| 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. |
TCTTGCTTTTTGAGGAGTAGATACTAGTAGTAGCTTAAAAGGTAAAGTTG
CAAACTTGGAATAGAAAGAGAAGGCATGAGGATTGATGCATAATGGCATG
TAAGTATTGTATGTATATTTTATATTAACAGACAAAGCAGACCCAGAAAC
ACATAGCATGGTAGGTTATGATGACTTAAGGATGATGATTCTTTTTGCTG
TTGATTAGCAAAAAGATGCAATTTTTTAAAGTGGGCATGGTCAGAAATCT
TGCAGCTCTTTGTCTCTCAATCATCTTGCTCATGTGAGAGAGAATTTGGA
GAGAAAGAGACTTGACAGCAATCTAAGATTTGCATTCTATAAATTGGCTT
GATGATGGACTTGGAATTTGAGAAGATCTGTGTAGTAGATGGAAGTCCTA
ATACTGTCCTTCTTTGTCCACGACAATTCTACAAAGTTGAAAGGGAAAAG
ACCAATAAACCTCATGATGCATTGAGCCCAAAACAAGGGTTTTCAGATAT
AAGGTTTCGTCGCTATAGTAGAGCATCCTGTAAACGATCTCAATCTAAGA
GTACTGTCCCGGAAGGAAATAAAGTTCTAAAAAGAGGTTCTGTATATCAG
AGTTCTCAAGAAGTAACAATGAAGGATTTAGGTGATGTTGGGGATAGGAG
AAAAATTGAATTTCCACAAGGCAGTGTCAATGCCTTATCAATTGGGGTAG
TAAATTCGCTGTGTGACTCAGATGAAGATAGCTCATCAGTAGAGCATAGA
TCATCAGCGATGTCTCTCAACTCGGAATCAAGCACATCAGTAACTAGCAC
ATCAGTAACTAGCAAACCATGTACCTCTAAGGAGTTTTTCAGTAGCTCCC
GGCAACCTATTTTGAAAAGAGAGGTATCGTTAAATAGCTTCTTAAAGATT
TCCTTGAAATCCGAGGACGGAAAAAATCAGTCAGCTAAATATGCAGAGAG
AAAAGAAGTTGAGGCATCCATGTGCAATAACGATCCAACTTTTAGTCTTC
CAAGAGATGACAGCGGGCTTAAAAAGAGGGATACTGGTTCTGTCATGCAA
AAATCATTATCTGCTAGACCAGTCCTGCCCTATACGCATCCTCGATTGGA
AAGCAATTGCTCCACACCAGGCACTCTATTTTCTGGCTTAAGCCCCACGA
GAGAGACATCTGAACCGCTTCCCGAGCTGAAATCACAGAGAAGTCCTCTG
GGCTCTGTTGATGAGCATATTCCCATTGCAAAAGTTAGCATCAAAAGGAA
CAAGAGATTACATAGATCGCTCTTGCCTGATTTTTCAAAAACATCATGGA
ATACATGTGAGTCTCAAATTGTCAAGGAATACAGTAAGCCTCCACTGCCT
TGTTCACCAGCTCATTTACATGGCCATCTCAAGTTTAAAAATAGACATGG
GATGCCGTATTTTGAGTTCTTAGTGAAGAGTCCAGAAGACAAAATTATAG
CCAAGACATGGAAAGTTGGAAATGCTTTGAATTGGCTATACACCTTCCAC
ACCAGTCAAAACAAAAGTAGAGCTATATCTCCTAATTGGGGGATAAAAGA
GAGCAATAAAGAATCCGCTATGGTGGGACAGATGCAAGTATCTTGTTTAT
TGCGTTCAGATCTCAATGATGCTGGAGCTTTAGAAAACTCCACAGTGACA
GAATTTGTGTTATATGATATCAAGCAGGCAAGAAAAGATATAGCCGCTAA
AAAGGACTCTTTCTCTTCACTTGAAGCTGCTAAACCTCTTACAAGTGTTA
AAACAAACTTAGCCGGGGGAACATGCAAGTTGCACGAGACTTCTGATCTG
AGAAAATATAGTGATCAACCAAAAAATGTCTTTAATGGTGGTCACTCTCC
GTGGGAGCCAGCAGATTTACATCCAAACAATGAAATTGCGGCAATCGTTA
TTCAAGTTCCACTAGAGAAGAGGGAAAGCTTGAAGGAAAAAAGAAGGAAT
CAGAAGAGTAACCAATCATACATCAACTTGCATGATTTTGAAGGATTGGA
TCAGAGAACAAACTGCTTGTCCCAGACAAAGGTGAATGTTGTAACCTCTT
CTGGAAATCATGGTTTGCCAACTGCAGAATGTCCTGGCCCTTCACGACTA
CTAGATAGATGGAAATCTGGCGGAGGCTGTGACTGTGGAGGCTGGGATAT
GGGCTGCCCCCTTGTTACTTTTGACAATTCCAACCGATGTCCTGAGGACC
ATTCCCCCATAAACAACCAGCAGCCTTGGAAACTTTATATACAGGGAGGA
AAAGAGAAATCACCAGCATTCAGAATGACAGGAACCAAGGAGGGAGAGTA
TGAAGTTGATTTTCATGCACAATTAAGTACATTACAGGCTTTCTCAATCT
GCGTCTCTATCTTGCATAGTACAGAGGCTACCGATGCAGCTAAGCAGTCG
AGAGATGACAAGTTTCAACAATGTGATTCTCTGAGTGGGCTTTTAGATGA
GGATATTAAATATATATTTGAAAATGTGCAAGATGAGAAAAAGAAAGCTC
CAGCATCTTTTGTACTCAATCCACCCTTTTCTCCCATTGCTCGAGTATAG
TCTCAGCATATACTCTTCGCGATGAAGCAATGACATTTGAGCATCTCATG
CCGGGGTTGGACTATTTCTAATGACGTTTGAGCATCTCATGCCGGGGCTG
GACTATTTCTACCAAATTTACTCTGATCAATTAATTCAAGCCTCACAGTC
TTGTATTGCGGAAAAGTGGAGTATTGTTGATAACATGTTCGGGTGGCCAT
TATCCATTTCTTGCAGGTTACAAGCTGTTCTCACTGATCTAGCACTTCCA
GCATTTCTTATAGTCTTATATCCATAGAAATATATAGAAGGCACCATACT
TTGCATATAATCATTAGCTAAAGAGGTGTAATCATTTAAGTACATATAAT
TAGTCAGTAGTGAGTAGTAAAAGAAAATGAAGTTGGTTGCAGTTAGAAAA
GGGTCTCATGAGTCTTGAGCTTATTCATTTATTAAAAGTGTAAAAATGTG
CATGTTAGATAGATTTATATATGTATTTTATTCCTCGAA
MMDLEFEKICVVDGSPNTVLLCPRQFYKVEREKTNKPHDALSPKQGFSDI
RFRRYSRASCKRSQSKSTVPEGNKVLKRGSVYQSSQEVTMKDLGDVGDRR
KIEFPQGSVNALSIGVVNSLCDSDEDSSSVEHRSSAMSLNSESSTSVTST
SVTSKPCTSKEFFSSSRQPILKREVSLNSFLKISLKSEDGKNQSAKYAER
KEVEASMCNNDPTFSLPRDDSGLKKRDTGSVMQKSLSARPVLPYTHPRLE
SNCSTPGTLFSGLSPTRETSEPLPELKSQRSPLGSVDEHIPIAKVSIKRN
KRLHRSLLPDFSKTSWNTCESQIVKEYSKPPLPCSPAHLHGHLKFKNRHG
MPYFEFLVKSPEDKIIAKTWKVGNALNWLYTFHTSQNKSRAISPNWGIKE
SNKESAMVGQMQVSCLLRSDLNDAGALENSTVTEFVLYDIKQARKDIAAK
KDSFSSLEAAKPLTSVKTNLAGGTCKLHETSDLRKYSDQPKNVFNGGHSP
WEPADLHPNNEIAAIVIQVPLEKRESLKEKRRNQKSNQSYINLHDFEGLD
QRTNCLSQTKVNVVTSSGNHGLPTAECPGPSRLLDRWKSGGGCDCGGWDM
GCPLVTFDNSNRCPEDHSPINNQQPWKLYIQGGKEKSPAFRMTGTKEGEY
EVDFHAQLSTLQAFSICVSILHSTEATDAAKQSRDDKFQQCDSLSGLLDE
DIKYIFENVQDEKKKAPASFVLNPPFSPIARV
| Relationships |
|---|
| The mRNA, XM_017379562.1, is a part of gene, LOC108208930. |
| The polypeptide, XM_017379562.1, derives from mRNA, XM_017379562.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |