| 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. |
CTCGGAAGTTGTCAATTTTGTTGCTTTTTCTAATCATTTTTAGGGTTTCT
AGAGTTTAATATCTGATTATGAAACTGTGTTGAGTATCTGCAATTTTTAA
TGTATAGGCAATCATGAGCAACGAGGGAGAAAAGACTTGCCCTCTCTGTG
CTGAAGAGATGGATTTGACTGATCAGCAGTTGAAGCCGTGCAAGTGTGGT
TATGAGATTTGTGTTTGGTGCTGGCATCACATAATAAACATGGCTGAGAA
AGACAATGTAGAAGGCAGGTGTCCAGCATGTCGCACCCCTTATAACAAGG
AAAAAATTGTGGAAAAGGCAGCTCAATGTGAAAGGTTGTTGTCTGAGTTG
AATGTGGAGAAGAAAGGGAAGTCAAAGTCGAAAAGTAAAGCACCTGATGG
TAGAAAGAACCTAAGTAGTGTTCGAGTGATTCAACGAAATCTTGTCTACA
TTGTGGGGTTACCTCTTACTTTGGCAGATGAAGACCTCCTACAAGGAGCG
GAATACTTTGCTCAATATGGGAAGGTGCTTAAAGTGTCAATCTCTCGTAC
GGCAGCTGGGACCATTCAACAATTTCCAAATAGCACTTGTAGTGTATATA
TTACTTATTCAAAGGAGGAAGAAGCAGTTCGTTGCATTCAGTCAGTGCAT
GGTTACACATTGGAGGGTAGACCATTAAGGGCCTGCTTTGGAACCACAAA
ATATTGCCATGCATGGCTGAGGAGTGTGCCATGCATCAATCCTGATTGTC
TATACTTGCATGAAATTGGTACACAAGAAGATAGTTTCACTAAAGATGAA
ATAATATCAGCATACACAAGAAATAGAGTTGAACTGAGTGTGGGTGCCAC
AATCGACACGCAACGTCGATCTGGGAGTGTATTACCACCACCAGCAGACG
ACTTCTGTAATGACAGCTGCTCCTCATCTGGAATACATCATAATAAAAGC
TCAACGGATAACCTTGACATCTCTTCTCAAAACATATTGGAGTCATCTGT
CTGGCAAACTCCGGCAAGCAGTGTGAGGGGCTCTCCACCAAATAGTGGCA
TTTCAGTCGCATTTTCAACTGCAGTAGTGAGCCCAGCCAAAGTCTCCTTA
ATGCACAATACTTCAGGAAAGAAACTTAATGGAGAAGGTTGGTTTCCCTT
ACAGAGGAATAAATCTGTTCCAGTAGCATCTGTGGGAATACAGGATGTAG
ATAAGCAACAAAAGTCATCGAATACTTCCACCAAGATTGGACATTTTGAT
AAACTAGTGACAAGTGACCAGATATCTACGCCATCGCCAAAAGTAGATGG
GTCCACAAGCATGCCAGATATCACAGTGCAGTCTTGCGGTATTAATTCAG
AAAGAAATTCACATCTACCTGTAGAGAGTAAATTTAAGGAATTATGTTCT
GATATGTTGTCTTTAAATATAATTACTCATGGGCCACAGCACGTAGACAC
AAAATACAGAGAACTCTTGTCAACAGATGCTGCAGCAAAGGATGCATCCT
CCAGTAAGGATCCTGTTGCAGCAAGGGATCTGTCTGAATTTAAATTAGTG
TCGCCGTCGCAAGTAGCAGAAAGTGATACTTGTAAAGTTAAGGATGATAT
ACAATCTTTTAATATACAAAGACGCAGGGATCCTGAAGTTACCAATAGCA
CAGATAGTAGTATAGGTCAGTTATCAGATAGTTCTAGGGATCTACATTCT
CAAGAGTCTTTCCATATACCCAGCACCAATTTTGATCTAAATAATGTAGA
TAATCAACCTAGCAAGTTTTCTGTTCCGCAAGCATATAATGCCCCAGTTA
TTTCGAATGGTTATGCTGGGAACCAGACTAGAAGTTTTGATTTGGATACC
AGTGCTAATGATTCTTCTTATATGCTACAAGATGAACTGAAATTGCATGA
TGGAAGACATGGCAGTGCGTTAGTAAACCACGATAGTATTTTAGCAGACG
GAATGGGAGAGAGCAGCATCATATCAAATATTTTGTCAATGGACTTCGAT
TCATGGGATGAATCTTTGGCTTCACCGCAGAATTTGGTTAAGTTACTAGG
TGAAACTGATAAACAGCTGGGTTCTCTTGGTGCATCGAATACGAAGAAAG
TACAAAACAGCAATCAGTCTAGGTTCTCTTTTGCAAGAGAGGAACATCAA
GCATCCAATTTTGGGCCATCATCTGCTGGCGTTGAGCAAACTCTTAGGAA
TCATTCTTTTACAAATGGTTTCAAGGACAATGGAAACCATTATCGCAGTG
GTACTGCCAATGGTTATTCTACTTTGAGTGCGCATCAACCTGGTGATTTT
GCAAGCACCCATTTTCATAATTCACCGAACAGGTTTTCTGTCAGGGGAGC
GCGTGCTTCAAATAGTCAACCATCACCAACAAGCATGGCAAGCTCAAATG
GACCTTCTAAGCAGAAATCTGATACAGGTGGCATTTCAGTCGCATTTTCA
ACTGCAGTAGTGAGCCCAGCCAAAGTCTCCTTAATGCACAATACTTCAGG
AAAGAAACTTAATGGAGAAGGTTGGTTTCCCTTACAGAGGAATAAATCTG
TTCCAGTAGCATCTGTGGGAATACAGGATGTAGATAAGCAACAAAAGTCA
TCGAATACTTCCACCAAGATTGGACATTTTGATAAACTAGTGACAAGTGA
CCAGATATCTACGCCATCGCCAAAAGTAGATGGGTCCACAAGCATGCCAG
ATATCACAGTGCAGTCTTGCGGTATTAATTCAGAAAGAAATTCACATCTA
CCTGTAGAGAGTAAATTTAAGGAATTATGTTCTGATATGTTGTCTTTAAA
TATAATTACTCATGGGCCACAGCACGTAGACACAAAATACAGAGAACTCT
TGTCAACAGATGCTGCAGCAAAGGATGCATCCTCCAGTAAGGATCCTGTT
GCAGCAAGGGATCTGTCTGAATTTAAATTAGTGTCGCCGTCGCAAGTAGC
AGAAAGTGATACTTGTAAAGTTAAGGATGATATACAATCTTTTAATATAC
AAAGACGCAGGGATCCTGAAGTTACCAATAGCACAGATAGTAGTATAGGT
CAGTTATCAGATAGTTCTAGGGATCTACATTCTCAAGAGTCTTTCCATAT
ACCCAGCACCAATTTTGATCTAAATAATGTAGATAATCAACCTAGCAAGT
TTTCTGTTCCGCAAGCATATAATGCCCCAGTTATTTCGAATGGTTATGCT
GGGAACCAGACTAGAAGTTTTGATTTGGATACCAGTGCTAATGATTCTTC
TTATATGCTACAAGATGAACTGAAATTGCATGATGGAAGACATGGCAGCG
CGTTAGTAAACCACGATAGTATTTTAGCAGACGGAATGGGAGAGAGCAGC
ATCATATCAAATATTTTGTCAATGGACTTCGATTCATGGGATGAATCTTT
GGCTTCACCGCAGAATTTGGTTAAGTTACTAGGTGAAACTGATAAACAGC
TGGGTTCTCTTGGTGCATCGAATACGAAGAAAGTACAAAACAGCAATCAG
TCTAGGTTCTCTTTTGCAAGAGAGGAACATCAAGCATCCAATTTTGGGCC
ATCATCTGCTGGCGTTGAGCAAACTCTTAGGAATCATTCTTTTACAAATG
GTTTCAAGGACAATGGAAACCATTATCGCAGTGGTACTGCCAATGGTTAT
TCTACTTTGAGTGCGCATCAACCTGGTGATTTTGCAAGCACCCATTTTCA
TAATTCACCGAACAGGTTTTCTGTTTCTAGAGCACCTGTAACAGCCCCTC
CTGGATTTTCCGGGCCTACCAGAGCTCCACCTCCAGGCTTTTCCTCTTTT
GAAAGGATGGAACAGACATTTGACGTAAACTCTGGGAATCATTTGCTCAA
CAATTCATCTTACTTGAGAAATGCTAGTCAGTCACCTTCTAGTATGTATA
ATGATTCCACCAATGCAGATATAGAGTTTATTGACCCTGCAATATTGGCA
GTAGGTAAAGGCAGACTTCCTAATGGGTTTAATAACCCTAGTTTAGACAT
GAGGTCAACTTATCCTACCCAGATGAGTAATTATGAGAATGAGGCAAGAT
TGCAGCTAATGATGCAAAGATCTGTTTCACCACAGCAGAACCCCAGATAT
GTCGAAATGGGTAACAGTTTTTCTTCTTATCCGGATAATTATGGAATGCC
TCCAACGATTTTTGAGCAGGCTTTGGCAAACAATGGATCCCAGTATTCTC
AATTTGGTCTTTCACAGTCCAGAAATCAACTTGTGTCGAGCGGTAGTTGG
GATGGTTGGAAAGAGGTTCTGAGTGGAAATGGCTCAAATGCGGCAGAGTT
TCTTAGATCGGAGAGATTGGGAGGAAATAAGTACTTTAGTGGTCGCCAGG
ATTCGAAGTACCGGATTTCCAGTTCTGGAGATTTATATAATCAAACATAT
GGGATTTGAACTTTGTCTAGTGGACTAATCCCTTTAATGTTGAAACTGAT
ATAGAATGACTATATCCAACTTGTCATGACAGCAGTGAACTGTAAAAATG
TGGCTGGATCTTGACTGGTTTTACTGGTTAACCTGCTGATTGGCTGGATC
TTGACTGGTTTTACTGATTAACCTGCTTATTGGTGGAGTGAACGTTCTGA
TAACCGTCTCCTCCAAAACCAGCAGGAAACTAAGCTATCAAGTCTTGGTT
TGAAGCTGCATGATACAGAAAGGTACACAAGATCCTATTGATTATGGTTT
ATTATGCTAGAAGAGCCCAGGATCGAAACTGTGAATCAGGATGAAATCGC
AGGTTATGAACTTTAGTGTTTACTTTCTTGTTGCTGGAAGTGGCTCTTAA
ATTATTGCTTCAGCTGTCAATTTGTGCTATAGAAGTTTTGAGCAAATACT
GTCTGCTGGAAGTAGCTCTAGTTTTGTTTACCTTGTTGCAAAAAGAGACA
ATTTGTTTACAGTAGTTTTGAGCAAATACTGTGCAAGTTCAGTGTTTTAT
CATGCTACATGCTGTGAGTTCCAAGTTTCCTTGTTTTTCTCCCAAATATA
AAGGATTATTATCCCACTTAGA
MSNEGEKTCPLCAEEMDLTDQQLKPCKCGYEICVWCWHHIINMAEKDNVE
GRCPACRTPYNKEKIVEKAAQCERLLSELNVEKKGKSKSKSKAPDGRKNL
SSVRVIQRNLVYIVGLPLTLADEDLLQGAEYFAQYGKVLKVSISRTAAGT
IQQFPNSTCSVYITYSKEEEAVRCIQSVHGYTLEGRPLRACFGTTKYCHA
WLRSVPCINPDCLYLHEIGTQEDSFTKDEIISAYTRNRVELSVGATIDTQ
RRSGSVLPPPADDFCNDSCSSSGIHHNKSSTDNLDISSQNILESSVWQTP
ASSVRGSPPNSGISVAFSTAVVSPAKVSLMHNTSGKKLNGEGWFPLQRNK
SVPVASVGIQDVDKQQKSSNTSTKIGHFDKLVTSDQISTPSPKVDGSTSM
PDITVQSCGINSERNSHLPVESKFKELCSDMLSLNIITHGPQHVDTKYRE
LLSTDAAAKDASSSKDPVAARDLSEFKLVSPSQVAESDTCKVKDDIQSFN
IQRRRDPEVTNSTDSSIGQLSDSSRDLHSQESFHIPSTNFDLNNVDNQPS
KFSVPQAYNAPVISNGYAGNQTRSFDLDTSANDSSYMLQDELKLHDGRHG
SALVNHDSILADGMGESSIISNILSMDFDSWDESLASPQNLVKLLGETDK
QLGSLGASNTKKVQNSNQSRFSFAREEHQASNFGPSSAGVEQTLRNHSFT
NGFKDNGNHYRSGTANGYSTLSAHQPGDFASTHFHNSPNRFSVRGARASN
SQPSPTSMASSNGPSKQKSDTGGISVAFSTAVVSPAKVSLMHNTSGKKLN
GEGWFPLQRNKSVPVASVGIQDVDKQQKSSNTSTKIGHFDKLVTSDQIST
PSPKVDGSTSMPDITVQSCGINSERNSHLPVESKFKELCSDMLSLNIITH
GPQHVDTKYRELLSTDAAAKDASSSKDPVAARDLSEFKLVSPSQVAESDT
CKVKDDIQSFNIQRRRDPEVTNSTDSSIGQLSDSSRDLHSQESFHIPSTN
FDLNNVDNQPSKFSVPQAYNAPVISNGYAGNQTRSFDLDTSANDSSYMLQ
DELKLHDGRHGSALVNHDSILADGMGESSIISNILSMDFDSWDESLASPQ
NLVKLLGETDKQLGSLGASNTKKVQNSNQSRFSFAREEHQASNFGPSSAG
VEQTLRNHSFTNGFKDNGNHYRSGTANGYSTLSAHQPGDFASTHFHNSPN
RFSVSRAPVTAPPGFSGPTRAPPPGFSSFERMEQTFDVNSGNHLLNNSSY
LRNASQSPSSMYNDSTNADIEFIDPAILAVGKGRLPNGFNNPSLDMRSTY
PTQMSNYENEARLQLMMQRSVSPQQNPRYVEMGNSFSSYPDNYGMPPTIF
EQALANNGSQYSQFGLSQSRNQLVSSGSWDGWKEVLSGNGSNAAEFLRSE
RLGGNKYFSGRQDSKYRISSSGDLYNQTYGI
| Relationships |
|---|
| The mRNA, XM_017395592.1, is a part of gene, LOC108221735. |
| The polypeptide, XM_017395592.1, derives from mRNA, XM_017395592.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |