| 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. |
GCCTTCTACACGTACTGTGCTAATAATAACTCCCAGCTCTCACTGTCCTC
ACTGATTATTTAAATACGGACAACTACGAAACTCCATTCACTCAGATCAA
AAATACACAATCACACCCAGAGAGATAACTATAGAGATAGAGAGATCGTC
GAGAGAGATTAGTATTTTGAAATGCTTCGTTTGAATCACACCTCTCGGCC
ATGGTCTTCACCTATTCCTACTCAAATTTATCCTTCCCGCAGGGAAGTGG
GAAGAAAATTCTTGTATGGTGTGGGACAAAGCAAATAACAATAAGATCTT
GAAGGTGGATCTCAAAAGTCGTCTTCAGCATGTGCAGGGTAAAGATAAAC
TTATGATGTCGTATCTGTCATGCTATTCCCTGGGTAGAATGACACAACAA
ATATCCAGCAATGCAGTGTTTAATATGCTTAAAGACATACTACTCTTTGT
GATTCGGACGTCTGCAGCTACAAGCTCTCCTTTTGCTTGTATATCAAACT
CCCTGAATAAGCCAACACCTCTTAAGTTGGATATAATTCTGCCTTCAATA
CGAGATATTAGATGGAATTTTGCACGATTATTGTATTTGTTCAACATACG
GCTTGAGAGAAATGTCGCGACGTTTTTAGTGGTGCTTCTTGTAGCATGCT
TTTCATTTGTTATGATTGGAGGTCTTCTCTTCTATAACTTCAGGGGTAGT
ACACAGTCTCTAGAGGACTGCTTTTGGGAGGCTTGGGCATGCCTTATTTC
TTCCTCTACTCATCTACGACAAAGAACACGCGTTGAGCGTGTAATTGGCT
TCATTCTTGCTATATGGGGGATCCTTTTTTATTCTCGCCTGTTGAGCACG
ATGACAGAACAGTTCAGACACAATATGCAAAAGCTTAGAGAAGGAGCACA
AATGCAAGTTCTGGAAACTGATCATATTATCATTTGTGGAGTTAACAGTC
ATCTGACCTTCATATTAAAACAGCTAAATAAGTATCATGAGTTTGCTGTT
CGATTAGGTACTGCGACGGCTAGGAGGCAACGGATTCTTCTTTTGTCTGA
TCTCCCTAGAAAACAAGTGGATAAAATTGCAGAGAACATTGGTAAAGATC
TCAATCACATTGACATCCTTACAAAGAGCTGCAGTCTGAGCATGACAATA
TCATTTGAAAGAGCAGCAGCCAATAAGGCACGTGCCATTATTATATTGCC
AACAAAGGGGGATAGGTATGGAATTGATACGGATGCATTTCTATCTGTGC
TTGCCCTTCAACCCCTTCCAGATATGGGTTCTGTCCCTGCCATTGTTGAG
GTCTCGAGTTCCAATACATGTGAACTCTTAAAAACGATATCAGGATTAAA
GGTCGAGCCTGTGGAAAATGTTGCTTCCAAATTATTTGTTCAGTGCTCTC
GGCAGAAGGGACTGATAAAAATTTACAGACACTTGCTTAACTATCGAAAA
AATGTATTCAATCTTTACAATTTTACTAACCTAACAGGGTTGAAGTACAA
GCAAATACGGCGTGGATTTCAAGAGGCAGTTGTATGTGGTATTTATCGAA
GAGGAAAAGTAGATTTCCACCCAAATGATGATGAAGTTCTAGAGCAAGAT
GACAAAGTATTGTTCATTGCACCTATTCCTGGAAAGAAAAAACCATATTT
AGCATCTCCAGACGTTATCAGTGAAGATGTCAGTGGCATTCATAATCTTG
TACAAGTGAATAAGAATGTTGAATCCCTAAGTTTCGCCCAACATATGGAA
AAGCTGCGGTTTGAGAATATAGTCAAACGGCCCAAAAAATCAGGTTCAAA
GGCTTCAGACTGGACAGTAGGACCCAAAGAATGGATCCTAATGGTTGGAT
GGCGACCTGATGTTGTGGAAATGATTAATGAGTATGACAATTATCTTGGA
CCCGGCAGTGTGTTGGAGATATTATCGGATGTGCCAATAGAAGATAGAAA
TAGGGCCAGAGACCTTGCTGGTCAAGGCAAGCTAAAAAATGTGAAGGTTT
TCCACAGGATTGGAAACCCAATGGATTACACCACTTTAAAAGAAACCATA
ACAAATATTCACAAGCCATCCACGAAAGGTGGAGATATTCCATTTTCTAT
TGTCGTGATTTCTGACAGAGAGTGGCTACTTGGAGATCCGTCCAGAGCAG
ATAAGCATTCGGCATACTCTCTACTTCTAGCTGAAAGTATCTGTAACAAA
CTTGGTGTAAAGGTCCAGAATCTAGTAGCTGAAATTGTTGATTCAAAACT
TGGAAAACAAATTACAAGAATTAAGCCATCCCTAACTTATATTGCAGCAG
AGGAAGTAATGAGCCTTGTAACTGCTCAAGTGGCAGAAAACAGCGATTTA
AATGAGGTCTGGAAGGATATTCTGAATGCAGATGGTGATGAAATATATGT
GAAGGACGTTGGCCTATACATGAAGGAGGGGGAGAATCCATCGTTTGCTG
AACTCTCTGAAAGAGCGCATTTACGAAGAGAGGTCGCTATCGGTTACGTG
AAAAATAATAATAAGGTCATAAATCCAGTCTCCAAGTTGGAACCCCTCTC
ACTTGAACTAAATGATTCACTAATTGTAATATCGGAGCTGGAAGGAGTAC
AGCCTCTGCCTTTGGGATCTGAGAGTTAGGTATCTTCACAAGTGCTTGAT
GCTTCTCTGTGTTCTGCCTGGGAACACGTTGTTTCCTTAAATGTGTGCTA
AAGTGTGACGAGCAGGTCGAGCAGGTTCGATATCGCAAAATCGATATTAC
GTGAACTGGATATAATCGCAAGATAATATCGATACACTTGCATGGAAGTA
TCTGTAGACCAAGGAGTGAGATATGGCCTCTTGAAGATTCGAACAGGATT
CCCTTTTTCACTTGGCAACGTTTTGGCCCTCCCGTCTTGTAGAGGCAGAA
TGCAAAGTGTGAGATATTCTTAGTTAACTTCGTTTTCCTCTGATAATTCA
TAAGGTGTTTTCGGATTTGGTTTTTTACCAGAATGCAGTGCACGAGGGCA
AACATGTTGTAATCGTTATGATCAATAATCAACAAAATGAAAATCAAATT
ACTTTGTCTCTCTACA
MVWDKANNNKILKVDLKSRLQHVQGKDKLMMSYLSCYSLGRMTQQISSNA
VFNMLKDILLFVIRTSAATSSPFACISNSLNKPTPLKLDIILPSIRDIRW
NFARLLYLFNIRLERNVATFLVVLLVACFSFVMIGGLLFYNFRGSTQSLE
DCFWEAWACLISSSTHLRQRTRVERVIGFILAIWGILFYSRLLSTMTEQF
RHNMQKLREGAQMQVLETDHIIICGVNSHLTFILKQLNKYHEFAVRLGTA
TARRQRILLLSDLPRKQVDKIAENIGKDLNHIDILTKSCSLSMTISFERA
AANKARAIIILPTKGDRYGIDTDAFLSVLALQPLPDMGSVPAIVEVSSSN
TCELLKTISGLKVEPVENVASKLFVQCSRQKGLIKIYRHLLNYRKNVFNL
YNFTNLTGLKYKQIRRGFQEAVVCGIYRRGKVDFHPNDDEVLEQDDKVLF
IAPIPGKKKPYLASPDVISEDVSGIHNLVQVNKNVESLSFAQHMEKLRFE
NIVKRPKKSGSKASDWTVGPKEWILMVGWRPDVVEMINEYDNYLGPGSVL
EILSDVPIEDRNRARDLAGQGKLKNVKVFHRIGNPMDYTTLKETITNIHK
PSTKGGDIPFSIVVISDREWLLGDPSRADKHSAYSLLLAESICNKLGVKV
QNLVAEIVDSKLGKQITRIKPSLTYIAAEEVMSLVTAQVAENSDLNEVWK
DILNADGDEIYVKDVGLYMKEGENPSFAELSERAHLRREVAIGYVKNNNK
VINPVSKLEPLSLELNDSLIVISELEGVQPLPLGSES
| Relationships |
|---|
| The mRNA, XM_017400481.1, is a part of gene, LOC108225567. |
| The polypeptide, XM_017400481.1, derives from mRNA, XM_017400481.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |