| 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. |
ACAAACGCGATCATTAATCCACTCCCCGTTTCACTTTCCTTTTTCAGCAC
ATTTCAAACACTCTCTTTCTAGAGAGAGAAACACTCGCCGCGCTTCTAGA
GAGAGAAACACTCGCCGCGCTTCTAGAGAGAGAAACACTCGCCGCGCTTC
TAGAGAGAGAAACACTGCAAACTCACCCTAACCTAGCCCCCATGGAAACT
ATCTCACCTCCACTTCACAAAAAAAGCTACCGCTCCGGCAATGTCGCCGC
CGGGAAGACGCCGTACGACGACGTTTTCGCGGCTCGGCCGAAGGTCAAAG
TTCCGACTCTCTCTCCTCGCGACGAGGACTACTCCGAGATTTTCGAGGTG
TTTCACGCTTCCCGAGGCTCTTCTATTCCTGTGCTTGATCTTCCTGCTGT
TGGTGAAGATGAGGATCCTGATGTTTACTTTGATGTTCGGAGCTCAGGGT
TTGACTACTCCGAAGTTTTCGGGAGCTCTAACGGTTTCGATTTCGCGCTG
TACGAGCAGCTGTTTCAGCAATCCAAAGCTGATAATGATTCGTCTAATGA
AGTTTGGACTCCAGCTCAAAGTGAATCTCTCTCAGATGAATCAGATCCTT
CTGGTTGCTCTGAAAAGAATCAAAGCTTGTCAAGTGGAGATATACACCAG
TCATATGATGATACAAAGCAGTTCAACATATCATATCACAAGGCCAATCC
AAAAGGCAAGGATAATATATTAGATGCGATGACACATGTTACTCAGTTAG
ATGCTATTCCTGGATATAGCTTCATTATCAGTGACACCTCACCGTCGAAA
CATGTAGAAGTTGAAAGTTTACCCGTGCAGATTGAGAGGAACACAGATTG
TGGTGGAGCAGTTACAGAAGGAAAACGACTTAGGAAAACAGTATCACAAC
CCCCGATCAGTGATATTGGTTTACAAGGTTGTAAAACCGAAGCCAGTGTT
TTGGCTCACAATGACAAATCCAGGTCTCCAGGGAAGGCATTTATATCTGT
GTCTGATGTAAACCTCAGGACTCGACCTTCTCATTTGCCACCCCCCTCAA
GACCACCACCCTTGTTTGCTGACAGAGCCGAGAACTCCAGTAGACTAAAT
TCGAAATTCAAAGCTTCCAAAAGTTATGTATTTGAAAGGACAAATGCTGG
CGATTCACAACCTTATTTTGACGTGGAAATAGATGCAAGTTCGTCAGCTG
CAGCATCTGCTGCGGCTGTAAAAGATGCAGTGGAGAGAGCTCAGGAGCAA
CTAAGTAATGCGAAAGAAATGATGGAGAGGAAGAAGGATGGTCTCGAAAA
CCGTACAAAGTCACATTTCAAGAAGGATATAGGTCAGAGGGGTGAAAAGA
ACATCAAATTTGATATGTTGAAAAGTTCTAAAGGTGACATATTTTCTCCT
AAATATGCAAGAGAAGGAAGTGAAATTAAAACTTTTGCTGAAGAAAATGA
AAAAAAGGCGAGGAACATGATCCATGTTGCCTCAAGTGCAACAGAAGGAA
AAGAAGATATACACAGTAAACAGGGGAAAGAACATATGCAGTCTCAAGTA
CCACATGAAACTGAAGGAACTGTTGCATGGAGAGAAGCAACTCAATTATA
TGAAGTGGTCGAAGAAAAGAAAATTAGTGAGGCATGTAGATCAGCAGATC
ATTCAACGTCTAGTGACTCTGGAGTTGGTGAAACAGGTATTGCCACTGCT
GTTGAGCTACAAGAATGTCAAATGCAAACAAAAGCAACCTCGGCGGACCA
TGAATGTCAAGGAAATGTGGAGAAATTTGAAGTGTTCAAGGGTGGCCATG
AACAGGTAAAAATTAAAGCAGCCCAAGGATCAATTTGGCAGGAAGAGCAT
CAGGAGAAATCAAAATTGGCGCAGATGGGTGATGAATGTCAACATATGGA
CAAGGAAACCAGAGGGGCTTTACAACCTGGAGAAACAAATGACAAAGCAA
ATGCGGTTGATAAATATGAGAATGATGATATCGGGACACAAGATCAGTTA
GAAGAAAATGAGGTGATTTTTATACAGAAAATTGTGGGGGCTAATGAAAG
CTATGAAAAGGTAATCGAAATTATGGAAGCTCCTGAACGGAAAGGTAGTG
GAATGGAAAGAACTGCATCTTTCGACAGCATTGAAAATACAATAAAATTT
AGCGCAGATGTTAAACAAGAGCGAGGAAAATTCAATGAGGCCACAAGGCA
GAGTGCCAAAGACAAGCTGGAAAAAGAAGTTTTTGAAAATCATGGAAATG
AGAGTAAACATGTGAAGACTTATGAAATGGGACAGAATAAGGAAAAACAA
GATGAAGTGGCTGAGTGTAAGGGAAAAACAAATCAATTGGAAGAGGTTTT
TGAGCAAGAAGAGAGCAACAATAGACTAGGAGTTGATCTTAAATGGCAAG
AATGCAAGAAAGAACAGAACTTTGTCAGTGAAGCAGAAAAGATTGAGAAG
GGTTCTAAAATTACTATTGAGCAGTGGCAGAATACAGAAAGAGAAGAGAA
GGCTTCTGAAGAAGCGGCAAGTGAGGAGCGGCCAAATGATTTGAGTGAAC
AAGATGAGACTGAGAAGAGACTCAAAGAGGCCTGGGAGAAGAAAGAAAAA
TGGAAAAGATCACGCGAGGCTCGTGAAAGTGAGAAGAGGGTAGAATTGTT
GTTTAAGGAGGATGAGATAATGGATAGATCAAGTGAAGCCAATGTGTGGA
TCAAAGAAGGAAAAGGCGAAGGATTTATTGAACACGACATTGTTCAGGAG
CAACTTATGAGGGTAGTAAGCGATGGGATACTGAATTTGAACCAAGGAAA
CTATACTACAATGGAGGAACCCAAGATATTTGATGGTGGAAGCGGGCATA
TTCACGAGCCTTCTGTGCCCGTGGAAAATGAAAGCTTAGAAATGGAGCAC
AAAACTCATGAAAGGGAAGTTGAAGTTAATAATGAGCCCCAAGAAGCAAA
TGTTAACTCTAACCTGGATCAAAATGGCTTGCAATATGAAGGAATTAATG
ACAAAAATAAAGACGAGCCACTTTGTCAAATTGGCATCACGGATATGTAT
AATGAAGATGGCATTGATCAAACAACAGGAATACACATTAAGAAAACTAG
TGGAACTAATGAAATGGCTTCTGATATTGAGAATGCAAACATTTCAACGC
ATACACGGAGAGAGGCAAGGAGGAACTTCAAAGGTATCCAACCCGACCAA
CACGCTTTTAACCAGGCAGAAAATGAGGATAAATTCACGGCACCTCGAGT
GGTGAAGAAGTCCGTCGAAAATGAAAGAAAACCGGGTAATGTTCTGCCAG
CTAAAAAGTTTACTAGCCAAAATCCAGAAGTAGAAGAGACTAATTTTCAA
AAGAAGACTAGATTAGAAGAAAGGGAAAAAGAAAGATTAGAAAAGGAAAG
AGATCTGGAAAATGATTTCTTAAGAAAGCTAGAAGAAGAGAAAGAGAGAG
AAAGAGAAAGAGAAAAGGATCGCATGGGTGTTGATACAGCTACTCGTGAA
GCTCGTGAAAGGGCATTCGCTGATACTAGGGAAAGGGCAGAAAGGGCAGC
AGTTGAAAGAGCAACTGCTGAAGTTCGACAAAGAGCACTGGCAGAAGCCC
GGGAAAGATTAGAGAAGGCATCTGCAGAGGCTAGGGAGAGGCTAATTGCT
GATAAGGCTTCAGATGCCAGGCTCAAGGCTGAGCGTGCTGCAGTAGAAAG
AGCAACTGCTGAGGCTCGAGAACGTGCTATTGAAAAAGCAAAGGCTGAGA
AGGCTTCTTATGAGTCACGTGACCGAGTAGAGAGACCTGTGACTGACAAA
TTTTCTGCTTATTCCAGGAATGGTGGATTCAGACAGTGCTCTTCATCCAA
TAACCTGCAACATCAGGGGATGGGGCCTTCCCGTGATTTGAAACATTCGC
ACTCTTCGGTTTCTGGTGGACTTGAAGGTGAATCAGCTCAGAGGTGTAAA
GCTCGATTAGAGAGATATCAGAGAACAGCTGAGCGTGCTGCAAAAGCTCT
GGCGGAGAAGAATATGCGTGATCTTATAGCTCATAGAGAGCAAATAGAGA
GAAGTAGACTCGCAGAATCCCTGGATGCTGATGTTAAACGATGGTCAAGT
GGGAAAGAAGGGAATTTGCGTGCTTTGCTTTCAACATTACAATATATCTT
GGGGCCTAATAGCGGCTGGCAGCCCATACCACTAACTGATGTGATAACTG
CTGCTGCTGTAAAGAAAGCTTACAGAAAAGCCACTCTTTGTGTTCACCCT
GACAAATTACAGCAACGGGGTGCTAGTATACATCAAAAGTACATATGTGA
AAAGGTTTTTGATCTTCTCAAGGAAGCATGGAACAAGTTCAACTCAGAGG
AGAGATAGACAGGCTTTCATCTGCGTGTACACAGTAGCACTTAAGTTACC
CCACATTATGTAATTATGCCGTCAGGTAGCAAATCTTTGTTTCTTATAGG
TTGCTTATCTAGTTTCTATGTAAACTTTAAGTTTCCAAGGAACAGGGAAC
AGGATAGATTAGTAAACGAAAAAGATATCCTCTTTTCTTGAACCTGTTAG
TCGGATAATGATCCTCTTAATTTGTTGGACTTTGTTCCAGTGGACATATG
GAGAACTTGGTGACTAAAA
METISPPLHKKSYRSGNVAAGKTPYDDVFAARPKVKVPTLSPRDEDYSEI
FEVFHASRGSSIPVLDLPAVGEDEDPDVYFDVRSSGFDYSEVFGSSNGFD
FALYEQLFQQSKADNDSSNEVWTPAQSESLSDESDPSGCSEKNQSLSSGD
IHQSYDDTKQFNISYHKANPKGKDNILDAMTHVTQLDAIPGYSFIISDTS
PSKHVEVESLPVQIERNTDCGGAVTEGKRLRKTVSQPPISDIGLQGCKTE
ASVLAHNDKSRSPGKAFISVSDVNLRTRPSHLPPPSRPPPLFADRAENSS
RLNSKFKASKSYVFERTNAGDSQPYFDVEIDASSSAAASAAAVKDAVERA
QEQLSNAKEMMERKKDGLENRTKSHFKKDIGQRGEKNIKFDMLKSSKGDI
FSPKYAREGSEIKTFAEENEKKARNMIHVASSATEGKEDIHSKQGKEHMQ
SQVPHETEGTVAWREATQLYEVVEEKKISEACRSADHSTSSDSGVGETGI
ATAVELQECQMQTKATSADHECQGNVEKFEVFKGGHEQVKIKAAQGSIWQ
EEHQEKSKLAQMGDECQHMDKETRGALQPGETNDKANAVDKYENDDIGTQ
DQLEENEVIFIQKIVGANESYEKVIEIMEAPERKGSGMERTASFDSIENT
IKFSADVKQERGKFNEATRQSAKDKLEKEVFENHGNESKHVKTYEMGQNK
EKQDEVAECKGKTNQLEEVFEQEESNNRLGVDLKWQECKKEQNFVSEAEK
IEKGSKITIEQWQNTEREEKASEEAASEERPNDLSEQDETEKRLKEAWEK
KEKWKRSREARESEKRVELLFKEDEIMDRSSEANVWIKEGKGEGFIEHDI
VQEQLMRVVSDGILNLNQGNYTTMEEPKIFDGGSGHIHEPSVPVENESLE
MEHKTHEREVEVNNEPQEANVNSNLDQNGLQYEGINDKNKDEPLCQIGIT
DMYNEDGIDQTTGIHIKKTSGTNEMASDIENANISTHTRREARRNFKGIQ
PDQHAFNQAENEDKFTAPRVVKKSVENERKPGNVLPAKKFTSQNPEVEET
NFQKKTRLEEREKERLEKERDLENDFLRKLEEEKEREREREKDRMGVDTA
TREARERAFADTRERAERAAVERATAEVRQRALAEARERLEKASAEARER
LIADKASDARLKAERAAVERATAEARERAIEKAKAEKASYESRDRVERPV
TDKFSAYSRNGGFRQCSSSNNLQHQGMGPSRDLKHSHSSVSGGLEGESAQ
RCKARLERYQRTAERAAKALAEKNMRDLIAHREQIERSRLAESLDADVKR
WSSGKEGNLRALLSTLQYILGPNSGWQPIPLTDVITAAAVKKAYRKATLC
VHPDKLQQRGASIHQKYICEKVFDLLKEAWNKFNSEER
| Relationships |
|---|
| The mRNA, XM_017363001.1, is a part of gene, LOC108195963. |
| The polypeptide, XM_017363001.1, derives from mRNA, XM_017363001.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |