| 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. |
CCGACGATCTCTATATATACCGCTACACATATACTCCAGTTTCTTCAATA
ATCTCTCTCCCCCCTCTCCATCTCTCTCGTGTATAAATCTCTCCCGCTGG
CCCCATATCTCTCTGCTCTCCAAGATTTCGCTCCAGTAAGAAATTCCCAG
CTTCTTCATTCTCCTCGAGGTTTTCAAAAACCCATCAATTCTTGAATTCT
CGTGTTTAAATTAGGGCAATTCATCACAATTCCTGCAATATCCAGAGTTG
ATTTGGAAAAGATGGGGCTAGAGCAAGGTAGTTGTAGTACATCTCAGGAT
GCTCGTGATGAAGATGATGAAGATGAATATGAAGAGGCTGAAGGCGGTAA
CCGTCTTTTAGGATTCATGTTTGGAAATGTTGATGGTGCTGGTGATCTTG
ATATTGATTACCTTGATGAGGAGGCAAAGGAGCATCTGGGCGCATTGGCT
GACAAGCTTGGTTCATCATTGACGGATATAAATTTGTCAGTACGATCTGT
ACAAACATCTGCAGATGCAATTGAACAAGATTACGATGAGAAGGCAGAAG
ATGCTGTAGATTATGAAGACATTGAGGAACAGTACGAAGGACCTGAGGTC
CAAGCTATAACAGAAGAGGACTATTTATTGCCAAAGAAAGATTATATATC
TTCCCAAGCATCAGCACCTGTTAAGGGCACAACTTCTCTGTTTGATGATG
AGAATTATGATGAGGAGGAATCTGAGAAGGAAACCGAGGCTGATGAAAAC
AATGCTGAAGTTCAAACTACTAACTTATCAGGTGATAGTGATAACCATGC
AGTGCTTTCGCAAGTGGAAGATCTCCGGGGTGATATAGTCAATGGTGCTT
CTGAAACTGAAGAACCAACTCCGTCCTTGGAAGATTTTCTAAAGGAGGAA
GATGATATCCTAGAAGAGCTAGTTGATAATCAGAATATGACTCCACTTCC
GATCTTATACACAGAGGATGGAGCAGTAATTTTACGTTTTTCTGAAATTT
TTGGTATCCACAAGTCTTCGAAGAAATCAGAAAAGAGGGAGTGTAGGTAC
TCTGTTCCTAAAGACAAGTACATGTCCATGGGTACTGCTGATGTCCTTGA
AGATGATGATGAGACATTTTTCAAAGGATTATGCCAAGGCTTTACTTGGA
AGTGTCGGACTCATGTAAATGATGATATTTTACCCATTAAAGATAATGAA
TCAGATCTAGAAACATTACAATATGTACAGCATCCTGGAATAGTAGCTTC
TGTAGTTGATGAGGACCGGAGGGACACTTGTCTTAGTGATGAACCGATGA
AGAAAGATATAGCAATAGATCCATTTTTAGAGAAGATTACACCTCTCTCC
CCTGAACTTTACCTTCTTGAACAGCAGGACTGGGAAGATCGAATCATTTG
GGACAATTCCCCGGAATTAAGTGACCGTTTTGCAGAGACTTTAGAGATCT
CTGGACATGACTCTGGTGCTTCATTTGTTGAAAATTTAGAGTCTAATATA
GAGGAGCAACATAATCATCAAGAGCTGCGGATGGAAACTGATGAGACAAG
CAATGCAATTTTCCAGCGTAGCTATCCTGTATCTGTGGAGCCCTTTGGCT
CTAGAAAAATTTCAGATTTAGTTTCATCAGCAAGACAATTCCATCCCCAA
CTTCTGAGGTTAGAGTCTCGGCTTGAAAACGGTTTGGATAATGGAAAGGA
TAGTAGCACTACTGAAGAGGTCGGGCATCGTGATGCAATAAGGTCTTATA
ACAAGGTGTCTCTGCTTAACAAAGACTTACTGGAAGGGTCTTGGTTAGAC
AATGTAATTTGGGAACCACATCAATCAATGACAAAGCCAAAACTAATACT
TGATCTTCAGGATGAGCAAATGCTTTTTGAGATTTTGAATGACAAGGACG
GCAAGCATCTGAAGCGCCACGCAGGAGCTATGATCATAACCCGCTCTGTG
AAGTTCAACGGTGATTTGGTAGAGACAAATGGTCACGGTACATTACTGGG
GGAGTCATTCAATATAGCTAATGATAAATTTTACTCGAATAGGAAATCTT
CGCAGCAGCTAAAATCACATTCTAAGAAGCGAACTGCTCATGGTGTCAAA
GTTTTGCATTCAATACCTGGACTTAAGCTGCAAACGATGAAAGCAAAGCT
AAGCAATAAGGATATTGCCAATTTTCATCGGCCAAAAGCTTTATGGTATC
CGCATGACAATGAGGTTGTACTCAAAGAACAAGGAAAATTACCTACACAA
GGATCAATGAAAATTATACTGAAGAGCCTGGGTGGTAAAGGCAGTAAACT
TCATGTGGATGCCGAGGAGACCATTGCTTCTGTCAAGGCAAAAGCCTCCA
AAAAGCTGGATTTTAAGCCATCAGAGGCAGTGAAGATATTTTATTGTGGA
GTGGAACTTGATGACGATAAATCTCTTGCCCTGCAAAATGTTAGGCCCAA
CTCTTTGCTGCATCTTGTTCGTACTAAAATACATATGTTGCCAAGGGCAC
AAAAGGTTCCTGGTGAGAATAAGTCGTTGCGTCCTCCTGGAGCATTCAAG
AGAAAAGCTGATCTTTCAGTAAAAGATGGCCATGTTTTCTTAATGGAGTA
CTGTGAAGAAAGACCTTTACTAATTGGAAATGTTGGAATGGGTGCTAGAT
TATGCACCTACTACCAGAAATCATCCACGGGTGACCAAACTGGAACTTCC
TTGAGGAGTGGAAGTTCTGGTTTAGGAAACCTTCTCACCCTTGATCCATC
TGATAAATCTCCTTTTCTTGGTGATATAAGAGCTAGTTGCAGCCAGTCAT
GCATAGAAACTAATATGTATAGAGCTCCTATTTTTCAACATAAAGTATCG
TCAACCGACTTTCTATTGGTTCGCTCTCCAAAGGGGAAGCTTTCCATAAG
GCGAATTGACAGAATTGATGTTGTTGGGCAACAGGAACCACATATTGAGG
TAATGTCCCCTTCATCCAAGGGTGTTCAGATGTATACAATGAACAGGTTA
TTGGTTTATCTCTATCGTGAATTTCGTGCTGCTGAAAAACGTGGTTTGCG
CCCTTCGATCCGAGTGGATGAGCTCTCTGCCCAATTCCCTAATATGAATG
AAGCTTTTCTTCGCAAAAGGTTAAAGCATTGTGCTGACTTTCAGAAGCAA
TCAAATGGTCTGTTTTGGGTGATGAGACGCAATTTTCGCATTCCGCTGGA
GGAGCAGCTGAGAAGGATGGTAACACCAGAAGATGTATGTTCCTACGAAA
GCATGCAAGCTGGCTTGTACAGGCTCAAACGATTAGGAATCACAAGGCTG
ACATCTCCTACAGGCCTTTCTTCAGCAATGAATCAACTTCCAGATGAAGC
TATTGCTTTGGCCGCTGCATCTCATATTGAGAGAGAACTACAGATAACTC
CATGGAACTTGAGTAGCAATTTCGTTGCTTGTACGAATCAGGACAGAGAA
AATATAGAGCGCCTGGAAATCACTGGTGTTGGTGATCCTTCTGGACGGGG
CCTAGGTTTTAGTTATGTTCGTACTGCTCCAAAGGCACCGATTTCAAATG
CAGTTGTAAAGAAAAAAGCAGCTGTCAGTAGAGTAAGCTCTACTGTCACA
GGAACTGATGCAGATTTACGCAGGTTGAGCATGGAGGCTGCTAGGGAGGT
TCTTCTTAAGTTCAATATCCCCGAGGAACAGATAGCAAAACTGACTAGGT
GGCATCGGATTGCTATGATTCGCAAGCTTTCAAGTGAGCAAGCTGCCGCA
GGTGTCAAGGTTGACCCAACTACAATCAGTAAATATGCACGCGGGCAGCG
AATGTCATTTTTGCAGCTTCAGCAGCAGACGAGGGAGAAGTGTCAGGAAA
TTTGGGATAGACAAGTTGAAAGTCTTGCTGCTGTTGATGGTGAAGAAAAT
GAGAGTGATGTTGAAGCAAATAGTGATCTTGATTCTTTCGCTGGGGACCT
GGAAAATCTTTTGGATGCAGAAGAATTCGAAGAAGGAGAGGAGCGTAATT
ACGAGTCCAAGCAAAATAATGCTGATGGTGTTAAGGGGCTAAAAATGAGA
AGGCATCCTTCCCAAGCTCAAGCAGAAGAGGAGTTTGAAGATGAGGCTGC
TGAAGCAGCAGAATTATGTAGAATGCTTATGGATGATGAGGAGGCTGAGC
GGAAGAAGAAAAAAAAGATACGAATGGTTGGGCAGCAATTGAGACAGGCT
CAGGGGTCACACGGTTTTGATAGTGTGGAGAGAGTAAAGAAGACCAATGC
AGGTTTTAAACAACATACCCCTGCTATTCAGCCTCGAATCACACCAAAGG
ATAGTTTTAATATGGATATGAAGCAGCAGGATGAAAGGTTTCCTGATAGA
AAGAACTTCTCCACCAAGTTAAAGGCAAAGAAAAAAAATGAAATCGAACA
CTTAGGGTTTTTAAAGAAGGTGAAAATATTAGGAGAAGGAATCAAGACTC
TGAAGGAAAAGAAATCAGCAAGAGATAGTTTTGTATGTGGAGCTTGCGGT
CAGCTTGGTCACATGAGGACCAACAAGAATTGCCCCAAATATGGGGAAGA
TCCAGAAACTCAGCCTGAAACTAGAGATACAGAAAAGGCGTCAGGAAAAC
TTAATTCTCTGGATAAGACAGCTGTTTCGCAGCAGAGACCTCTACTGAAA
AAGAATACACCCAAAAGCATGGCAAAAATTCTTTTGGCAGAAACTCCTGA
AGAAGACAAGTCTAGTTCAAAGGCAAAAATTTTGAAGGTCAAATGTAGCT
CCACTGACAAGCTTCTAGATAAAGCAACTCCAGCCACCTCCCAGATTTCT
GATATGCCTTTAACATCAGATACAGATACCGCAAGTAGACCTACAGTTAA
AGTTAATAAAATAATTTTTGCTAATAAGACCAGACCTGAAGACACCCAGG
TCGAACAGCACAAGCCATCAATTGTGATAAAACCACCTGTGGAGACGGAT
AGAGAGCAGCCCCGTAAGAAGCTTATTATAAAACGACCAAAAGAACACAT
TGATAATGATCAGATCAGCCAGGAAGAAAGCACTGACCTAGATTCTCGAA
AGACCAAAAAAATAATTGAGCTGTCGAGTTTCGAGGATTATAGAGAGCAG
GATAGCAGTGTCCATTTTGCTGAAGCATCCAGAAGAAGAAATAGAGATAA
CAATCGAATGTGGGAAGAGGAGCAGAAGATGAGGGATGCGGAGAGAAAGA
GAGAAGAAAGGATAAGAAGGTTTCAAGAGGAGCAGGCAATCAAGCTAGAA
GAACAAGAAAGAGTAGCTAATATTAGAAGATATGAGGAAGTCATCAGAAT
AGAGAGGGAGGAAGAAGAACTACAGAAGGCAAATAAGAAGAAACAGAAGA
GTAAAAGAACTGACCTCAGAGATGACTATATGGATGACTTTCCCCCTCGA
AGAATTGATAGGAGGATTCCTGGAAGGGAGCGAACTGCAAAGAGGCAGTC
TGTGTTTGAGTCAGCAAGATATGGTGCCGAACATGCCCCCCCTACAAAGC
GTCGTAGAGGGGGAGGGGGAGAGGTTGGCTTGGCAAATATCTTAGAGAAT
ATTGTAGAGATTCTCAAGGAGAAGATAGAAATTTCGTACCTGTTTCTAAA
ACCAGTACTGAGAAAGGAAGCCCCTGACTACCATAGAATTGTGAAGAGAC
CTATGGATCTTTCTACAATCAAGGAGAAAGTCAGAAACTTGGAATACAAG
AGCCGCAGGGATTTCAGGCATGATATGTGGCAAATCACGTACAACGCTCA
CCTTTACAATGATAGGCGGAACCCTGGCATTCCACCACTTGCAGATCAGC
TTTTGGAGCTTTGTGACTACTTATTGGCTGAAAATGATGCAAGCTTGACC
GATGCTGAAGCTGGCATTGAAAGTGGTTAGGGTCATAAACCCTTGGTAGA
CAAGTTGAAAGAAAGCGGCAAAAAAGTAGATCAAGAAATGGAGGTAAAAG
ATGCCTTGGTGTGCATTGGTTTGCTAAATCATTTGCAGCCCCCACCATTG
CCTACAAAAGTATCTTGAAGTTGGGTTGCTTGACTGCATTCGTTAACAAA
CCTACCGCAGGTAAATTACCAGATCAGTTGTTTCCTGAACTTGATACCTC
CCTAGGCCCAGCTTCTCTGTTTGTATAGATTATGTTTTAGAACTGGGAAA
CTATGCCTTCGGCTCTGCAGCTGGTATTTTCAGACTCTGTAATTATGTAG
GAGTTCGATATTAGATTCTTCAGTACTTTAGTCTTGATATACACCCTCTG
ATTTCTTATACCATTGTATAAGTGACTATAGCCTTTTATCTTCGTTCAGA
GGATATCCTGTAATTTGTCCTGTTGGTACTTTTTTTTTTTTAAAGGTGAT
TTAGTTGAGACTTGAGA
MGLEQGSCSTSQDARDEDDEDEYEEAEGGNRLLGFMFGNVDGAGDLDIDY
LDEEAKEHLGALADKLGSSLTDINLSVRSVQTSADAIEQDYDEKAEDAVD
YEDIEEQYEGPEVQAITEEDYLLPKKDYISSQASAPVKGTTSLFDDENYD
EEESEKETEADENNAEVQTTNLSGDSDNHAVLSQVEDLRGDIVNGASETE
EPTPSLEDFLKEEDDILEELVDNQNMTPLPILYTEDGAVILRFSEIFGIH
KSSKKSEKRECRYSVPKDKYMSMGTADVLEDDDETFFKGLCQGFTWKCRT
HVNDDILPIKDNESDLETLQYVQHPGIVASVVDEDRRDTCLSDEPMKKDI
AIDPFLEKITPLSPELYLLEQQDWEDRIIWDNSPELSDRFAETLEISGHD
SGASFVENLESNIEEQHNHQELRMETDETSNAIFQRSYPVSVEPFGSRKI
SDLVSSARQFHPQLLRLESRLENGLDNGKDSSTTEEVGHRDAIRSYNKVS
LLNKDLLEGSWLDNVIWEPHQSMTKPKLILDLQDEQMLFEILNDKDGKHL
KRHAGAMIITRSVKFNGDLVETNGHGTLLGESFNIANDKFYSNRKSSQQL
KSHSKKRTAHGVKVLHSIPGLKLQTMKAKLSNKDIANFHRPKALWYPHDN
EVVLKEQGKLPTQGSMKIILKSLGGKGSKLHVDAEETIASVKAKASKKLD
FKPSEAVKIFYCGVELDDDKSLALQNVRPNSLLHLVRTKIHMLPRAQKVP
GENKSLRPPGAFKRKADLSVKDGHVFLMEYCEERPLLIGNVGMGARLCTY
YQKSSTGDQTGTSLRSGSSGLGNLLTLDPSDKSPFLGDIRASCSQSCIET
NMYRAPIFQHKVSSTDFLLVRSPKGKLSIRRIDRIDVVGQQEPHIEVMSP
SSKGVQMYTMNRLLVYLYREFRAAEKRGLRPSIRVDELSAQFPNMNEAFL
RKRLKHCADFQKQSNGLFWVMRRNFRIPLEEQLRRMVTPEDVCSYESMQA
GLYRLKRLGITRLTSPTGLSSAMNQLPDEAIALAAASHIERELQITPWNL
SSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYVRTAPKAPISNAVVK
KKAAVSRVSSTVTGTDADLRRLSMEAAREVLLKFNIPEEQIAKLTRWHRI
AMIRKLSSEQAAAGVKVDPTTISKYARGQRMSFLQLQQQTREKCQEIWDR
QVESLAAVDGEENESDVEANSDLDSFAGDLENLLDAEEFEEGEERNYESK
QNNADGVKGLKMRRHPSQAQAEEEFEDEAAEAAELCRMLMDDEEAERKKK
KKIRMVGQQLRQAQGSHGFDSVERVKKTNAGFKQHTPAIQPRITPKDSFN
MDMKQQDERFPDRKNFSTKLKAKKKNEIEHLGFLKKVKILGEGIKTLKEK
KSARDSFVCGACGQLGHMRTNKNCPKYGEDPETQPETRDTEKASGKLNSL
DKTAVSQQRPLLKKNTPKSMAKILLAETPEEDKSSSKAKILKVKCSSTDK
LLDKATPATSQISDMPLTSDTDTASRPTVKVNKIIFANKTRPEDTQVEQH
KPSIVIKPPVETDREQPRKKLIIKRPKEHIDNDQISQEESTDLDSRKTKK
IIELSSFEDYREQDSSVHFAEASRRRNRDNNRMWEEEQKMRDAERKREER
IRRFQEEQAIKLEEQERVANIRRYEEVIRIEREEEELQKANKKKQKSKRT
DLRDDYMDDFPPRRIDRRIPGRERTAKRQSVFESARYGAEHAPPTKRRRG
GGGEVGLANILENIVEILKEKIEISYLFLKPVLRKEAPDYHRIVKRPMDL
STIKEKVRNLEYKSRRDFRHDMWQITYNAHLYNDRRNPGIPPLADQLLEL
CDYLLAENDASLTDAEAGIESG
| Relationships |
|---|
| The mRNA, XM_017386051.1, is a part of gene, LOC108214203. |
| The polypeptide, XM_017386051.1, derives from mRNA, XM_017386051.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |