| NCBI Gene |  |
|---|
| Relationships |
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| The exon, LOC108205241.exon3, is a part of gene, LOC108205241. |
| The genetic_marker, MK009339 1_6966269, is located in gene, LOC108205241. |
| The exon, LOC108205241.exon2, is a part of gene, LOC108205241. |
| The exon, LOC108205241.exon1, is a part of gene, LOC108205241. |
| 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. |
TTGGGTGACCCGAAACCGCCAATTTTAACCGATAATCTCTCTCCCTCTCT
TCTCGCTCTCTCTCCCTGTCCATCCGCTGTAAACACACAGACACGTATAT
AATGAAATAACTAATACTCCACTTCATATAAACCCTGATTTTGTAGACCT
TTTTATCTGTCAATCACACACTCTAATCCAACTCATCTTCCTTAATTAAA
AAAACCCACTCCCCCTATTTCTCCTTCATCATCATCATCTTTCCTTCTCT
TTCCTCTCTCATCTTTACCCCCCACCTCTCTCCCTCTCTCTCAAATTACA
TTCTCTCTCTCCCTTCCTACAATCTCTCTGACATAACATTTTCTCATCCA
CTTCCGATGCCCCTAACCTAGGGTTTCAAAACCTCCCTCTCTCTGTCAAT
GCTCCAAACTTAGTCTTCCAAATCCACACACATTGTGTTCAAAATGAGCA
CTCTCTCTCCGCTCTCGCTCCTCCTCCTCTTCTCTCTCATCTCCGCCTCC
CTCGCCGTCGACTCCGATGAGCTCCGATCACTCCTCGAGTTCAAGAAAGG
CGTAAAAACCGATCCTTTAAGCAAACTCGCCACTTGGAACATTCAAAACC
CCAACTCAGATCCAACCGACGCCGTTTGCTCTTCTTTCTACGGCGTCTCC
TGCGAATACAACTCAAATTCATCCGGTCTAGTCACCGGCATTGCGCTGGA
CCGGCTCAATTTAGGCGGAGACTTGCGGTTTTCGACACTAAATGGACTCA
AAGGACTTAAAAATCTGAGTTTGGCAGGTAATTCACTAACCGGAAGACTT
GTACCTACACTAGGTTTAATCACTAGTTTGCAGCATTTAGATCTAAGTGA
TAACTCGTTCTACGGGCCAATTCCTGGGAAATTGAATGATTTGTGGGATT
TACGGTACTTGAATTTGTCGAGAAATAAGTTTGTTGGTGGTTTTCCGAGT
GGAATGGAGAGGTTGCAGCAGTTGAAGGTTCTTGATTTGAGTGGGAATGG
ACTTTGGGGTGATGTTAGGGGGTTGTTTAATGGATTTAGGAATGTGGAGC
ATGTTGATTTGAGTGGAAATGAGTTTTTCGGGTCGGTTTTGGTAGATGCA
GGCAATATTTCCGGGTGGGCTAATATTGTGGAATATGTGGATTTGAGTAG
TAATAATATCAGTGGGGGATTCTTGAGTGGGGATGTTGTTTTGTTGTTTC
GGAAGTTGAGAGTTTTGGATTTGGGGGATAATCAGTTGACTGGTGAGCTT
CCTTCGCTTGGGGATTTGCCAAGTCTCCGTGTTTTGAGGTTAGGGAATAA
TCAGTTTTATGGGTCGATTCCAGAGGAGTTGTTGGGGAGCGCGGTCCCCG
TAGAAGAGTTGGATCTCAGCCGCAATGGGTTTTCAGGTGAGAATGTGGCA
TCTGTACATATGACATTTACTGTATGTTATTTGTTCTGTTCAGTTTATAA
CTGAAATGGTATAAGAATCAAAGTATTTTTCTTCTTGTATTTGTTACTGT
ATATAACATCGAACAATGTATGGAATGACTATCAGCACTTTCAATATATT
GCAGCTTGAGCTATATTATCTTTGAATCACCACCAAATTATACATACGCG
CATACATGTGGTATTTGCTTGATCGTTCTGACTTCAAACTGACAAATATA
GTACCCAGGTGCCACTTGTTAAAGAATAATAAAAGTAGGACTGCACCTTG
TGCCTCTTTATTATGAGTGACTGTGTGCCTTTGTTTTTGTGTTTAAAAAA
TGTTAGCAGTATATGACATAGGCAAACAAAGGTCTTCCTTTGGTTGGCGT
TGTGGTAACTTATTTTTCGTTTTTATGTGCGTTTTTTTTTTTGGATTGAT
GCTAATGCTATTAGTGGTTGTGTAATTAGTTTTATATGTAGATTCAGAAT
ATAGTTCTACTGCTAGGTTTTATGCAGTAATCTAAGTTGTCAGATCATGA
TTGCAGGTTCGATCCCTAAAATTAACTCAACTACTCTGAGTACATTGAAT
CTATCGGTGAATGCGCTCTCTGGTTTATTGCCACCTTCAGTTGGAAGTTG
TAAAATTGTTGATTTGAGCAGAAATAGTCTATCTGATGAGATTTCAGTTG
TGCAAAACTGGGAAGCGAATTTGGAAGTTCTTGATTTAAGTTCAAACAAT
TTGGGTGGAATCATTCCTAACTTTACTGCTCAATCGCAAAACTTGGCTAT
GCTGAACCTGCAAAACAATTCTCTAGTTGGTAGCCTACCTGCTGCGCTGG
GAACCTACCCTAGACTATCCGCGGTTGACCTGAGTGTTAACAAACTTGAT
GGGTCTATTCCGCGTAGCTTCCTTACTTCAGTGACTCTGGTGAGCTTTAA
TGTATCAGGGAATCAGCTTTCAGGACCCATTCCTCTACAAGGATCCCATA
CCAGTGAATTATTGGTTTTACCTTCTTATCCGCTGATTGAGTCACTTGAT
CTTTCAGATAATTCCTTATCTGGACCATTGCAAGCAGAAATAGGAAACTT
GGGAAGGCTTAAATTGCTGAATCTTGCAAAGAATAAGTTATCTGGAGAGT
TACCAGATGAATTGAAAAAACTTGTTGGTCTGGAGTATCTGGATCTATCC
AATAACAATTTCAGTGGTAAGATACCTGATAAGCTTCCATTAACTTTGAA
GGGCTTTAATGTGTCTTATAATGATCTATCAGGAAGTGTTCCTGGAAACC
TGAACAAGTTTCCAGATTCTTCATTTCATCCTGGAAATGTCTTGCTAAAC
GCCCCAGATGGTAGTCGATCTAATGGAGGGGCTCCTGTACAGCCTGGAGG
GGCTCCTGTACAGGCTGCAGGGGGGAGAAAGAACCACAAATCAAAGACTA
ATATCAGGACAGCTATTGTTGTAGCTTCTGTTGTAGCTGCTGTAATGATA
GCCTTCATTCTACTGGCTTATTATCGAGTACAACTTCAAGATTTCCGTGT
AAGAAGTGGATTTAGTGCGCAAACTGCTGGGAGAGATGTTAAAGTTGGTA
GATTCAGCCGCCCTTCAATATTTAAATTCCATTCAAGTGCTGAGCCACCT
ACTTCATTAAGCTTTTCTAATGATCTCTTGCTAGCATCAAAATCAATGTC
ACTATCAGGGCAGAAAGAATTTATTGAACCTGTTTTACCCTCAGGAAAGG
CTGCTACCTCAGATCCAGTAATCTTAATCTGCTTGATAGTTACCCCGAAA
CATCAGGAAGAAAGTCATCTTCAGGTTCGCCCCGATTCATTGAGGCAATT
GAACAACCTGTAACACTAGACGTGTATTCACCAGATCGGCTGGCTGGAGA
ACTTTTCTTTCTTGATAATTCACTGGCATTGACAGCTGAAGAGTTATCTC
GAGCACCAGCAGAAGTTCTTGGTAGAAGTAGCCATGGCACATTGTATAAG
GCTACCCTACGTAGTGGGCTTATGTTAACTGTGAAGTGGTTGCGAGTGGG
ATTGGTTAAACACAAAAAGGAGTTTGCGAAGGAAGTCAAAAGGATTGGTT
CAATTAGGCATCCAAATATTGTTCCGTTACGAGCATACTATTGGGGTCCA
AGAGAACAAGAAAGGCTTGTTTTGGCAGACTACATTGATGGAGATAGTGT
GGCTCTACATCTGTATGGTAAGAGATAGCGAGTGATTATGTATTATGTGA
TAGTTTTACTCTATGCCTTTCTTGTATATATCCTGTTAGAATCACCCTTT
TTTCCCTCATCCACCTAAATGCACAGTTCTACCCTCTTCTTTTAGCTTGA
GCCTTGTAGTTTCAGTTTAAGATCTTGTATTAGCTTCTTGCGCACTGGAT
ACCAGTAAGGATATATACACATATATTGTCATAGTTTTGGTGAGTTGGAT
CATGGATAACAGCGAATTGTGTTCTGGTTATTTGTCGAATTTTTGTGTTA
AAACTTATAGGCATCATATTACTTGTAAGGTGTGGTTGTGACTGGGTTTC
TTTTTACTCTGAGACTGGCACATGATTATCTGAGACCTAGTGAGTATAAA
TCTTTAAATTATTATTTTACTTTTGCCCAACATTTCTCGTCACCTGACCG
AGCATCTAGTAATGGTTCTATGATAAGTGAGTTTGTGCAACACACAATGG
GGCTAAGTGCTGTCATGTCTTTGATCTCTTTCCCCTCGTACATTTTAATA
GCCTAGAAATATTTAGGGTGTTTGTTGGAATCTTATGAGTAACACACATC
AAAGTTTCGGTTCAGGCATGTTGATACTAAGCTGTCTCTGTCTCTTAGAT
ATCCAGTGTATCTTTTGTTCTAAAAAATTCAGGATACAGAGACATGCAAG
TCAAACTCCATATGATCTTGTGGTAAACGAATTTATGTTTCTCTGAATGG
GTTAATGTGCTTTATGTGACACGTTAACACCAAAATTCCAGGGTATTAGA
TCTAAAAAAACAACAAAGTCGAAGCCCCAAATCCAGATCTTATATATGTT
GTTATCGGCTCTTATTTTAATGTCTTGCATATTGATTATGTACTCATTGT
TATGCAGGCAGAAAATTATTCTACATAGTTTTGCTTTTAACAGTCTTTAT
CATGTGCAGAATCAACACCTCGGAGGTACTCACTGCTTTCATTGAACCAA
AGGTTCAAGGTTGCTGTTGATGTTGCTCGTAGTCTTGTGTATCTTCATGA
GAAAGGGATGCCTCACGGAAACTTGAAGCCAACAAATGTCATACTGGCAG
GCTCTGATTATGATGCCCGCCTTACAGACTATGGTCTCCACCGACTCATG
ACACCAGCTGGCATTGCAGAACAAATATTGACCTTGGGAGCTCTTGGATA
CCGTGCCCCAGAACTAGCAACCATGAGTAAACCAGTCCCGACCTTTAAGG
CTGACGTGTATGCATATGGAGTCATGTTAATGGAATTGTTGACTAGAAGA
AGTGCCGGTGACATCATCTCAGGTCAATCGGGTGCAGTTGATCTTACAGA
TTGGGTTCGACTGTGTGATCAAGAAGGGCGAGGCATGGACTGTATAGACA
GGGATATTGCTCGTGGTGAAGAACATTCGCAAGAAATGGATGAATTACTT
TCAATATCAATAAGGTGCATTCTCCCTGTAAATGAAAGGCCTAACATGAG
ACAAGTTTATGAAGATATCTGTTCTATATCAGCCTAGTGTACGAAATTTC
TTCCACGCCCTTCTTTCATAACTTCATTGCTGATTTCTCATTATTTCATC
TTTCTCCTTTGTAATCAAAATTTTCCCCTTCAATTTTTTTGTGTAAAGGG
ACGAATGTCCATTACTTGATTGAGACGGTAGTATTTTTCTTTTGATCTTT
TAGTGAAAAGGGTGTCCATTCTTTTGTTCTCCAA