| 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. |
CCAACCCACTCAGTTTGTCTTCCCATCTTAAAACAAAACAAACATATTTC
TCAATCCGCGTGTGCCCTTTTCCGTCATTTCGCACCCTCCCTCAGCAATT
ACACACTGCTCATCATCGTCTTCCTCATACACGCATATATAGACACGCAT
ATTATCTGTGTATTATTATCGATTATTCGGCTTCTCCAAACCCTAGCTTT
CGCCGAGGTGATTTCTCATCCATTTTTCGATTTTGAATGGTAGGTTGATA
TTTGTATGACGAGTGGTGATTTGTTATGTTGAATGGTGATTGAGACACGT
AGAGTAAACTGTTTAAGATTTGATTCCGAGATGTCCTCTAAGAATAGGGA
GAGTATGTCGACTGATGAAGATGAGTTTTTGGATGATGTTTTTTCGGATG
AGGAGGATGACGATGATGATGAATTTAATGATTGTGATTCTGGCGCGGGT
TCTGATGACTTTGATTTGTTAGAATTGGGGGAAACTGGAGCAGAGTATGT
ACAAGTTGGGGATCAGACTTGTAGTATTCCGTTGGAGTTGTATGATCTTT
CCGGGTTTGGTGATATTTTGTCTATGGATGTGTGGAATGATGTTTTGACA
GAGGAAGAAAGGTTTGATCTGACAAAGTTTCTACCAGATATGGATCAAGA
GATGTTTATGCGGACGTTGAAGGAGCTGTTTACAGGTTGTAATATGCATT
TTGGTAATCCCCTTGATAAGCTTTTTAAATTGTTTAAAGGTGGGCTATGT
GAACCACGGGTTGCACTTTATAGGCAGGGTTCGATTTTCTTTCAGAACTG
CAACCATTATCATCATCTCCAGAAGTATCAGAACTCGATGGTCACTAATT
TTCATCAGATAAAGGATGCTTGGGCGAATTGCAAGGGATACAGCATTGAA
GAGAAGATCCGAGTGTTGAATATTATGAAAAGTCAAAAGAGCTTAATGCA
TGAAGATATGGAAGACTTGGAAACTGACTCGGAAAGGGAAGAATCGGTAG
ATGGCATTTGGAATAGGAGGCTGATGAACCAGAAAGTAGGACAGAAAATA
AGTCATTATTCTGAGGAAAAGCTGAGTTCAGCCTTTGGTTACTCTTCTCG
AGAGAAGCAGGTGGCACTTGATACAGCACATTATGAAAGGCAAAATCCAA
AAGGGACCTTGAAAGTAACTGGGTCGAAGAAATCTGCTTCAAAAGAATCA
GCAGGTTGTTACTCTGCTGGTCGTCAGGGCATGAAAATGAGGTCAAGCCC
TTATGGTTTTGCATCAACTTCTTCAAGATATGACATGGCTTCTGGAAACA
ATTCACACGCTGCTTTCAGGATGAGAAATCGGGTACCAGATGATAATACT
GACGGAGAAGCATTGTATAAAGTAGCTGTCCAGAGCAATCGGAGTTTCCT
AAGCACTAGTCGAAAGGATGATCCTGCTAACTCTAAAGTTTCGGAGAAGT
ATGAAAATTACGGAGGTGATAAATATTCTGATATCTTCACAGGCTTACCT
TTGTCTTCAAAAAAGGATTTTTCTGCCTACAATAGGAACAGAACTGTGAA
TCAGTTATCAGATATTGAGTTGTTAACAACAAAGCCATCTAAATCTGTGT
TTTCTCATGAATACGTCAACAATCTTGAATCCCCTGATAACATGCAGCAC
TTAAATGTTGGTGAGAGAGTGAAGTTTGAGAAAGGGCACTCTTCAAATTT
ATTGTTGAAAGGAAATCGGGCTGAGTTATCAGATAGAGGTGATCCCTTTC
GGCATGGGATAGCTAAAGAAGAGCATTTCTCAACTGATTTATCACCTAAA
TATGGTAATTTAAATGTTAAAAGCAAGTCCAAGTTTGAAAAGAACTCTCC
TGATATTAAAGTGAATGATAGATCTGGTTCAGGGTATAGAGAGAATTCAA
AACATGAGAACAGGGGCGCGATAGCTAATCAGGATGGACGACGAGTTGTG
CCAAATGTAAAGCGCCGAAAAACTTTCACTTCAGATTCAGACTCATCTGA
GCAATATGAGGATGATAATCCTTTGATGAGGAGCAAGTGGGCTTATCCCG
GTGGTGCCTCAGGTATGAAATCTGTTTCATTTCCTAAGCAGGCTAAATTT
GTCAAAGGGGATGAAAAGATTGATGGATGTGGTGATGAAATTTCCAACAT
CCAGAAGAAGATGGGTTTCCATGGTACACATTCATATATTTCAGAAGACA
ATTTCAGCATGAAAGCAAAACAAAAGAATAAGATGGATGATATTGGCAGA
AATTTTCCTGGACCAGGTAGGATGACTGGTTATAATTACGATGATGATTG
GGGAGAGTGGTCCAAGTTTGGTAGGAATGGTCATGTACAAAATGAACAGA
GCGAAAGGATTTTAATGGCATCCGTGCCTCCTTACAATGTTGGCAGGATG
GAGAAAATAGAGACCATGCATGGCTACTCAATGGCTGACAATGAAGATGA
TTCACTTAAAAGTATATTGGCAAAGCATAACAACACTTCTGGTAAGATGC
AAAATAAAGGTAAAGATATTGGAGCAAGGGACCGACATTTTGAAAGATCT
GACATGCAGTTATTAGAATGCAATTCTTCGATGAAAAAGCGGAAAGTTAA
GGATGATATGATGATAAACGTAACTGAGCCAAATGAAATTGGTACTCCTG
AAAAAGGAGTTTCTGATCTATCTTCTACTGTAGTGTTAGCTGGAGAAGAT
GTCGAAAGCAAATCAGTGAAGAAGCAATTTACATTGATTACTCCTACTGT
TGATGCTGAATTTTCGTTCTCAATCATTCATCTTCTGTCAGCTGTTCGCA
TGGCAATGACAACCATACTTCCTGATGATCCCGTGGACATGGGAAAGCAT
AATGGCAACAATAATGGAGTGCTGAAAGATGATGATGAGGAGAGTAAGCA
GGAGGGCATTGGTGGGGAACTATCTCACCTAAACAGGGATATAATGAACA
CTGAGCGAACAACCGAGCTGAATCTTCCATCTCTTACTGTTCAGGATATT
GTTAACCGTGTAAAATCAAATCCAGGAGATCCTTGTATTCTTGAGACTCA
AGAGCCACTTCAGGATTTGGTCATAGGTGTTCTTAAATTATTATCATCTA
AATCACCTCCTTTAGGAGCAAAAGGTTGGAAAGCAGTCTTGAAATATGAA
AAATCTACAAAATCCTGGTCCTGGATTGGTCCACGGAGTCCTTCAGATCA
GGAAACTACCGAGGAGGTGACATCTCCTGAAGCTTGGGGTCTCCCACGGA
AAATGCTAGTTAAGCTAGTCGACTCATTTGCAAATTGGTTGGAAAGTAGT
CAAGAGACCCTCCGACTAATTGGAAGTCTTCCTGCCCCTCCGTTGACATT
AATGCAGCTTAACATTGATGAGAAAGAAAGGTTTAAGGACTTGAGAGCTC
AGAAGAGTCTAAACACCATAAGCCAAAGCTGTGACGAGGTAAGAAGTTAT
TTTCGCAAGGAGGAAGTTCTCAGATACGCAATACCTGACAGGGCCTTCTG
CTACACTGCTGCTGATGGTAAAAAATCCTTTGTAGCTCCCTTAAGAAGGT
GTGGTGGTAAACTAACATCAAAAGCCCGAGAGCACTTTTTGTTGAAGCAG
GATCGCCCGCCGCATGTTACAATTCTTTGCCTTGTCAGAGATGCAGCTGC
TAGGTTGCCTGGAAGTATTGGAACAAGGGCTGATGTCTGTACTTTAATTA
GAGATTCCCAGTATGTAGTGGAAGATGTCTCTGATGCACAAGTCAATCAA
GTTGTTAGTGGGGCCTTGGATCGTCTGCATTATGAACGTGATCCTTGTGT
TCAATTTGATGGTGAGAGGAAATTATGGATGTATTTGCATAGAGACAGAG
AAGAGGAAGATTTTGAGGATGATGGGACGTCATCTACTAAAAAGTGGAAG
AGGCCAAAAAAAGAAGCTCCTGACTCATCTGAACGGGGATTGGTGACTGT
GGCTAATAATGCGAGTATAGAAGGGGGCCAAACTCAGATTGAACCAAGCT
CTAATCTTATTGTTGACTCTACATGCATGGATGAAGATAAAAGGGTGGAT
CATCTGTATTATAATGATGGGCAGAATGAAGTCAACCTTGAGGGTCTTGA
CCAGCCTGGGATACATTATAGCTCTGATCTTATTGTTGACCCTTCCGGCA
TGGTTGACCATAAAATGGTAGATCATTTGCATTATGATGATAGACATATG
GAAGTCAACATTGGGGGTCTTGGCCTAATTGGGATTCGTTCAGGCTCTGG
TCTTAATGTTGATACTTCATGTATGGATGATGGTAGAAGGGTGGATCATT
TGCAGTATAGTGATAAACATATGGAAGTTAGCATTGAGTGTCTTGACCAA
ACTGGGATTCATTTAAGCTCTGAAGTTCGTGTTGACCCTTTATGCATAGC
TGATAATAAAAGAATGGATCATTTGAATTACAATGATAGAGAAATGGAAG
TTAACATTGATGGTCTCGAATCTAAGCAAGGGATCATGGACCAAGGTCCT
CCAATGGTGTGGCAGGCTCATGGCTTAAATTCCATCCAGGAGAACAGCTT
GTTATGCATAGAAAATTCCAGACCCGGTGATTTTGACAATAGGAATTTGG
GCAGATGAAACCAGCTTATGTTAGGAAGAAGCTCATCCGGAATAATGCTC
AAGGTGAGCTAGTGTTTCTCAGCCCCTACTCCAAATCAGCTGGTCATAGA
TTTAGTTGGATTTGGCTGTTGGTATTTTTGTGAACTATCTTATCTGTAGT
GTCAATTATTTTGCCTTTTTAAGTGATACTGTGTAGTGGAAGCAAGCAGC
AATAATAATATCTCTGGTGGTAATAAATAAAAATAGAACTTTAAGACCAA
MVIETRRVNCLRFDSEMSSKNRESMSTDEDEFLDDVFSDEEDDDDDEFND
CDSGAGSDDFDLLELGETGAEYVQVGDQTCSIPLELYDLSGFGDILSMDV
WNDVLTEEERFDLTKFLPDMDQEMFMRTLKELFTGCNMHFGNPLDKLFKL
FKGGLCEPRVALYRQGSIFFQNCNHYHHLQKYQNSMVTNFHQIKDAWANC
KGYSIEEKIRVLNIMKSQKSLMHEDMEDLETDSEREESVDGIWNRRLMNQ
KVGQKISHYSEEKLSSAFGYSSREKQVALDTAHYERQNPKGTLKVTGSKK
SASKESAGCYSAGRQGMKMRSSPYGFASTSSRYDMASGNNSHAAFRMRNR
VPDDNTDGEALYKVAVQSNRSFLSTSRKDDPANSKVSEKYENYGGDKYSD
IFTGLPLSSKKDFSAYNRNRTVNQLSDIELLTTKPSKSVFSHEYVNNLES
PDNMQHLNVGERVKFEKGHSSNLLLKGNRAELSDRGDPFRHGIAKEEHFS
TDLSPKYGNLNVKSKSKFEKNSPDIKVNDRSGSGYRENSKHENRGAIANQ
DGRRVVPNVKRRKTFTSDSDSSEQYEDDNPLMRSKWAYPGGASGMKSVSF
PKQAKFVKGDEKIDGCGDEISNIQKKMGFHGTHSYISEDNFSMKAKQKNK
MDDIGRNFPGPGRMTGYNYDDDWGEWSKFGRNGHVQNEQSERILMASVPP
YNVGRMEKIETMHGYSMADNEDDSLKSILAKHNNTSGKMQNKGKDIGARD
RHFERSDMQLLECNSSMKKRKVKDDMMINVTEPNEIGTPEKGVSDLSSTV
VLAGEDVESKSVKKQFTLITPTVDAEFSFSIIHLLSAVRMAMTTILPDDP
VDMGKHNGNNNGVLKDDDEESKQEGIGGELSHLNRDIMNTERTTELNLPS
LTVQDIVNRVKSNPGDPCILETQEPLQDLVIGVLKLLSSKSPPLGAKGWK
AVLKYEKSTKSWSWIGPRSPSDQETTEEVTSPEAWGLPRKMLVKLVDSFA
NWLESSQETLRLIGSLPAPPLTLMQLNIDEKERFKDLRAQKSLNTISQSC
DEVRSYFRKEEVLRYAIPDRAFCYTAADGKKSFVAPLRRCGGKLTSKARE
HFLLKQDRPPHVTILCLVRDAAARLPGSIGTRADVCTLIRDSQYVVEDVS
DAQVNQVVSGALDRLHYERDPCVQFDGERKLWMYLHRDREEEDFEDDGTS
STKKWKRPKKEAPDSSERGLVTVANNASIEGGQTQIEPSSNLIVDSTCMD
EDKRVDHLYYNDGQNEVNLEGLDQPGIHYSSDLIVDPSGMVDHKMVDHLH
YDDRHMEVNIGGLGLIGIRSGSGLNVDTSCMDDGRRVDHLQYSDKHMEVS
IECLDQTGIHLSSEVRVDPLCIADNKRMDHLNYNDREMEVNIDGLESKQG
IMDQGPPMVWQAHGLNSIQENSLLCIENSRPGDFDNRNLGR
| Relationships |
|---|
| The mRNA, XM_017395868.1, is a part of gene, LOC108221994. |
| The polypeptide, XM_017395868.1, derives from mRNA, XM_017395868.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |