| 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. |
AGAACAACTTATCTTATCCATGCTCTTCTTGCTACGATTCTCTCATCCAA
AATGATTTTCCTTCCTGTCCAAACTCACTCACTTTCATTCCCATTTCACT
TTCCTTGTAATTTTCATGACCAGCAACAATGCAACACAAGAATAAGCATC
ACGCTTCCCAACCACACTTTCTCATCCCCACGCTCCTCTCGTTTCCTTCC
TCTTCATCGCCCTGCCACTCGCCATTTTAAGGTGATGGCAAATGCGAGGA
AAGAAAACAAGGTTTTGGAAGCTGGTGAAGTTGAATTACTTATGGCCACT
TGCATAACTCGCACTCTTTCACCTGCATTGACGCTTGAGCATGGTCTCGA
TCAAATCGACAACGCTATTCGCCATTTGAAGTCCAATCCTCCTTTTACTA
CGATTGGAATGTACAGGTTTGAGGTTCTGGTGTCTCCCAGTACAAGAGCT
TTGAATTGGTTTTCTTCTCAACCTGAATCATCTACGATATATCCTCAATT
TTTTATGTCCAATGAGATTGAAAACTCCACAAGTGTGTCATTTCGTTTGG
ATACAATCCGAGGGGTTTTTGGAATAGGCACAGCGGTTTCCTTTAAGGGA
TCTTATTCTTCTGCCTCAGCTCATTGTGCCTCTTTTAAAAGTTATTTTTC
AGATTATTCAACACTCGTTGCGGCTTATGGGTATATGGATCTGAGGTCTG
ATCCTGGGTTCTATGGGACAGGTTTATCATATTTTTTCGTTCCTCAGCTT
GAATTAATTGAGCTCGATGGGATTTCTATTTTATCTATGACACTTGCGTG
GAATGATTCTTCCCTTTGTAAGTTCAAGGAGGCTGTTGAAGCTAATGAGT
TATCACTGTACCAGGCCAGAGATTATTTATGGCCCAGAACAGGGGAAAGC
GACAAGAAATTTATCAACTCGACTCTTACAAGACCTGAAGTGCTTACAAA
TGACAATGCTCAGATGGTGGCCCTGAATGCTTTGTCTGTGTCTGAAAGGG
ATCTTATGCATGATCCCACCGAAATGAAAAATGGTGCCCACTCTCATCAA
TTCACTGTTCGATTTTCTCCTACTATTACTATTTCTTGCAACATGTATCC
ATCAAATTATGTTGCTAAAACGAGTAATGCTTTCCAAGACTATGCGAACA
TCAATACCTTGTGGGCGTCCCTTATTATTGAAGAATGTTCACGACTTGGT
TTAACGTACTTTTGCGTAGCTCCTGGATCACGATCATCTCCGCTGGCCCT
TGCTGCTTCTGCTCACCCGCTTACAAATTGTACTGTATGCTATGATGAGA
GATCACTTGCATTTCACGCTATTGGTTATTCAAAAGGTTCTCATATACCA
GCAGTAGTAATTACATCATCAGGAACGGCAGTTTCTAATCTTCTTCCTGC
TGTTGTGGAGGCGAGTCAAGATTATGTGCCACTTCTATTACTCACAGCTG
ATCGTCCTCCAGAGCTTCAAGATGCTGGGGCAAATCAATCAATTAATCAG
GTTAACCATTTTGCTCCGTTTGTGAGGCACTTCTATGGTCTTCCAGTACC
TACAGATATTATACCTGCAAGGATGGTACTTACTTCAGTTGACTCGGCAG
TATATTGGGCAACTTCTTCGCCTTGTGGTCCAGTTCATATAAATTGTCCT
TTTAGGGAACCACTGGACAGTAGTCCAAAAAATTGGATGCTGAGTTGTTT
GAAAGGATTGAATTCTTGGATGATGAGTGCTGACCCATTTACTAACTACG
TAAATATACAACATACGTTTCCATCGAATGAGGCACATGGCTCTCTGAGA
GAAATTGTAAATATTATGAAAGGAGCCAAAAGAGGTGTTTTGGTACTAGG
CGCCATCTCTTCAGAGGATGACATATGGGCTGCACTTCTTCTGGCCAAAC
ACCTTCTTTGGCCCGTTGTAGCTGATATCTTGTCAGGTTTACGAATGAGG
ATGTATACGAGTTCATTTTCTGAAATACGAGGGAATTTTGTTTTTGTTGA
TCATCTTGATCATACCCTACTATCAGATGCAGTCCGGGATTGGGCACAGG
CTGATGTTTTTGTTCAGATTGGAAGCAGGATTACGAGCAAGCGCATTTCA
CAAATGCTAGAAGATTGCTTCCCATGCTCATATATACTAGTTGACAAGCA
TCCAAATCGTCATGATCCTTCACACATTGTAACACATAGGATCCAATGTA
CTGCTGCTCAGTTTGCTGATCATGTGCTTAAAGCTTCAATAAATGGGATC
AGCAGTAACTGGACTAGTTTTCTCTGTGCATTAGACACAATGGTTTCTCG
GGAAATTTCATTTTTAATTCATCAGGAGCAGTCATTGACGGAACCCTATA
TTGCACATGTTATTCTTGAAGCTCTTAACTGTGGATCAGCAGTGTTTGTT
GGAAACAGCATGCCTATACGTGACGCGGACATGTATGGATCTAACTGGAC
AAATTGCACACATAGTAATGACATTCTATTAAGCTCAGGATTGCCGTGTC
ATGGGATACGAGTGTCTGGAAATAGGGGAGCTAGTGGTATTGATGGTTTG
CTTAGCACTGCTGTTGGATTTGCTGTGGGATGTAAAAAAAGAGTGCTTTG
TGTGATTGGAGATGTTTCTTTTCTGCATGATACAAATGGATTAGCACTAC
TGAAACAAAGGATACCCCGGAAACCAATCACAATACTGGTGATAAACAAC
CATGGTGGTGCAATTTTCAGCTTCCTTCCTGTTGCGGCAACAACAGAGAA
GAGAGTACTAGAGCAGTTTTTCTACACTTCTCATGATGTGTCAATTCAGA
ACTTGTGCTTGGCACATGGCATAAAACACGTGCATGTTAACAGAAAAGTG
GATCTGCAAGATGCTTTAATTAGTGCTCAACACGAAGCCCTTGATAGTGT
AATAGAAGTTGAAAGTTGTATAGAAGGAAACACATCCTTTCACAGCTGTT
TGAAAAAATTTGCAAGTCATGCAGCAGATCACTCTTTCAATGTCCTAACA
AAACTTTCACTCTCCAATTCAGCCTTAAGAGGATCTACCTATTGTACAAT
TCAGAAGTTGGAGTATTCCTTGTATAGAATTAGGCTATGTGCTCCACCTA
CTTCAGCTCGTGTTACTCGTGACAGTACTACATTTTACAGAGAAGGATTT
GTTTTAGCTTTGTTTCTTAAAGATGGAAATGCTGGTTTTGGCGAGGTTGC
ACCTCTTGAAATTCACAAAGAAAATCTGCTAGATGTGGAAGAGCAACTTC
GATTTCTTATGCATGTCATCAAAGGAGTTAATATTGAATTTATGCTTCCC
CTTTTAAATGGCTCGTTTTCTTCTTGGATATGGAACAACTTAGGGATTCC
GCCAGGTTATATTTTTCCAAGTGTTCGATGTGGTCTGGAGATGGCAATAC
TCAATGCCATTGCAGCTACAGAAGGTTCTAGTTTGTTAAATATACTCCAG
CCACTGACAGAGAGTGAAAAACAAACGTCTGCAGTACCACCAAATGTGAG
AATATGTGCTCTTCTTGATGTGAAAGGAACTCCCTCGGAGGTGGCTTATG
TTGCTGGCACACTTGTCAAAGAAGGATTTACTGCAATAAAGCTAAAAGTT
GCACGGAGAGCAGACCCTACTGAAGATGCTGATGTCATAAAGGAAGTAAG
AAAGATAGTTGGAAGCCAAATTCAACTGCGTGCTGATGCAAATCGAAAGT
GGATCTACGAAGATGCAATACGTTTTGGTTCTTCTGTTAAGGACTGTGAC
CTGCAATATATAGAGGAGCCTGTTAGGGATGGAGATGATATAGTTAGATT
TTGTGAAGAGACTGGTTTACCTGTAGCACTTGACGAAACCATCGATAACA
TTCAGGGAAATCCTCTCAAAACTCTTGAGAAGTTCAGTCATGCTGGAATA
GTTGCCATTGTTATCAAACCAAGTGTTGTCGGAGGATTTGAAAATGCAGC
ATTGATTGCAAGATGGGCTCAGCAGCAGGGGAAGATGGCTGTTGTCAGTG
CTGCATTTGAAAGTGGCCTTGGTTTGTCAGCCTATATACAATTTTCTTGC
TATCTCGATTTGAAAAGTGCAGAAATATATAGACTGATGAATAAGGAAGC
ACCAGTACCTGTAGCACATGGTCTTGGAACTTATCGTTGGTTAACACAAG
ATGTGATTACAGAGCCTTTAAGTATAACTCGTAATCCTTTTAATGGCTTC
ATGGAAGCCTCTTCTGCAGATGCTGGCCGACTCTTGCGAAATATTCGACT
TGATCAGAATTATATCGTCAGTAGGAACTCTGAGGAGAAAGTTCGTCCTT
ACCAGTTACAAGTTCACTCAAAGGGTTTCTCCATGTCCATTAATGTGCAT
GAGATTGGAAAAGATACTAATGAAAATGTCGTCGTGTTTCTTCATGGCTT
CCTCGGAACTAGTGAGGAATGGATTCCTGTCATGGAGGCCATCTCAGGAT
TTTCAAGATGCATTGCGTTTGACCTACCTGGACATGGAAAATCAAAGATT
GAAGTTGACACTGTTACTGAACCTGCAAAAGAACATATTTTCTCAATTGA
GGCAGTGTCAGATATTATTTGCGAGTTGCTTTCTTCTATCAACGCACCCA
AAGTAACTTTAGTTGGTTACTCAATGGGGGCAAGGGTTGCTCTATACATG
GCCCTAAGATGCGTTGATATGGTTGAAGGAGCTGTTGTAATATCTGGAAG
CCCTGGGTTGAAAGATGAGCCTGCTAGAAATATTCGTAGGATGAAAGATG
ATTCCAGGGCTTGTTCGCTTACTTCATATGGTTTAAAATGCTTTCTAGAC
ACTTGGTATGCAGGAGACCTGTGGAATAGCTTAAGATGCCATCCGAATTT
TAAGGCGATAGTCACCAGTCGCATGAGACACAATGATGTTCATGGTCTTG
CAAAAGTGCTTTCTGATTTAAGTGTTGGAAGACAACCACCTTTGTGGGAA
GACCTGAAACACTGCAAATCACCACTTCTGTTGATTGTGGGTGAAAAAGA
TGATAAATTTAAGCGACTTGCTCAAGAGATGTGTTCTACAATCAGTCAAG
AATCTAGGGGCAACAGGAAGTCCACAACTTGTGAAACAGTAGAAATCCCG
GGTTGCGGGCATGCTGTCCATTTAGAAAATCCTCTTCCAGTTGTTAAAGC
AATTAGAAGCTTTCTAACGAATAAAAGAGTCTGATCAGGTCTTATTTCCT
TACCAAAAGAAGAAGAGATATATGACTCGTAACTGTAATTCTTATACCAA
GTGGTTTTGATTTGAAGGAAATACTGAGTTTCAGTGTGACATTAAACTAT
TTTTCATAGGCATGCACAATTTGACTGGTATAAAGAGATTTTATTGTAAT
CA
MIFLPVQTHSLSFPFHFPCNFHDQQQCNTRISITLPNHTFSSPRSSRFLP
LHRPATRHFKVMANARKENKVLEAGEVELLMATCITRTLSPALTLEHGLD
QIDNAIRHLKSNPPFTTIGMYRFEVLVSPSTRALNWFSSQPESSTIYPQF
FMSNEIENSTSVSFRLDTIRGVFGIGTAVSFKGSYSSASAHCASFKSYFS
DYSTLVAAYGYMDLRSDPGFYGTGLSYFFVPQLELIELDGISILSMTLAW
NDSSLCKFKEAVEANELSLYQARDYLWPRTGESDKKFINSTLTRPEVLTN
DNAQMVALNALSVSERDLMHDPTEMKNGAHSHQFTVRFSPTITISCNMYP
SNYVAKTSNAFQDYANINTLWASLIIEECSRLGLTYFCVAPGSRSSPLAL
AASAHPLTNCTVCYDERSLAFHAIGYSKGSHIPAVVITSSGTAVSNLLPA
VVEASQDYVPLLLLTADRPPELQDAGANQSINQVNHFAPFVRHFYGLPVP
TDIIPARMVLTSVDSAVYWATSSPCGPVHINCPFREPLDSSPKNWMLSCL
KGLNSWMMSADPFTNYVNIQHTFPSNEAHGSLREIVNIMKGAKRGVLVLG
AISSEDDIWAALLLAKHLLWPVVADILSGLRMRMYTSSFSEIRGNFVFVD
HLDHTLLSDAVRDWAQADVFVQIGSRITSKRISQMLEDCFPCSYILVDKH
PNRHDPSHIVTHRIQCTAAQFADHVLKASINGISSNWTSFLCALDTMVSR
EISFLIHQEQSLTEPYIAHVILEALNCGSAVFVGNSMPIRDADMYGSNWT
NCTHSNDILLSSGLPCHGIRVSGNRGASGIDGLLSTAVGFAVGCKKRVLC
VIGDVSFLHDTNGLALLKQRIPRKPITILVINNHGGAIFSFLPVAATTEK
RVLEQFFYTSHDVSIQNLCLAHGIKHVHVNRKVDLQDALISAQHEALDSV
IEVESCIEGNTSFHSCLKKFASHAADHSFNVLTKLSLSNSALRGSTYCTI
QKLEYSLYRIRLCAPPTSARVTRDSTTFYREGFVLALFLKDGNAGFGEVA
PLEIHKENLLDVEEQLRFLMHVIKGVNIEFMLPLLNGSFSSWIWNNLGIP
PGYIFPSVRCGLEMAILNAIAATEGSSLLNILQPLTESEKQTSAVPPNVR
ICALLDVKGTPSEVAYVAGTLVKEGFTAIKLKVARRADPTEDADVIKEVR
KIVGSQIQLRADANRKWIYEDAIRFGSSVKDCDLQYIEEPVRDGDDIVRF
CEETGLPVALDETIDNIQGNPLKTLEKFSHAGIVAIVIKPSVVGGFENAA
LIARWAQQQGKMAVVSAAFESGLGLSAYIQFSCYLDLKSAEIYRLMNKEA
PVPVAHGLGTYRWLTQDVITEPLSITRNPFNGFMEASSADAGRLLRNIRL
DQNYIVSRNSEEKVRPYQLQVHSKGFSMSINVHEIGKDTNENVVVFLHGF
LGTSEEWIPVMEAISGFSRCIAFDLPGHGKSKIEVDTVTEPAKEHIFSIE
AVSDIICELLSSINAPKVTLVGYSMGARVALYMALRCVDMVEGAVVISGS
PGLKDEPARNIRRMKDDSRACSLTSYGLKCFLDTWYAGDLWNSLRCHPNF
KAIVTSRMRHNDVHGLAKVLSDLSVGRQPPLWEDLKHCKSPLLLIVGEKD
DKFKRLAQEMCSTISQESRGNRKSTTCETVEIPGCGHAVHLENPLPVVKA
IRSFLTNKRV
| Relationships |
|---|
| The mRNA, XM_017363206.1, is a part of gene, LOC108196102. |
| The polypeptide, XM_017363206.1, derives from mRNA, XM_017363206.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |