| 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. |
GTATAACTCCATTCTCTATATTATTCAACCCTCTTTCGTCGGTTACAATA
CACAAAATATGTAAACACAAATTCATATTCATATATATCCAATCTACAAC
CTCAATATTACGCAATTCTTGATCAACCAATTCAATCAATACAGACATAG
CGTGAAGAACCAAAATTCTTGTCTTAAGACAGATTGGTGATTCTGACAAA
AGAAAGAGTCAAAAAGTTTCTTTTTCAAGGCTGTTTTGCTTCAAGGTTAT
TAGAATTGTGTTTTACTGAATTATCTGTTTAATCCTTTGGAGCATTGCAC
GTGGACTTACATCGGATACTGTAAAGTTGCATAAGGATTCTATTTTCGTT
CTGTGCTTACCTTGATCGTCTCACCAAGATAACGAAGCTCATATTTGGGA
ATTGTTCTAAACTTGTCTCCTCGTGGTGAGTGTCTGTGTTACTTTGATTA
CCTGTATGTTATTCTTGACCAGTGTTTTTTATTTTTCTAGTAAATAAATA
TTGAACATATTGCGGAACTATATCACACATTGGTTATATATGTTTAAACT
ATCACCATTTGGCATTTGTTTATATGAACTTCAGCTCAATTTATTGATGT
GAGGCCACAAGATACGTCAGGTGTGTATATGTGAGTCAATGTTGAACTTC
TTCTTGGTATACATATTTGTTTTTACAAATGTGTCAGAAATTAGCGAGAG
TCAACATTACCCAACCACTTTGACGAACATAAGACTATGCCAGGAGTTCC
GATTACTATGAAGCATATTATTGCTCCCAAGTTTGTACCAGTTACAGATG
GAGGTGACTTATAAGTATAGTATGATTCTGCAACGTGGTCCACAAAATCC
CGTGGATTTCTAATTTCCGGGAAAGTCCGCCCTCTTCACCTCATAGTTAA
GAAGATGACAGACTTTCTTTAAATGCCGTTAACTAGTTAAATATTTTGGA
TAGTGTTAAGGCATGTATTTTCCTCGACTCTTTCCTATAGTTCATTGACG
ATGTATACTAGAGATGTGAAAGTAATTGATTGAGTTCTTGAAAACATTGG
GGGGCTTGAAGGTAAAAAATCTCGAGACTGCGGCCTGGCCGGTCTCTAAA
TTACCCTCTAAAGACCAATATAGAATCAGGTTGGTGCTGGTATGTTTGGA
GGTTCTGTATGGTAGTATTGATGGAATGTAGGCATGATATTGTTGCTATA
TCTGTGTTTATTATTATTATATTTAGTATTATTATCATTATCATTATCAT
TATTATTATTATTATTATTATTATTATTATTATTATTGGTAATTTTATAC
ACTACATGAAACATTATTAGCGTTTGAGTTTCTACATTTCTTCGTGTTCT
GTTCAGGCTTTTGGCTATACAGAGAATATTTCGCTTCATTTTTGTTTAAC
CTAAAAGTGTTCGAAGTTAAAAGATAATGCTAAAAAGAGTGTAAGATTTG
TTAAATTACTTTGAAAATATAATATATATGTATACTGTATAAATCGTTAA
ATTGTAAAAAATTACTATTTTTGAATGTCATCCTTTGCTTTTACTTATCT
TGTCATGTACACATCTGTGTGTGTGTTCTCGTCATACTGGTATCTGACAG
GAAAGTCCTTCGAGTGTTGTTTGGGTTGGACTTTGGAGAAATTCCCTGAT
TGCTGGGTACTTTTAGAACTGCGTCTGCTTTTCTTGTCAGTTTGTAAGAT
TACTTGAAATTTGGTGCTCCACTCTCCTTTTTTAATTATTTTTTGTTTTA
GGCCTGTGGGTGTTAGTATAGACTATAGATGCTTAGTTGGATCATTGGCA
TTACCTCTTACTGAAAATGCTATTTTTTTTAGTATTTAGTAGTGGATCCC
TGGGAGCCATCTTTTGGGGAAATATTCAACCTTAACTTGCAGAATAAAAT
TAAAAGAAAATTGAGGGCATCAGGTTTTAATTTGGGCCTCCCATAGTACG
AGCTCCTACCACGATAGCTTGGTAAGCTGCCAACTCCCATAATATCTTAG
GTAGAAGACTAGAAGGCCTTTATAGACCATATATCCGTAAGTTGATGGTA
ATATTCTGATGGAGTTTACAGGTGTGTAAATATGACACGGAATAATGTTA
CTGTAGAAAGCAGACCAGTGGAATAGTTTTGTTGTTAGTTTCTAGCTACC
TTAAGTTTACTTATAATTTATAATGAACTGGTAACTTGATTATTTGTATT
TTTCTTATAAACACTTTAATTTTAAACTTGTATCTTTTAACTTGGCTAAA
AGAACAAATGTATATGAATTTTAACAACAAACTGCAGATAATAGATCTGT
AAAGGGATTAAAGCATGTAGAAAAGAGAAAATAACAGAAGTCATTGATAT
CCCACCAATTTATTAACACGCTGTCTCTGTTCATTCTGAGGATTCAACTG
TGTATTTGTGAAACACAAGATATCTTGATACTTAATAATTAACATTCAGT
TCCTTGTTTCCATGCTCTTGTTGGACTAGCACTGCTGTCCTGATCATTTC
AATATTTGAGCAACATACTACATTCATTCAGTGAAACATAGATGGCTAGT
AGAAAACGAAGCTTATCAAATGATGTAGATAGTAATGCCCTCCACAAGGA
ATGGGATGAAGCTTCATGCCCCATTTGCATGGACCACCCCCACAATGCTG
TTCTTCTTTTGTGCAGTTCCTACAATAAGGGTTGCAGATCTTACATTTGT
GACACCAGTTACAGGCATTCCAATTGTTTGGATCGCTTTAAAAAACTCAA
AGCACAGGATGAGAACAGCACCTCTCCACCTGCATTGTTACCCAGGGATC
TGCACAGAGACACTAGAAATAACACAAGTGACTCTACTTCAGTTCGTGCT
CAGAATTTAATTCCTAATAATGCCATAGCATCTGAAGATATATCTGGAAG
ATCAATTGAGAGTAGAAGCAATGTTGCTAGTAGGTACTCTGGCAGGCCAG
CAGGAGATATGGAAGATGGAGGTTCTGATGTATCCAGAAGGATTGTTCCA
GCAGAGATCAATGACGGGAACTCTTCAGAACCAAGGTCAAAGTTGAGATG
CCCTTTATGCCGTGGGGATGTACTTGGCTGGCAGGTTGTTGAAGAGGCCA
GAAAGTATCTTAATACGAAGTCTCGGAGTTGCTCTCGTGAAACATGCTCT
TTTTCTGGTAGCTATGGAGAACTGCGTAGGCATGCTAGGAGAATTCATCC
ATCAGCCCGACCTTCTGATATCGACCCAATTCGAGAACAGGCATGGCGCC
ACCTTGAGAATCAGAGAGATTATGGTGATATTGTCAGCGCCATTCGTACA
GCCATGCCAGGTGCTGTTGTTTTTGGGGACTATGTAATTGAAAATGGAGA
AAGAGCACCTGGTGAGAGAGGAAGGGGTTCAGGTGAGCGTGATGGACCTT
GGTGGACAACATTTTTCTTGTTTCAGATGCTGGGCTCAATGGATCATGCT
GCTGACCGTAGGAGTGGGAGGTCAAGGGACTCTACCAGGTTTAGGCGCTC
TAATGGATCTGGACGGAGGTACTTGTGGGGTCGAAATTTGCTGGGAGCAC
ACGATGATGACGATGACGATGATGACAATGATTCGGATGTTAATATATTA
AGTGATACAAATGAAGATGTCTCTCCCATCCCAAGAAGACGTCGACGATT
GACAAGATATAGATCAAATGAAGACCGATCATAGTCGAAGCATAATCTGG
CAGTTTCCCTCTTTCTAGAATAGCAAACAGGACCTCCAATCTTGTCCAAG
AACTTGGCTTCCTTGTCCAAGAACTTGGTTTCAAGTCTGCTTCATATAGC
TGTATTAAGGCACCAGACATCATAATATCGGTGTGTTTCTGTAAAAGAAT
AGGCGAAGAACAAACAAAAGAAAGTGTTCAGTTTGGTTCTTGTTTGGTCG
TCTGTACAGTTTTCATTTAGTTTGTTTTGTTGGATTTATTGTCGAACTAA
CAATGTCACCTTCATTTCATTTACATATCCTGCTCTAGTTATAAGGTGTG
GCTCTTGCAATGGAAAAATATTGTTCATTTGAATGTTGGATTAATGTAGT
TTGAAAATTCATTCAGTGGGATA
MASRKRSLSNDVDSNALHKEWDEASCPICMDHPHNAVLLLCSSYNKGCRS
YICDTSYRHSNCLDRFKKLKAQDENSTSPPALLPRDLHRDTRNNTSDSTS
VRAQNLIPNNAIASEDISGRSIESRSNVASRYSGRPAGDMEDGGSDVSRR
IVPAEINDGNSSEPRSKLRCPLCRGDVLGWQVVEEARKYLNTKSRSCSRE
TCSFSGSYGELRRHARRIHPSARPSDIDPIREQAWRHLENQRDYGDIVSA
IRTAMPGAVVFGDYVIENGERAPGERGRGSGERDGPWWTTFFLFQMLGSM
DHAADRRSGRSRDSTRFRRSNGSGRRYLWGRNLLGAHDDDDDDDDNDSDV
NILSDTNEDVSPIPRRRRRLTRYRSNEDRS
| Relationships |
|---|
| The mRNA, XM_017396958.1, is a part of gene, LOC108222960. |
| The polypeptide, XM_017396958.1, derives from mRNA, XM_017396958.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |