| 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. |
TTCGATTTCGAATTTGATTACAAACTGCAGAGCGAACTCAAAAATTCGAA
CTCACACTCCCACATCCCTCCGATTCATCAAAACAACCAGCCGGCGACTC
TCCCACTCTCCGGCCACCGCATTCCTCCCCACTCGCCGCTTCTTCCACAA
TCTCCTAATCAACTCATTTCACCACTCTCTCCAACTCAAAACACTAAAAC
CCCAATTTCAAAACCCTAAAACCCCAAAACAACAAAAACCTAAAACCCTA
ACCTTCGGAATGTTCTCTCCGGGCACAAAGAGAGCCAAGCCGCGCCCAAC
TACACAGCCACCCGAAGCTGCCTCGCCGCACACACCACACCACATTGCTA
ACCGCCCTTCCACCGGCACTCCCGCCCCCTGGGCCTCCCGCCTCTCCGTC
CTCGCCAGGATTTCACCAGGGAAGAAAAGTGACAAGGATGACGAGGATCC
AAATAAGCCTGTATATGTTGGAGAGTTTCCTGAAGTAGTTCGCAATGAGC
AAGCTAATCTAATGCACAAGCAGTTGCATGGTGATGCATTTAACTCTGGC
GGGATTGACAAGGCGACATCCTTGGCATGGATTATTTGTGGAAGCAAAAT
TTTTATATGGGAGTACTTGGCGTCCGCTAAATCTAGAAAATGTGTCGTGC
TTGATATTCCCTCAACTGTATCAGATATTAGAGGTTCAAGCATAAATTCG
AGACTTGGGAATAACTGGTCACTTTGTATTATTATTAGGGATAGCATGCA
TAAGAGTAGAAGTAAATCTCTAAAACAGTACAGCTCTGTTGGTGTTATAT
TGTGTCATCTGAAAAGTCGAGCCGTAGTGTATTGGGCAAACATCTATTCT
GAAGGAACAACCTCTCCTGTCACAAGTATTGACAATACAGAAGCAAATTT
TTCGCCTGGTCAACAGAAAACGGGTTCAAACTATTACAACTCTTTTATTG
CTTCTGCTGCCACTTATCCATCTAATGTCTGTCTGGCTCTTGCTTGTAGC
TCTAGTGGTGATATTTGCCAATTCATCTGTAGCCCTAATGGTATCGAGCG
TAAGGTGGCTATTCATAATGTCTTAGGGTTATCCCTCCAAGGAAGTGATA
TCAACCAAGTCAACAGAAGTAAGGGATATCCGAGGTCATTAACTTGGCAC
TTTGCTAATCATTCTTTGGAAGAAACCGAAAGACAATTTCTTTTGTTGAC
AGACCATGAGTTACAATGTTTTACTGTCAACCTTAATAATTTTTATGAAG
TTTCAAAGCGCTGGTCGCATGAAATAATTAGCCCTGATGGTGATCTAGGT
ATTAAGAAGGGTCTGGCTGGTCAGAAGCGAATTTGGCCTTTGGACCTGCA
ACTCGACAATTCTGGAAAAATAATTACTGTTCTTATTGCCACTTTCTGCA
AGGATCGGGTCACCAGTTCAAGTTTCATAGAGTACTCTCTTCTGACCATG
CAATATAAATCTGGGCCAAGAATTTCGTCAGAAAGCACTGAGCAAACAGA
TGAGAATGTTTTGGAGAAAAAAGCTCCTCTTCAAGTAATTATACCAAAAG
CAAGAGTGGAGGATGAGGATATCTTATTTTTAATGAGATTAAAGGTTGGT
GGTAAACCGTCTGGGTCTGCAATCATACTTTCTGGTGACGGTACTTCTAC
AGTCTCACATTACTGGAGAGATTCCACACGGCTTTATCAGTTTGATCTAC
CCTATGATGCTGGGAAAGTTCTTGATGCTTCAGTCTTGCCTTCAGATGAT
GGTGATGACGGACCATGGGTCGTTCTCACTCAGAAAGCTGGATTATGGGC
AATTCCTGAAAAGGCGGTTTTGCTTGGAGGTGTTGAACCGCCAGAGCGAA
GTTTGTCACGGAAAGGAAGTTCTAATGAAGGATCTGCACAAGTGGAAAGG
AGAAACTTTCCCTTTTCCGGTAATATTGTCCCCAGAAGGGCTACTTCTGA
AGCATGGGATGCTGGAGACAAACAAAAAGCAGTGTTTACGGGGATCACAC
ATAGAACTGCTCAAGATGAGGAATCAGAAGCTTTACTGAATGTTCTTTTC
AATGATTTTCTTTTATCAGGTCAGGTTACTGGTGCATTCGACAAGCTAAA
TAGTTCCAGGGCATTTGAAAGGGATGGAGAAACAAGTGTTTTCACTAGGC
TCAGCAAATCAATTGTTGACACCTTAGCCAAGCATTGGACAACTACTAGA
GGTGCTGAGTTCGTGGCTCTATCTGTTGTTTCCAACCAACTCATTGATAA
GCAGCAAAAGCATCAGAAATTTCTACAGTTCCTTGCATTATCAAAATGCC
ACGAGGAACTGTGTTCTAAACAGAGACAATCATTGCAATTTATAATGGAA
CATGGTGAAAAACTTTCTGCTGTGATTCATCTGAAGGAGTTGCAGAACAA
CATTAGCCACCGCTCAAGTGGACTTGGCGGTACTTACTCTACAATGGAAA
ATAAAGTTTCTGGTCCACTTTGGGATCTGATTCAGTTAGTTGGAGAGAAA
TTGCGAAGGAATACTGTCCTCCTGATGGATAGGGACAATGCCGAAGTCTT
TTACAGTAAAGTTTCTGAACTTGAAGAAGTATATAGTTGCTTAGATAGAC
ATCTGGAGTTTATAATTACTGAGGAGATGCAACTACCTGTTCAGTTCGAA
CGAGCTTGCGAATTGTCAAATGCGTGTGTACTCTTAGTTCGCACGGCATT
GAATTACAGAAATGAGTATCACATGTGGTATCCATCTCCTGAGGGTTTGA
CACCATGGTATTGTCGAACTGTTGTACGAAGTGGGCTTTGGAGCATTGCA
TCTTTCCTGCTTCAGATCTCAAATGAATCAAATCGCCTTGACAGGCCCAA
AAGGTTGGAGTTTTATAGTAACTTAGAAGTTCTGGCTGAAGTGCTACTTG
AGGCATATTCTGGTGCGATAACAGCAAAAATCGATCTGAAAGAAGACAAC
TTAGGTCTACTAAATGAGTATTGGAGTAGAAGAGACACACTTTTTAGCTC
ACTTTATCGGCAAGCAAAAAGTTTTGTTGAACCCAGTTACCAGGATTTGA
GTGAAGGAGATGAAGAGCAGGGTGAGGAGATATTCAGACAGCTGTCTTCT
CGTTTATTGTCAATTGCTAACCGCCATGAGGGTTATCAAACACTGTGGAC
TATATGTTGTGATCTCAATGATTCAGACCTTCTTAGAAGTTATATGCATG
AGAGCATGGGGCCAAAGGGAGGGTTTAGCTACTATGTTTTTGAGCAACTG
TACAATAATAAACAATTTTCCAAGCTAATTAAACTTGGGGAAGAGTTTCC
AGAAGAGTTGCTTACTTTCCTAAAGCTTCATAATGACCTCCTCTGGCTTC
ATCAGTTGTTCGTTCATCAATTTTCCGCTGCCTCTGAAACTCTCCATAAA
CTGGCTTTTTCTCAAAATGCTGGCTTTAGTCCAGAAAGTGAGGTGCTTGA
ATCTCATCATCCAGTTATAGAACCTACACTGGCAGACAGGAAACGTTTTC
TGAATCTATCAAAGATAGCTGCATTGGCAGGTAAGTCTGCTGATTATGAC
ACAAAGTTAAAGCGGATTGAAGCTGATTTGAAGCTTCTGAAATTGCAGGA
AGAAATATTAAAACTCCTTCCTGAGAATGAAGAAACACGGAAGATTGGAG
AGCGGCTTCTTCCTTCACTTGAGCTTATTCAATTGTGCCTTGGAAGTCAG
CATCGAGAACTTTCTATTTGGGCTTTTGATGTTTTTGCTTGGTCTACATC
ATTTTTCATTAAATCCAACGCAAGCCTACTGGAGGAGTGCTGGAGGAATG
CTGCTAATGAGGATGAATGGGGGGAAATTTATCAAACTTCTATGAGTGAA
GGCTGGAGTGAGGAAGAAACCCACGAGTATCTTAAAGAAACTATCCTTTT
CCAAGCTTCTCGGAGGTGCTATGGACCCAATGCAGCAACTTTTGAAGGAG
GTTTCGAGGAAGTGCTTCCTCTGAGACAAGAGAATACTGATTCTTTTTCT
TTAAAAGAAACAGGTTCTGTTGAAGCAATCCTTATGCAGCACAAGGATTT
TCCTGAAGCAGGGAAGTTGATGCTGACTGCTATCATGCTGGGAACTTTTC
ATGCTGATTTGACGGTGGAAGGGAGTCCTTCTCCAATGGAGGGATAGTGA
ACAGTAATGATTAATATTTTTGTAATTTTGTTTAAATGAATTACGGTAAT
GCCTATTGTTGTAACTACAGTGACTTGCAATCATGAGTTGAGTTTCGAAG
AACAAGATCTCAAAGATTCAGCCTGTATTTATCATACTA
MFSPGTKRAKPRPTTQPPEAASPHTPHHIANRPSTGTPAPWASRLSVLAR
ISPGKKSDKDDEDPNKPVYVGEFPEVVRNEQANLMHKQLHGDAFNSGGID
KATSLAWIICGSKIFIWEYLASAKSRKCVVLDIPSTVSDIRGSSINSRLG
NNWSLCIIIRDSMHKSRSKSLKQYSSVGVILCHLKSRAVVYWANIYSEGT
TSPVTSIDNTEANFSPGQQKTGSNYYNSFIASAATYPSNVCLALACSSSG
DICQFICSPNGIERKVAIHNVLGLSLQGSDINQVNRSKGYPRSLTWHFAN
HSLEETERQFLLLTDHELQCFTVNLNNFYEVSKRWSHEIISPDGDLGIKK
GLAGQKRIWPLDLQLDNSGKIITVLIATFCKDRVTSSSFIEYSLLTMQYK
SGPRISSESTEQTDENVLEKKAPLQVIIPKARVEDEDILFLMRLKVGGKP
SGSAIILSGDGTSTVSHYWRDSTRLYQFDLPYDAGKVLDASVLPSDDGDD
GPWVVLTQKAGLWAIPEKAVLLGGVEPPERSLSRKGSSNEGSAQVERRNF
PFSGNIVPRRATSEAWDAGDKQKAVFTGITHRTAQDEESEALLNVLFNDF
LLSGQVTGAFDKLNSSRAFERDGETSVFTRLSKSIVDTLAKHWTTTRGAE
FVALSVVSNQLIDKQQKHQKFLQFLALSKCHEELCSKQRQSLQFIMEHGE
KLSAVIHLKELQNNISHRSSGLGGTYSTMENKVSGPLWDLIQLVGEKLRR
NTVLLMDRDNAEVFYSKVSELEEVYSCLDRHLEFIITEEMQLPVQFERAC
ELSNACVLLVRTALNYRNEYHMWYPSPEGLTPWYCRTVVRSGLWSIASFL
LQISNESNRLDRPKRLEFYSNLEVLAEVLLEAYSGAITAKIDLKEDNLGL
LNEYWSRRDTLFSSLYRQAKSFVEPSYQDLSEGDEEQGEEIFRQLSSRLL
SIANRHEGYQTLWTICCDLNDSDLLRSYMHESMGPKGGFSYYVFEQLYNN
KQFSKLIKLGEEFPEELLTFLKLHNDLLWLHQLFVHQFSAASETLHKLAF
SQNAGFSPESEVLESHHPVIEPTLADRKRFLNLSKIAALAGKSADYDTKL
KRIEADLKLLKLQEEILKLLPENEETRKIGERLLPSLELIQLCLGSQHRE
LSIWAFDVFAWSTSFFIKSNASLLEECWRNAANEDEWGEIYQTSMSEGWS
EEETHEYLKETILFQASRRCYGPNAATFEGGFEEVLPLRQENTDSFSLKE
TGSVEAILMQHKDFPEAGKLMLTAIMLGTFHADLTVEGSPSPMEG
| Relationships |
|---|
| The mRNA, XM_017397281.1, is a part of gene, LOC108223163. |
| The polypeptide, XM_017397281.1, derives from mRNA, XM_017397281.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |