| 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. |
TTTTAAAAGTCCAGAAACACAAATAGAAATGAAAGTTATATAATTTTACT
TCCGTTTTATAACTCGGGAGAGCAGGACGTCCGTTTCACTTGTTTTCCAC
CCTTTTTATAACTCGGGAGCAGGGCGTCGGTGATGCTGGTGGACTCAGGT
CTAGCCGTCTAGCCGTATACAACACGGTGGCTAGTACATAGTACTCCTTT
TTTTGTTTGTTTCCATACTACATTGACTCTCAGTCTACCATGCCTGTCCT
TGTCTACCATACTTCCATTGACTCTCAGTCTACCACTAACAACATTGTTA
GTGTTGTACATGGTTGATTGAATTGAGCACTACATCTGCCAGGAGAATTT
TCAAACAAGCATCCACACCAGACCGCGGCACTCGAAACATCTTACAGGAT
GAGAGCAGCTGGAGTTAACAGATACTGGACTCATGTAATATCTTTGTTCC
TCATCTCCACATCTGCTGCTGCTGCTGCATCTGGTGGAAATGAAACGGAT
CAACTAGCATTGTTGGCCTTCAAAGCAAAGATTTCCGATGATCCTCTAGG
AGTGTTTAGCTCCTGGAATATGTCTCTCCATTTCTGCCTCTGGGAAGGTA
TTACATGCAACAAACAGCACCAAAGAGTCGTCAGCCTAAACCTCTCCTCG
ACAGGTCTGGTAGGTTCTTTGTGTCCTGATATAGGAAACATGAGTTTTCT
GCGTGAAATCGATCTTTACAACAACAGTCTTCAAGGCCCAATTCCTCAAG
AAGTAGACCGTCTTTTCAGGCTAAAAGTTCTAAGCTTAGGCCGTAATGAT
TTGGAAGGAAAGATACCAGGCACCATAGGACGTCTGAAAAGTTTATTCTT
TGTCGATATCTCTTCAAATGAACTCTCTGGTATGATCCCTACTTCAATTT
TCAATATCTCGTCATTGTCTTCCTTCAATTTGGCCAGTAATCAGCTTGAA
GGAAGTATACCATCAGACATCGGATTGACTCTTCCAAATCTGAAACTGAT
TCGGTTATCATATAACAAATTAACTGGAAGCATTCCTGCATCGCTCTCTA
ATGTTTCCAAACTTCAAGCTATTGAATTCCAGTCCAACAACTTAAGAGGC
CCTGTATCTGTGGATTTTGGAAGATTGCCGTATCTTCAATTACTACGCCT
GTCGTATAATAATCTAGGATCTGGAGAAGAGGGTAACTTGAGTTTTCTTG
ATCCACTCACCAATTGCAGCAGATTACTAATATTGGAACTAGAAAGCAAT
AATTTTCAAAGGTCATTGCCCAGTTCAATTGCTAATCTATCAACTACGCT
ACAAATCATAAGCTTAGCATATAATCAGATTTCTGGAAGCATCCCTTCCG
GGATAGGTAATTGTATCAGCTTGATTCTTTTATCTTTACAAGGCAACAAG
CTCACGGGCATTATTCCCTCTGAAATTGCTAGGCTCGGGAAATTGCAACG
AGTTATTCTTTCTAACAACATGCTTTCAGGGAGCATTCCTGCATCCATTG
GGAACTTATCTTTGCTGGACGAGATTCATTTAGAAGATAATCAATTACAG
GGAACAATTCCGGCTGGTTTTGGAAACTGTCCAATGTTGGTTTTCTTGGA
TTTGTCTCGAAATAACCTCAGTGGAACTATACCTCGTAACTTATTTTCTA
TTTCCCCATTTTCTGTGAAACTAAATCTTTCTCGAAATCATTTAGTTGGA
TCACTACCAGCAGCTATTGGAGCTTTGGGAACTGTAGTTGAATTGGATGT
CTCAGAAAATGAGTTTTCTGGTTTTATTCCAGTAGAGCTTGGTCGATGCA
TCTCCCTCAGTTCACTATACATGCAAGGGAACTTTATTCAAGGTTACATC
CCTGAATCATTGACAAATTTACGAGGTCTGCAATATATTGATTTTTCTCG
TAACAAATTATCTGAGAATATCCCCGATTTCTTTGGAGACCTAATCTACG
TGGAATATTTGAATCTGAGCTGCAATAATCTCGCAGGAAAGGTGCCAATG
ATAGGGGTATTTTCAAATGCAAGTGCATTTTCAATAGTAGGTAACAAAAA
GCTATGTGGAGGGATACCAGAACTGCGGCTCAAAAAATGCAGTAAAAAAT
ATATTGGAACATATAACCAAATTATGGCTTGGGGACAGGTTTTCATCTTG
ATAGGCTCTATACAAGATCTTCTTATCATCAGTTGCGTATTTATGTCATG
GCATAGAAGGAAAAGAAGGGAACAACTGAGATACTCAGCATCAAATGTAA
TGATATCCCCCAACAAAATGTCATATGAGCTACTCCGTCAAGCAACCAAG
GGATTTTCACGAACCAACTTAGTCAGCGAGAGTGGTTTTGGGTTAGTGTA
TAAAGGAAAACTTGATCTTAAATACATTGGGATACCTGAGGGGGAGAAAG
CAGCTATAGCAGTAAAGATATTTAACACTTTGAATGAAGAAGCGGCCAAC
TGTTTCATCACTGAGTGTGAAACCCTGAAAAATATTCGCCACAGAAATAT
TGTTAGAATCATAAGTACATGTGAGAACCACAAATTTAAAGCTATTGTTT
ACGACTTCATGAAGAATGGGAGTTTAGAAGGGTGGCTGCATTCAACAAGT
AAAGCATCTCATGATAAGCTCAACATGCCTCAAATACTGAACCTTGATAC
CAAAATAAACATAGCGATTGATGTGGCTAGTGCACTTGATTATCTACATA
CTCAATTGGCCAATCCCTTAATACATTGTAATCTGAAGCCAAGCAATATT
TTGCTAGATAGAAACATGACTGCACATGTATCAAATTTTGGACTAGCGAA
GTTTAATACTGAGTTCAGCCTTACAAGCCAAAGCATTTTAACTGGATTTG
AAGGAAACAGTGGATATGTACCTCCAGAGTATGGTCTGGGAAGCATGGTG
TCAACTAAGGGGGATGTCTACAGCTATGGAATAATTTTACTGGAGATGCT
GACAGGAAAAAAGATAACTGACCCTATGTTTCAAAATGGTTTTAAGCTTC
AGAACTTTGTTTCCAATGCCTTGTCTGATGGTATAAAGGGAATTGTCAAC
CCAGTCAATCTATTTGAACTTACAAGAGAGAATGCAGCAGAGGCGGAGGA
TTGTCTAAGTATACTTTTCAACATTGGTCTGAAATGTGCGCTGGACTTGC
CACAGTTTCGACCAGACATCAGTGATATCTTAAGCATGTTGGAAACAGTT
AGGATCATCTTCAAGGCCAATACAGGTAGTCCGGAGGCCTATGCTAACAA
AACTTCCCAAGCTGCAGTTTTGATGGCTCAAAGAAACATGAAATCTCTAT
TATTGTACGGGGACAAAAAGATGCCTCCAGATTCAAGATCAATGTCGATA
TCACCATCGGTCACACTGTCATTCATGGATATCCATAAAGCAACTAATGG
ACTGTCATCAACCAACTTACTAGGCGCAGGTGGTTTTGGCTCTGTTTATA
AAGCAACATTTCATCAAGAGAATGTTCGTCTTCTCTTAAGGAATAGTGGG
ATAGAAGATAGGATTGGAACAGCTGTTGCAATTAAAGTATTTAACCTTCA
GCGTAGAGGTGCAGCAAGAAGTTTCAAGACCGAGTATAAAATCTTAAGAA
ACATTAGCCACATGAATCTTGTAAAGGTTATAACTGCATGTACAAGTAAA
GATCTGGAGGGTAACGATTTTCAAGCTATTCTTTATGAGTTCATGGATAA
TGGGAGTTTAGAAATGTGGCTGCATCCAACAAATAAAACATACCATGATG
GAGCCATCAGACCTCGAATACTCAGCCTACATGCCAGAATAAATTTAGTG
ATTGGGATAGCCTGTGCACTCAGTTATCTTCATTATCAATGTAAGAATTG
CATAATTCATTGTGACCTAAAACCAAGCAACATTTTGTTAGACAAAAACA
TGGTCGCGCGTATTGCAGATTTTGGGCTGGCAATTTCTCTTCCTGAATCC
CCAACTCTGAACCAAGGTAGCCAGTCCAGTGGATTACGAGGAACCACTGG
ATATATAGCTCCAGAGTATGGACTAGGATGCAAAATGACAACCAAGGGCG
ACACATACAGTTTTGGGATTTTGTTATTGGAGATTTTGACAAGGAGGAAG
CCTACTCATCGTATGTTTCGTGGAGGTCTTAACCTTCACAACTTTGTTTG
GATGGCTATGCCTGACAATGTGATGGACATTATTGACCCGCTTATGATGG
TAACGGCATCTGCAAATGAAGGGAATGAGAAACAAGTAGAGGAATGCCTG
ACTAGATTGTTCAGTATTGGTTTAGCATGCTCTAAGCCATCGCCGAAGGA
TCGGCCAAGCATGCTTTCCATACTACATGAGCTGGAGTCTATTAGGAACA
GCTTCTACATTAATTAGTATGTGTTGCCTCACTTTTTAAACTAATTACAT
GAACTTTACTACCTTAATACTGATTTGTACTATGCATGATAATATCACTA
AAGATCACTTGCATATTTTATGGACGTTGAAAGAATTATTTCTTTATTTA
TTGATGTATGTTATTTTTTTTTTCTAAGAAATAGGTTAATTTCCTGTAAA
AGAAACATACTGTAGTT
MRAAGVNRYWTHVISLFLISTSAAAAASGGNETDQLALLAFKAKISDDPL
GVFSSWNMSLHFCLWEGITCNKQHQRVVSLNLSSTGLVGSLCPDIGNMSF
LREIDLYNNSLQGPIPQEVDRLFRLKVLSLGRNDLEGKIPGTIGRLKSLF
FVDISSNELSGMIPTSIFNISSLSSFNLASNQLEGSIPSDIGLTLPNLKL
IRLSYNKLTGSIPASLSNVSKLQAIEFQSNNLRGPVSVDFGRLPYLQLLR
LSYNNLGSGEEGNLSFLDPLTNCSRLLILELESNNFQRSLPSSIANLSTT
LQIISLAYNQISGSIPSGIGNCISLILLSLQGNKLTGIIPSEIARLGKLQ
RVILSNNMLSGSIPASIGNLSLLDEIHLEDNQLQGTIPAGFGNCPMLVFL
DLSRNNLSGTIPRNLFSISPFSVKLNLSRNHLVGSLPAAIGALGTVVELD
VSENEFSGFIPVELGRCISLSSLYMQGNFIQGYIPESLTNLRGLQYIDFS
RNKLSENIPDFFGDLIYVEYLNLSCNNLAGKVPMIGVFSNASAFSIVGNK
KLCGGIPELRLKKCSKKYIGTYNQIMAWGQVFILIGSIQDLLIISCVFMS
WHRRKRREQLRYSASNVMISPNKMSYELLRQATKGFSRTNLVSESGFGLV
YKGKLDLKYIGIPEGEKAAIAVKIFNTLNEEAANCFITECETLKNIRHRN
IVRIISTCENHKFKAIVYDFMKNGSLEGWLHSTSKASHDKLNMPQILNLD
TKINIAIDVASALDYLHTQLANPLIHCNLKPSNILLDRNMTAHVSNFGLA
KFNTEFSLTSQSILTGFEGNSGYVPPEYGLGSMVSTKGDVYSYGIILLEM
LTGKKITDPMFQNGFKLQNFVSNALSDGIKGIVNPVNLFELTRENAAEAE
DCLSILFNIGLKCALDLPQFRPDISDILSMLETVRIIFKANTGSPEAYAN
KTSQAAVLMAQRNMKSLLLYGDKKMPPDSRSMSISPSVTLSFMDIHKATN
GLSSTNLLGAGGFGSVYKATFHQENVRLLLRNSGIEDRIGTAVAIKVFNL
QRRGAARSFKTEYKILRNISHMNLVKVITACTSKDLEGNDFQAILYEFMD
NGSLEMWLHPTNKTYHDGAIRPRILSLHARINLVIGIACALSYLHYQCKN
CIIHCDLKPSNILLDKNMVARIADFGLAISLPESPTLNQGSQSSGLRGTT
GYIAPEYGLGCKMTTKGDTYSFGILLLEILTRRKPTHRMFRGGLNLHNFV
WMAMPDNVMDIIDPLMMVTASANEGNEKQVEECLTRLFSIGLACSKPSPK
DRPSMLSILHELESIRNSFYIN
| Relationships |
|---|
| The mRNA, XM_017364786.1, is a part of gene, LOC108197226. |
| The polypeptide, XM_017364786.1, derives from mRNA, XM_017364786.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |