| 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. |
AAGAGTAAAGGAGCTCCGAAGTAGAAAAACAGAGTAGAGCAGAGAGCCAG
GGACTAGTAGTATACGGTATAGTTCGCGTATCTAGGGATCCCTACGATCC
CGTTAGGTGCTCTATCACTGTCGCATACTCTCCAAGTTTGTTTCAACCTG
TTCAAACAAACCCCCGATTTATACATACACACACCACTACACCCTCTCTC
CCTCTATCTACTCCACCATTGCCTCCCTGCTACCTATCTCTCCTCTCTCA
TGGAGAATTCGTCTCCAAACGGGCATCGTTTTAGAAGAATTTCCCGTCAG
TCCTTCGCTGGTAGTCTGAACTTAGATCCACTGCTTGATGAAAACTTGGA
ACAGTGGCCACATCTTAGTGAACTTGTTCAGTGCTACAGAACTGATTGGG
TGAAGGATGATAACAAGTATGGGCATTATGAGAGCATCGGCCCAATATCA
TTTCAAAATCAAATTTTCGAGGGACCTGATACTGATATTGAAACAGAAAT
GCATCTTGCTAATGCAAGGCAAAATAAGATCGATGATACTGATGACGACA
TCCCAAGTACTTCTGGGAGGCAGTTTACAGATGCCGCCTCCAAGTCATCA
AGCTTAAATGTTTTAAAGCATTTGGGAGAATCCCCACTGCCCACTTATGA
ACCTGTTTTTGACTGGGAAACTGAGAGGTCGACAATATTTGGGCAAAGGA
TCCCAGAAACTCAGCTAGCGCAATATGCCAGTGGATTGAAGATATCAGTT
AAAGTCCATTCCTTGTCATTTCAAGCGGGACTAGTGGAGCCATTTTACGG
CACTATCTGTTTGTATAACAAGGAAAGGAGGGAGAAACTCTCAGAGGACT
TCATTTTTTCTGCATTACCCACAGAAATGCAGGAGGCTAGCAGTTCCTAT
GAACCTCGTGGTATTTTTTATTTAGATACCCCATCAGCATCAGTTTGTCT
TCTGATCCAGTTAGAGAAGCCTGCCACAGAAGAAGGTGGGGTAACTCCCT
CTGTTTATTCACGTAAAGAACCGGTCCACATGACTGAGAGAGAAAAGCAG
AAACTCCAAGTGTGGTCCCGCATCATGCCCTACAGGGAATCTTTCGCCTG
GGCTATTATTCCATTGTTTGATAGCAATATTAATTCTTCCCCTGGCGGGC
CTGCTTCTCCTAGTAGTTCTGTTGCTCCTAATGTGTCCGTATCAAGTTCA
CAAGACGCCTCTGATCCTGTTGCAAAGTTAGATGGAAAACTAGGTTACTC
AAGCGGAAACTCTGTTGTAGTTGAAGTATCAAATTTAAATAAAGTTAAAG
AAGGGTATACTGAGGACTCACTCCAGGATCCCAAGCGGAAAATCCATAAA
CCTGTAAAAGGAGTGCTGAGATTGGAAATTGAAAAGCTCCAAGCTGGTCC
GGTTGACTTTGAAAATGCTTCAGAAGGCGGAAGCATTGATCATGAAGATC
AAATTACCGATTCAAGGTTTGCAAAGTGTCCCAGCAATGGTTCTGATGGA
CCTCAGAATGGGCATTCAAAAGTGAATTACTATGAAGGAAAAGAGTTACC
TCGAAATGGATCAATTGCTTTGGGAAATACAGATTTAAATACTGATGATT
TCCAAGCCTTCGACTTCCGAAGAACAACAAGAAACGAGCCGTTTCTGCAG
CCATTTCATTGTCTCTATGTTTATCCAATTACTGTAAGTTTGAGTAGGAA
AAGGAACCTGTTTATACGTGTTGAACTCAGGAAGGATGATGGTGATGCTC
GTAAACAACAGCCATTGGAGGCAATGCATTCAAGGGAACCTGGTGCATCC
CTCCAGAAATGTGCCCACACACAAGTTGCTGTTGGTGCTAGGATTGCTTC
TTACCATGATGAAATCAAAGTTTCACTTCCGGCAATATGGACACCATCGC
ATCACCTTCTGTTCACTTTCTTGCATGTTGATCTTCAGACAAAACTAGAA
GCTCCAAAGCCAGTGGTAATTGGATATGCATCACTCCCGTTATCAACACA
CGCACAGTTGAGATCAGAAATTTCACTGCCAATAATGAGAGAGCTGATTC
CGCACTATCTTCAAGACGGCGGAAAGGAAAGGATAGATTACCTCGAGGAT
GGCAAGAATGTATTTAAATTGCGATTAAGGCTGTGTTCATCCTTATATCC
AATTAGTGAGCGCATTAGAGATTTTTTTCTCGAGTATGATAGACACACAC
TCCGAACAAGTCCACCTTGGGGATCCGAACTACTTGAGGCTATTAACAGC
TTGAAAAATGTTGATTCAACTGCTCTGCTTCAGTTCCTTCAGCCAATACT
AAATATGCTTCTCCATCTAATTGGAAATGGTGGAGAAACTCTTCAGGTTG
CAGCCTTCAGAGCCATGGTCAATATACTAACGCGGGTTCAACAAGAGTCA
GTTGATGAGGCTGAACGGAACATTTTTCTAGTGAACTATGTGGACTACTC
CTTTGATGATTTTGGGGGTCGTCAACCACCTGTTTATCCTGGTTTATCAA
CTGTATGGGGAAGCTTGGCTCGCAGTAAGGCAAAAGGATATCGTGTAGGA
CCAGTTTATGATGATGTCTTGTCAATGGCATGGTTTTTCTTAGAGTTAAT
TGTCAAGTCGATGGCATTAGAGCAGACTCGGCTGTTCTATCACAACCTTC
CACTTGGTGAAGATATTCCTCCCATGCAGTTGAAAGAAAGTGTTTTCAGA
TGTATACTGCAGCTATATGATTGCCTTCTAACAGAAGTACATGAGCGTTG
CAAAAGGGGTCTAAGCTTGGCAAAACGCTTGAACAGTAGTCTGGCGTTCT
TTTGCTATGATCTTTTGTCAATCATTGAGCCTCGTCAAGTATTTGAATTG
GTCTCTCTGTACATTGATAAGTTCTCTGGGGTGTGTCAGTTAGTGCTTCA
TGATTGCAAGCTTACATTTTTACAGATTATTTGTGATCATGATCTTTTTG
TGGAAATGCCTGGGAGAGATCCTTCAGATAGGAATTACCTTTCTTCTGTC
TTGATACAAGAACTTTTCTTAACATGGGACCATGATGATTTATCTCTGCG
GGCAAAGGCAGCTAGAATCTTGGTAGTCCTTTTGTGCAAGCACGAGTTTG
ATGCTCGTTACCAAAAGCCTGAAGACAAATTATATATTGCACAACTGTAC
TTTCCCCTTGTTGGCCAGATTCTGGATGAGATGCCTGTATTTTATAATCT
TAGTTCTGTTGAAAAACGTGAAGTCTTGATTGTCATCTTGCAAATAATAC
GTAATTTGGATGATGCATCATTGGTGAAGGCTTGGCAGCAAAGTATTGCT
CGAACCAGATTATTTTTTAAACTGTTGGAGGAAAGCTTGGTTCTGTTTGA
GCATAGGAAACCTGCTGATAGCATGCTTATGGGCGCTAGTTCTCGCAGCC
CGGTTGCTGATGGACCTGTCTCTCCTAAATATTCTGACAGGCTTTCACCT
GCCATTAACCACTATCTATCGGAGGCATCAAGGCAAGAAGTCAGACCGCA
AGGCACTCCTGAGAATGGATACATGTGGCAGAGAGCAAATTCCCAGTTAA
GCTCTCCTAGTCAGCCATATTCTTTAAGAGAAGCACTTGCTCAGGCACAG
TCATCTAGAATTGGCGCTTCAACTCAAGCATTGAGGGAATCTTTGCACCC
AATCTTGAGGCAAAAGCTTGAACTTTGGGAAGAAAACTTGAGCGCTGCTG
TCAGCCTGCAGGTCTTGGAAATAACAGAGAAATTTTCCAGTACCGCTTCG
TCACATAGTATCGCCACAGATTATGGAAAACTTGATTGCATAACATCCAT
ATTTACAAGCTTCTTCTCACGTTATCAGCCGCTAGCATTTTGGAAAGCAA
TGTTTCCGGTGTTCACCAGTGTCTTTCAGCTTCACGGAGCAACACTAATG
GCAAGGGAAAATGATCGATTCTTAAAGCAAATTGCTTTTCATCTTTTACG
TCTTGCTGTTTTTCGAAATCACAATATCAGAAAAAGAGCTGTGGTGGGCC
TTCAGATACTCGTCCGGAGCTCTTTCTCTTACTTTACTCAAACGGCAAGG
TTAAGGGTGATGCTGACCATAACATTATCGGAGTTGATGTCTGATGTTCA
AGTGACCCAGATGAAGTCTGACGGAACGCTTGAAGAAAGTGGGGAAGCAC
GCCGTCTCCGGAATTCTTTAGAGGAAATGGCGGACGAGTCTAAAAGTGGA
AACTTAATCACAGAGTGTGGTCTACCGGAGAATGCACTTGGTACTATTCC
AGACGCATTAGCTGAGAAAAAATGGTCGTGGTCGGAGGTGAAAATCCTTG
CCAATAGCATTATTCTGGCTCTCGATGCTAGCTTGGAGCATGCACTCTTG
GCTTCTGTTATGAACACGGACAGATATGCTGCCGCAGAAAGTTTCTTTAA
ACTTGCAATGGCATTTGCTCCTGTACCAGATCTCCACATAATGTGGTTAT
TGCATCTTTGTGATGCACATCAGGAGATGCAGTCATGGGCTGAAGCTGCA
CAGTGTGCGGTGGGCGTTGCAGGTGTTGTAATGCAGGCTCTCGTAAGTAG
AAATGATGGAGTCTGGGGCAATGATCATATTACTGCACTACGCAAAATTT
GCCCCATGGTTAGCAATGAGATAACATCCGAGGCCTCTGCAGCTGAGGTA
GAAGGATATGGTGCTTCGAAACTCACAGTTGATTCTGCAGTGAAATACCT
ACAGCTAGCAAATAAGCTTTTTTCTCAGGCTGAGCTCTACCATTTCTGCG
CAAACATTCTCGAACTTGTAATTCCAGTTTATAAAAGCAGGAGGGCATAT
GGACAGCTAGCCAAATGTCACACAATGCTAACCAATATCTATGAATCAAT
TCTTGAGCAGGAATCAAGTCCAATTCCTTTCACTGATGCCACATATTATA
GAGTTGGATTTTATGGTGAAAAATTTGGCAAGTTGGATAAAAAGGAATAT
GTTTACAGAGAGCCCCGCGATGTTCGATTGGGCGACATAATGGAAAAACT
TAGTCATATATACGAGTCAAGGATGGATGGTAATCATACCTTGCACATAA
TTCCAGATTCTAGACAAGTCAAATCTGAAGAACTGCAGCCTGGAGTCTGT
TACTTGCAGATAACTGCTGTGGATCCTGTTATGGAAGATGAAGATTTGGG
AAGTAGAAGGGAGAGAATAATCTCTCTTTCTACAGGAAGCGTCCGTGCAC
GTGTCTTTGATCGCTTCTTGTTTGATACCCCTTTTACAAAAAATGGCAAG
ACCCAAGGTGGATTAGAAGACCAATGGAAGCGACGGACTGTTCTTCAGAC
TGAGGGATCGTTTCCTGCCCTTGTCAACAGGCTTGTTGTAACAAAATCAG
AATCTCTTGAGTTCTCTCCCGTAGAGAATGCAATTGGAATGATTGAAACT
CGCACGGCTGCATTAAGAAATGAGCTTGAAGAGCCTCGCAGTTCTGATGG
TGATCAGCTCCCACGTTTGCAGAGTCTACAGAGAATTCTTCAAGGCTCTG
TCGCAGTTCAGGTAAACAGTGGCGTCCTTAGTGTATGCACAGCTTTCCTG
TCAGGTGAGCCAGCGACAAGGCTGAGATCACAGGAGCTGCAGCAACTCAT
TGCTGCTCTCCTTGAATTTATGGCTGTTTGCAAACGTGCCATTCGTGTAC
ACTTCAGGTTAATTGGGGAGGAAGACCAAGATTTCCACACACAGTTAGTC
AATGGGTTTCAGTCACTGACTGCAGAGTTGTCTCATTACATCCCTGCCAT
TCTTTCCGAGCTCTGAAAATCACTAGTGGTCTTTGTTAGTGTAATGTGTT
CATATTGTTTGTACAAGTTTTCTGTAGGTTCATGTTGTGTTCTTGTTCAT
ATAATTATTCATCATTTGTTGATATATAATTTTTTTTATTCATTTTTGTA
TTTTTAACTACAGTGTTTTCCCCTTTTTAAGTAACCTGTCCAGTTTAGTT
TAACTGAATGTTCAAAAATTTGATTAGCACTATGGTAGGGTTTGACTTCA
TACAAGAGCAACAGAGCCTGTTTGTTTGTCGAAAA
MENSSPNGHRFRRISRQSFAGSLNLDPLLDENLEQWPHLSELVQCYRTDW
VKDDNKYGHYESIGPISFQNQIFEGPDTDIETEMHLANARQNKIDDTDDD
IPSTSGRQFTDAASKSSSLNVLKHLGESPLPTYEPVFDWETERSTIFGQR
IPETQLAQYASGLKISVKVHSLSFQAGLVEPFYGTICLYNKERREKLSED
FIFSALPTEMQEASSSYEPRGIFYLDTPSASVCLLIQLEKPATEEGGVTP
SVYSRKEPVHMTEREKQKLQVWSRIMPYRESFAWAIIPLFDSNINSSPGG
PASPSSSVAPNVSVSSSQDASDPVAKLDGKLGYSSGNSVVVEVSNLNKVK
EGYTEDSLQDPKRKIHKPVKGVLRLEIEKLQAGPVDFENASEGGSIDHED
QITDSRFAKCPSNGSDGPQNGHSKVNYYEGKELPRNGSIALGNTDLNTDD
FQAFDFRRTTRNEPFLQPFHCLYVYPITVSLSRKRNLFIRVELRKDDGDA
RKQQPLEAMHSREPGASLQKCAHTQVAVGARIASYHDEIKVSLPAIWTPS
HHLLFTFLHVDLQTKLEAPKPVVIGYASLPLSTHAQLRSEISLPIMRELI
PHYLQDGGKERIDYLEDGKNVFKLRLRLCSSLYPISERIRDFFLEYDRHT
LRTSPPWGSELLEAINSLKNVDSTALLQFLQPILNMLLHLIGNGGETLQV
AAFRAMVNILTRVQQESVDEAERNIFLVNYVDYSFDDFGGRQPPVYPGLS
TVWGSLARSKAKGYRVGPVYDDVLSMAWFFLELIVKSMALEQTRLFYHNL
PLGEDIPPMQLKESVFRCILQLYDCLLTEVHERCKRGLSLAKRLNSSLAF
FCYDLLSIIEPRQVFELVSLYIDKFSGVCQLVLHDCKLTFLQIICDHDLF
VEMPGRDPSDRNYLSSVLIQELFLTWDHDDLSLRAKAARILVVLLCKHEF
DARYQKPEDKLYIAQLYFPLVGQILDEMPVFYNLSSVEKREVLIVILQII
RNLDDASLVKAWQQSIARTRLFFKLLEESLVLFEHRKPADSMLMGASSRS
PVADGPVSPKYSDRLSPAINHYLSEASRQEVRPQGTPENGYMWQRANSQL
SSPSQPYSLREALAQAQSSRIGASTQALRESLHPILRQKLELWEENLSAA
VSLQVLEITEKFSSTASSHSIATDYGKLDCITSIFTSFFSRYQPLAFWKA
MFPVFTSVFQLHGATLMARENDRFLKQIAFHLLRLAVFRNHNIRKRAVVG
LQILVRSSFSYFTQTARLRVMLTITLSELMSDVQVTQMKSDGTLEESGEA
RRLRNSLEEMADESKSGNLITECGLPENALGTIPDALAEKKWSWSEVKIL
ANSIILALDASLEHALLASVMNTDRYAAAESFFKLAMAFAPVPDLHIMWL
LHLCDAHQEMQSWAEAAQCAVGVAGVVMQALVSRNDGVWGNDHITALRKI
CPMVSNEITSEASAAEVEGYGASKLTVDSAVKYLQLANKLFSQAELYHFC
ANILELVIPVYKSRRAYGQLAKCHTMLTNIYESILEQESSPIPFTDATYY
RVGFYGEKFGKLDKKEYVYREPRDVRLGDIMEKLSHIYESRMDGNHTLHI
IPDSRQVKSEELQPGVCYLQITAVDPVMEDEDLGSRRERIISLSTGSVRA
RVFDRFLFDTPFTKNGKTQGGLEDQWKRRTVLQTEGSFPALVNRLVVTKS
ESLEFSPVENAIGMIETRTAALRNELEEPRSSDGDQLPRLQSLQRILQGS
VAVQVNSGVLSVCTAFLSGEPATRLRSQELQQLIAALLEFMAVCKRAIRV
HFRLIGEEDQDFHTQLVNGFQSLTAELSHYIPAILSEL
| Relationships |
|---|
| The mRNA, XM_017371061.1, is a part of gene, LOC108202588. |
| The polypeptide, XM_017371061.1, derives from mRNA, XM_017371061.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |