTCTTCAAATAGTTCTCTGTTGGCTGGAGAAGGAAATGTCTCCACTAGT
TCAATTATTACTGCTGCGAAAGAGACAGTTAAGAAGAGAGTCGAAGCTGC
CACAGCTGCCTCAAAGCATGCTGAAAACTTGGATGCTATGGTTAAAGCTG
CTGAACTGGCAGCAGAGGCCGTTTCACAAGCCGGAAAAATTGTTTCTATT
GGCGATCCCTTGCCTTTGAGTGAGTTGTTAGGCTCTGGTCCTATGGACTA
CTGGAGAACTCCCCAGGTATTTCCTGAACAAGGGGTGATAGCAGGCATTG
ACCAACGGAAAACATTTGTTCCTGAAAAGCTTGTTCCTGCTCAACCACCA
AAAGATGGAGCAATTGTTACGGGAGAAGCAGTGGATCGTGGTACTATTGC
AAGTGTTGGAAAGAACTCATTGTCTACTCAAAGAGGCCACCGTGCATCTG
ACCCTGCTCTTGATTCATATGGGGGAACAAACTCTGAAATTGTTAAATCT
CGTGATGCCCAAAGAATTTCACCACTTACATCTCTTGAGAATGTAATGGT
GGAAGGTTGCTTTGTCGAGGTCTTCAAAGAAGGGGGTAAATATAAGGCAG
CATGGTATCCAGCCAAGATTTTGAATTCGGATGACGAGAAAGCTTTTGTC
TGTTACACTGAACTCCAAGCAGATGATGGGTCAGGGAAACTAAAGGAATG
GGTTCCACTTAAAGGGGATAACTCCAAGGCACCTATAATACGTATTCCAC
ATCCTGCAACTAGCATGTGCTTTGAAAGAAGTAGGAAGAGACGGAGAGCG
GCAGTGATGGACTATACTTGGTGTGTTGGAGACAGAGTTGACGCGTGGAT
GCAAGATTGCTGGCTTGAGGGAGTTGTGTCTGAGAAGAAAAATGATGAAA
CAACATTTAAAATATCTATTCCAGCTCTTGGAGGCACTTCAGCTGTTAAA
ACATGGAATCTTCGCCCAACCGTAACTTGGCAGGATGGAAAGTGGATAGA
GTGCCCCTCTGCAGTTCAGCAGTCCCCTACTCAGGGTGATACACCACAGG
AGAAGCGTGTGAAGTTGGGACATCCCGCTGTAGAGGCTGCTAAGGTGGAC
AAGAGTTTAAGAGGCAATGATCTCATGGAATCAAAGGAGCATGATGAATC
AAGACAACTTCCTTTACTAGCTAGTGAAAAAGAATTTAACATTGGGAATA
ATACTGGAGATATTAAACTTGATGCTCCAAGAATTGCAAGGACTGGATTG
CAGAAAGAAGGCTCAAGGGTGGTTTTTGGTGTTCCTAAGCCAGGAAAGAA
GCGTAAATTCATGGATGTAAGCAAACATCTTGACTCTGACCAATGCAATA
AAAATGCAAAAACAAGCGATTTAGTCAAAACTGCAAGATACTTGCCTCAA
GGAAGAGGGGGTGGTCGTGGTTGGAATAACAATACTAAAGATGATATCAA
AGAAAAGCAAGCTAAAGAAGACAAGGTCAAAGTTATCAGGTCTGGAGTGG
CACAGAAGACTAATGCTTTGCTATCTGCCAAATCTATGGGGAAAACTGTC
AGCAAGGAACAGAACAATCCAGCTCTGCGGGACCTTATGGAATTTGGCTC
CGTCTCTAATTCCCCTTCTGAAGGTCCAACTTCTTCAAAAGGTCCTAGAG
TTCCAAATAAAAGAGTACCCTCTTCAAGTACCAAAACCGTCCTTCTGAAT
AAAGGAAAGCATGCAGCTGGTGGAGAGGTTGATAAGAAAGTTGATCCGCA
TGTTACTGAGATTCGAAGATCAAACCGGAAGATTCAACCAACATCACGGC
TATTGGAAGGATTGCAGAGCTCTCTAATCGGTTCAAAGATGCCCTCTGTC
CCGCATGAAAAAGTTCAAAAAAACCTGAACAGAGGTGACAGTAGCAGCCA
TGGCTGAGCTTCTATGGATGAGGAAAGGTCTAGATTGGCACATCTGAAGT
TCACTGGATTCCGAAGGCAATGATTTCATGTCTGGAGGATAGAATTGAGA
CCGTGCTCTGCTGCTTCAGCTGTAGAATCTAGACCGTAGATATTTATAAG
TTATCATAATTTGATTCCTTACAGATCTTCAAGACTTTACTCCGTTAGCC
TGTACTGTATATGGAATCATGGATAATCACCCTTGATGGATGAAGATGGA
GACTTGTATGCAGTCCTTAATTTAGTATTCTTTTTTCCTAATATCTTATT
TGCTGCCCA
MDYDDKISEGHKSANAENSKSSPVVPPFALPKYDFDDSLQGDLRFEGLVE
NEVFLGISSQEDSQWIEDFSRGNNGIEFSSSATEPCSISRHNNVWSEATS
SESVAMLLKSVGQEERIQGETLIQELDTGNELGNLATEMEPNLKKDDKVE
SITTSQPTATPDSFLDRRNVNAVESKKDNVPVDGSSGVVSIVSSVILSEA
DEGPDDKCDDTTHLKVNIIDQPVDNLEGCNIDQGSAVTSQLGNVEVGACN
KGEKTSEPIQNPLGDTSSVACVDAHTFEVVNKDAEYSACTGVEVSIVELK
ENSFGNQPNSLERQNVEAVDIKTVNSSCPEHDMDSVVENENSENCSGGVA
VAEASSLLAADHKFTEQVEGSGIEYAENPDTSVSCIVSGSQCGIQLSSKD
SSDLRTSGVLEDNNSPEAQTSSFVVGGHVQMSKSHISSGQEDVHLFDKDV
SSLGTEDAKSLTTSLPPDESNKANIVQGAELLNSASNERGSEVTDEMNLS
SCGMPIDPPLLHGSKTTADGATFGEQEHKSQVANLLGTESSPQVSADLEP
FSFPESGQASRINQEAGPEGSKKVEACPSLISSEIKLVDDAALAAHKSNE
EIYLERSAELASSEVADAVLPSSQTLVPVESVPVSMLESSTISQKNDDVT
ATSGTELTENPSTKVDSPEKNEDSVSLACPSKCISDIGNMDGDASANSFE
ENVYTPAIISCAKAPLSEKEQKTRTIEVSIGDVQHPEATDGAAEMVQSVP
LDATFNNGEISTSQVNMSTGLTEGKIMKDMQLNPVQVHERSTDVKEYPSD
GNMGPPSVVSCVKIPISETGQTSRGKDASVSTVHHSEGTAGAGENVQSAA
LHMEHDNSNEGTNISMEVSSSTGLSESEIIKGSPSYPSIPVNKISTDVEG
YPLAADCSRIDLTMPEHSLENSEGPGPMSGKKRAGARGTSERKTRLGSVK
TTARTNSRKRGMQETPSKQFDEDKSMMISSLPGNSNAELSGIKVCGALPT
PMSTIPDLNTSVTPAYYQQPFTDTQQVQLRAQILVYGSLMQNSVPDEACM
IAAFGPSDGSGGCLWECAWRACSERIQTQKSDASNLETPVRSFSGSKGSD
QPVKKSKSSRQSKSTLPADRASSKDIPSPVVNPIIPLSSPLWNVSTPSGV
GLQSSGTYVDYHQPFGPLQPCQPQGTKGFGEQNPSWLSQINFPGQWVATP
QTSSLDVNASVSSKFCTEPVKLTPSKVSSVPSDPARKQTQFSVSTGGSAG
LSSGIHFQTDVTKTSVLPGQICDNTKHKKRKKVSVSKSPGQIPSLTLDQA
ASLSDTSNHISKKGTAPQAIFQNSLLAPSLPEMRSPAVNNASSMPNAATA
TFLGSTGRSSNNLPAVYPLVSSDQPTRVDQIVDKNSIMSEESLNAVEAAR
LQAEGAAAHAAAAVGNCNGVWSQLSKLKNSGLRFDDETKLSSAAMAIAAA
ASVAKAAAAAAKLASNIAIGAKLMADEVSTASVTRKDPHSTGMSMACSSN
SSLLAGEGNVSTSSIITAAKETVKKRVEAATAASKHAENLDAMVKAAELA
AEAVSQAGKIVSIGDPLPLSELLGSGPMDYWRTPQVFPEQGVIAGIDQRK
TFVPEKLVPAQPPKDGAIVTGEAVDRGTIASVGKNSLSTQRGHRASDPAL
DSYGGTNSEIVKSRDAQRISPLTSLENVMVEGCFVEVFKEGGKYKAAWYP
AKILNSDDEKAFVCYTELQADDGSGKLKEWVPLKGDNSKAPIIRIPHPAT
SMCFERSRKRRRAAVMDYTWCVGDRVDAWMQDCWLEGVVSEKKNDETTFK
ISIPALGGTSAVKTWNLRPTVTWQDGKWIECPSAVQQSPTQGDTPQEKRV
KLGHPAVEAAKVDKSLRGNDLMESKEHDESRQLPLLASEKEFNIGNNTGD
IKLDAPRIARTGLQKEGSRVVFGVPKPGKKRKFMDVSKHLDSDQCNKNAK
TSDLVKTARYLPQGRGGGRGWNNNTKDDIKEKQAKEDKVKVIRSGVAQKT
NALLSAKSMGKTVSKEQNNPALRDLMEFGSVSNSPSEGPTSSKGPRVPNK
RVPSSSTKTVLLNKGKHAAGGEVDKKVDPHVTEIRRSNRKIQPTSRLLEG
LQSSLIGSKMPSVPHEKVQKNLNRGDSSSHG
| Relationships |
|---|
| The mRNA, XM_017366965.1, is a part of gene, LOC108199235. |
| The polypeptide, XM_017366965.1, derives from mRNA, XM_017366965.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |