| 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. |
TGATATATTGGTAGTCATGGATTACATGATAAGGCTTTGTCTCTTATATT
TCTTAGTTAGTGATGAAGTCATAGATTACTAAACTAGATATTCTTGTCAG
AACTATTTGACATTGAACCCAAGTCTTGAATATTTTAGCTATATGAGATT
GACTTAACATCTGGGTATTCTTGAATCTTGATGGATTTTATGGGGTGATC
TATCCGAGTCTAATCGTGATTCTAAGGTGATTACTGGATAGTTCCAACTT
GAGAATAAGGAGTGTTCAGTTTCTCTGATTGGTATAATGGCTTCCAATGG
TACCATAGGACAGACTTGTCCACATCCAATGAAGGCTACTTCAAATGGAG
TCTTCCAAGGAGATAATCCTCTTGATTTTGCACTCCCTCTTGCCATTCTG
CAGATTTGTGTGGTTTTAATTGTCACTCGGGGTCTTTCTATTTTGTTAAG
GCCGTTAAGACAACCTCGAGTGATCGCAGAGATTGTTGGAGGAATTTTAC
TTGGACCATCAGCTCTGGGAAGAAACAAGGACTATCTGCAGGCAATCTTT
CCACCTAAGAGTATCACAGTATTGGACACTCTTGCTAATCTTGGTCTTCT
GTTCTTTTTATTCCTTGCTGGCCTGGAATTGGATCCTAGATCCCTTCGTA
GGACTGGAAAGAATGCCCTTGCCATTGCTATGGCAGGAATTGGCCTCCCA
TTTACAATAGGAATTGGTACATCATATGTCCTTCGACAGACCATTGCGAA
AGGTGTGAATGGGACTGCATTTTTCGTATTTATGGGTGTTGCCCTTTCAA
TTACTGCTTTTCCTGTCCTTGCCCGAATACTGGCAGAATTGAAACTTTTA
ACAACAGATCTTGGGAGAATGGCTATGTCAGCCGCAGCAGTCAATGATGT
TGCTGCATGGATTCTACTTGCCCTCGCTGTTGCACTATCTGGCAACAATG
TCTCTCCTATTGTCTCGTTTTGGGTCTTTCTTTCTGGGTGTGGTTTTGTC
GTTTGTTCGTTTCTCATTGTCCCACCAATATTTAAATGGATAGGCAAGCG
TTGCCATCAAGGTGAACCAGTGGATGAGACATATATTTGTGCTACATTAG
CAATTGTGCTTGCAGCAGGGTTTGTTACTGATGCTATTGGAATTCATGCC
ATGTTTGGAGCTTTTGTGATAGGAATCCTTGTTCCAAAGGATGAGCCCCT
TGCAGGTGCACTAGTGGAAAAGGTTGAGGATCTTGTATCTGGACTCTTCC
TTCCTTTATACTTTGTTTCAAGTGGACTGAAAACGAATGTAGCTACAATT
CAGGGGCTTCAATCATGGGGTCTTCTGGTGTTGGTCATAATCACAGCTTG
CATTGGAAAGATTGTCGGAACTGTTCTGGTTTCTCTTTCCTGCAAAATGC
CTCTGACTGAGGCTCTCGCAATGGGGTTTCTAATGAACAGTAAAGGTTTG
GTTGAGCTCATCGTCCTCAACATTGGCAAAGATAGAAAGGTACTGAATGA
TCAGACATTTGCTATTATGGTTCTAATGGCTCTCTTTACAACTTTCATCA
CCACTCCAATAGTCATGGCCATTTATAAGCCTTCTAGAAGAGGAAGAAAA
ACTGATTACAAGCACAGAACAATTGAGAGGAAAAACTCAAACACGCAACT
TCGGATATTGGCTTGTTTCCATAGCTCTAGAAGCATCCCTTCTATTATAA
ATCTTCTAGAGGCTTCCAGAGGAATGGATAAGCGTGAGGGACTATGTGTA
TATGCGATGCACCTCAAGGAGCTCTCAGAGAGGTCTTCAGCAATATTAAT
GGTACACAAGGCTAGAAGGAATGGCTTACCCTTTTGGAACAAAGGATTGC
GTACAGATTCTAACCAAGTAGTTGTGGCTTTTGAGACATTCTGTCAGCTA
AGCCAGGTGTCTGTAAGGCCAATGATATCAATATCTTCTCTCTCTGACAT
GCATGAAGACATTTGCACAACTGCTGAGGGTAAGCGAGCAGCAATCATTA
TTTTGCCATTCCACAAGCACCAAAGGTTGGATGGCTCTTTGGAGACCACT
CGAACTGACTTCCATGGAGTCAACATGAGGGTTCTCAAGCATGCTATGTG
CTCAGTAGGGATATTTGTTGATCGTGGACTTGGTGGAACAACGCATGTGC
CTGCAAGCAATGTCTCCTACTCTGTAACCGTCCTCTTTTTTGGTGGTCGT
GACGATCGTGAAGCCCTTGCTTACGGGGCACGCATGGCTGAGCACCCCGG
CATCAGATTGACCGTAATCCGATTCATAGTTGAATTAGAGTCTCTTCGAG
AAATTATCCCAGTTGAGAGAAATGCTGATCTTTCTGCTAAATTGGTTTCT
CAAGACGATGAGTTTTTAACTGAATTCAAGGACTCACAGTCCAATAACTG
CTCTATAACATACGAGGAAAAGTTTGTCAGAAATGTTGCGGAAACCGTTG
GCATTATTGGTGAACATAATCGATGCGATCTGTTTCTGGTCGGCCGGTTG
CCTGAGGGTGAACTAGCTTTAGCTTTGAATAGGAACACTGAATCCCCAGA
ATTAGGACCTGTCGGGTGTTTGTTGACCTCATCAGAATTTTCAACAACAG
CCTCCGTGTTGGTGGTACAACAATATTACGAAAACCTGTCTACAGATTTT
GGGGATCTGCTTGACAGAGATACAGAGGCCACCATCAGGGAAGGAAAGCC
ATGCAAGCGAATCGTGCTACACTACCACGACATTATCTTCAATGGCACAA
ACAAGGAGAATGCAACATCTGCTATTTCCGCCAATGCAACTGCCCTTGGC
AAGTTCAAATTCGGACAGCTGGTAATCTTCGATGATCCTTTGACAGAAGA
TCAAAATCTCTTGTCTCCACCTGTGGCACGAGCTCAAGGCTTATACTTTT
ATGACATGAAAAGCACATATAATGCTTGGTTTTCATGCACTTTGATCTTC
AATTCGACTCAACACACAGGTACCATCAACATGATGGGTGCAGATATGAT
GGACTCAGAAACTAGGGATCTTTCTGTCGTCGGAGGGACCGGGGATTTCT
TCATGACACGAGGCATCGCAACTTTTACCACTGATACCTTTCAGGGTGCT
GCGTATTTTCGACTTAAAATGGATATAAAGTTGTATGAATGCTATTAGAA
GAGCTGTCTGTGGAACTCGCATAGTGAAGTTACTTCAGTGAGTCAGTGAC
TGTATTTTCTTAGCAGAAATGAAGTGAGTAATGAATAAGCATTGTTTTCT
TTTGAGCAGATTCTCTAATCTCTATTGAGTATCAGGAAATGATTTTATAA
TTAGGATGCTCATA
MASNGTIGQTCPHPMKATSNGVFQGDNPLDFALPLAILQICVVLIVTRGL
SILLRPLRQPRVIAEIVGGILLGPSALGRNKDYLQAIFPPKSITVLDTLA
NLGLLFFLFLAGLELDPRSLRRTGKNALAIAMAGIGLPFTIGIGTSYVLR
QTIAKGVNGTAFFVFMGVALSITAFPVLARILAELKLLTTDLGRMAMSAA
AVNDVAAWILLALAVALSGNNVSPIVSFWVFLSGCGFVVCSFLIVPPIFK
WIGKRCHQGEPVDETYICATLAIVLAAGFVTDAIGIHAMFGAFVIGILVP
KDEPLAGALVEKVEDLVSGLFLPLYFVSSGLKTNVATIQGLQSWGLLVLV
IITACIGKIVGTVLVSLSCKMPLTEALAMGFLMNSKGLVELIVLNIGKDR
KVLNDQTFAIMVLMALFTTFITTPIVMAIYKPSRRGRKTDYKHRTIERKN
SNTQLRILACFHSSRSIPSIINLLEASRGMDKREGLCVYAMHLKELSERS
SAILMVHKARRNGLPFWNKGLRTDSNQVVVAFETFCQLSQVSVRPMISIS
SLSDMHEDICTTAEGKRAAIIILPFHKHQRLDGSLETTRTDFHGVNMRVL
KHAMCSVGIFVDRGLGGTTHVPASNVSYSVTVLFFGGRDDREALAYGARM
AEHPGIRLTVIRFIVELESLREIIPVERNADLSAKLVSQDDEFLTEFKDS
QSNNCSITYEEKFVRNVAETVGIIGEHNRCDLFLVGRLPEGELALALNRN
TESPELGPVGCLLTSSEFSTTASVLVVQQYYENLSTDFGDLLDRDTEATI
REGKPCKRIVLHYHDIIFNGTNKENATSAISANATALGKFKFGQLVIFDD
PLTEDQNLLSPPVARAQGLYFYDMKSTYNAWFSCTLIFNSTQHTGTINMM
GADMMDSETRDLSVVGGTGDFFMTRGIATFTTDTFQGAAYFRLKMDIKLY
ECY
| Relationships |
|---|
| The mRNA, XM_017367610.1, is a part of gene, LOC108199678. |
| The polypeptide, XM_017367610.1, derives from mRNA, XM_017367610.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |