| Relationships |
|---|
| The mRNA, DCAR_023802, is a part of gene, DCAR_023802. |
| The genetic_marker, MK009696 7_5492146, is located in gene, DCAR_023802. |
| The genetic_marker, MK003085 K0529, is located in gene, DCAR_023802. |
| 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 | |
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins. Data from this analysis can be viewed in JBrowse here. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| DCAR_023802 | DCAR_023802.mRNA | mRNA | DCARv2_Chr7:5491881..5500408 |
ATGCTGCTTGCTACAATCTCATGGCTAATCCTAAACATCTTGCTCTTGCT
CTCCGGTATTGAACCTATCTATGCCACTCCTCCCGACGTCTCGCTAACCA
AATCTACATGTCATGATGCATGTGGTACAATACCTGTAAGATTTCCCTTT
GGTACAGGCTTTGGCTGTGGCCATCCTGATTTTGGCAGAACAATCAAATG
TAGTAGCTCCGGAGCACTGCAGTTCTCAACTAGCACTGGCGTTTATACGA
TATCCTCAATAGACTACTCAGCCAACATTCTTATACTTCAAGACCCTTTC
ATGTCAACTTGTGCTTCAATGCAGAACTCTGGAAGCTTTCATCTGGACAG
CATGACACCATTCAAATACGTGGAGGAAGATACATTCGTTCTGCTAGGAT
GCTCTACGACGTCTCCTTTGTTTGATGCAAATGAGGATCTATGTGACACG
GGGTCTGGTTTGCATATATGCAGAGGATTGTATTCTTGCAAAGGAGTGAC
AGGCATTGGATTAGAACCAAATGCGCCAATCTCTACTTGTTGTGTGTATG
ATCCCCCGTTTGCTGTTGGTACCAGTGCTGTCAGTAATGGTTTAGATCTT
CCTAAGCTGCAATGCTCATCATATGCATCCATATTCGGGTTTGGGGGAGA
TGAAGGGAATCCGATGAAATGGCAATATGGGATTTCACTGCAGTACAATG
ACTCGTACTACTCTGATGAAACATGCAAGAATTGTGTCACAAGTGGGGGT
ACGTGTGGCTTTTCTGCTATAGATCAGTCGTTTGCTTGCATTTGTCGAAA
TGGCATCAACACAACTTCCAATTGTTTTGGCCGAGGTTAGTTCCTGACAA
CAGCTACATATCTGAAAATTTTAAAAGACACAATCTGTCAAAAATTGAAC
TAAATTTTCTGTTTGTGGTTCGACGTATGATTTTAAAGTTTAATATAATC
AGGGCACGCTTGGAGCGGGGGCTGGAGACTTAAAAGCCAGATCATGATAA
GTGTAGGAGGTACAGAAAACTCAACGCAGTCTGTTTTGCTCTCAATTTGC
ACAATAGCCATGAGCTTATTATTTTCTTTCATGAAGAGACCTGATATTAA
GCTGTTTTTTGTTCTTTAGTTTCAGTACCTTTTTGGTTAAACAAATGACA
TTGTTCTTGACCTGATTATATGTTAGTTTGAGTAACATCTAACTATTTAT
GTTTTCACTTGTCAGGAATCTTGATTTCGGTGATGCTGTGTTTTCCTTGA
AAGCGGGCAAATGCAGAAAGTACTACGCAGGTTCCAGATACTATTGAGTT
GGGAGGATTTATTTCAAGTTGTTCGTTATTTTTCACTTAAGCTTGCTCAT
TGAAATCGTTGATACGGATTTCACACCAAACTGGTCACCGGTTTCACTCA
AATATCTCAAATAAGTCACCCATTTTAAAGAATATATTATTTAAAATATT
TAATCGAGCATATCACTCCATAAGAGTAAGATGATATCAACCATCTATAG
AGAAAATGTTAAATATTTGAGAAGTTTTTCAGTTAGTCAACATTTTATTC
CATGTTGCCCCACGTACTGGAATGCTGTTCCTGTTCCTCCCGCTTCTTAA
CATTTGTAAGATGTATATAAGATGTAGATTACCGCACTTAAAAAAAAAAT
CTTGTTTTGTATAAAATTTAAACATTATCTTTTTATGCAAAAAAATAAAA
ATAAAAAATTATTAAAGTATATATTATGAGAACCGTAACACACGTGTCGA
ACCCCCTCCTCAGTGTTATGAGAGGAGGGAGACGGGGGATTACGTGGCAA
TTGAATTAAAGAATAAAAGTAAAAAATATGATAAAATTAAAGAAGTGAGG
AGATGATAAATGTCTGATTTTTCAGAAAAACCTGTTGTTGACGATTTATT
TATATATTTTTATATACCTGTTTATCATATTTTATTTTTCAAATGTAAGT
CACTTTTTTTTATAAAAAAATACATAGACGCATAATTTTTTTTTGAATTA
ATGTTTATTTAGAGTGTGTTTCGGTGTACTTGAAAAAAAAAATACACATT
CACATATTATTTCAAAAATAAATATCTTACCTTTGAAAAATAAGATAAAG
AAGGGGACCGTTGGGATATTTAAATATACAAATAAATAACATTAAATGTA
ATATTTAATGAGAAATCGAGTTAGAATTATAAAATAGAAAATACGAATCC
TCTGAGTATGGTCGAAACCGTCATCTTGAAGTAGTGTTGAATCGATAAAA
TATTTTAATAAAATATATTTCTTTTTCGGAAACGAAATTTATATTATTGA
GAAAAGTAACAAGTCATAAATTAGTAGGAATTTCATTCGGAACATGATAT
TTTTTGACGAGGAAAGTAATAATGTAGTAGGAGGGTTACTCATCTGGAAA
GACGGTGAGTAGTCAACAACCACTCTGTAGCTGCTTACCTGTCATTATCA
TCATCAATCTACACATACACACATAATTCAATCACAATCACTACTTACAT
TTCACTGTATCTATATTTTTACACATCTTTCGGTTTTTCAATATTTTCCA
AAAGCGTGAGCTCCATCTCACTGAACAAGTCTCGTAACAATAAACAGCAA
ATATTATTTTATTATTATTTTAATTGAATTTTTGTCAAACTGAGCTGAAT
TGACGGAGATGATGGAAGGGGAAGGGGGAGGAATGAAGGCGGCGATAGGA
GTGAGAGCGATGGAATCGTTAGGGTTAGGGTTTGATTTAGCGAGTGATTT
TAGGTTGAAGTTTGCGAAGAAGTGTCCGGATTCTGCGGATGGGAGATTGG
TGGTTTTGGATGATAGTAGTCGGAGAGATGTTGTGCTTCCTGGCGGCGGC
GGCGGTGTTATTCGGAATGTTCCTGATTCTATTCGGTGCGATAAAGGCGA
TCGTATTCGATTCAAGTCTGATGTTCTCACTTTTAATCAAGTAATTCGCT
CTTTTCTTTGTTTCATGTTGTTTGATGATTGTTTTGTGCTATTTTTAATT
GGAATTTAGTGAAAGTTGCCTGCTTTCGGGGTTTTGTTGGTGTGTACTGT
GTACTTTAGGATTTAAGATTATGTAGTTGTAGTACGTTTGAAATGATTGC
GTGTTGCGTGTTTGATCTCTGAATTCAATTGAAATATTTTGGAATTAAGT
AAGTATATGTTGAGTCAATTCTAATTTGAGCTTGCTGCAAATGGTGGAAG
TGATGAATTATGAGCTGTAGAGCTCAGCAATGAGGTAGTGTGGTGAATTA
TGATGATGATGATGCTCACCATTTGCGATGGTTGCGTATAGTCTCGTGGA
ACTAGTATGAGTATGTAAAGCTTCTTTTGAAAAATACTGTGTTAGTTTAC
ACTTGATGTTGAACTTCTTTTAAGGAATGTACAACAATCTATGACAACTT
TTCGCTTTCCAAATTTAATATCGAGGATGGCGTTTACTAAGACACGTAAC
TGTGTATGTCTTTTTCTGCCTGATATACTAATGTTATATTAAAAGACGGC
TGCTTTTTGATGAACCACTTAGAAGTGAGAATCCTCTTATGCTATTGACT
TTATTGTGCGGCCGACTAGTTGGGAGGATCACTTGACAAAGTTTCATTGG
GTCCTCAAACTGCTAGGATGTATAGTATGTATATGTTTACACACTTGCAT
CCAGTGACATGAATGTGTGGTTACGTGTGAGCTCCTCTTATGCCCGATTG
CTGTCCTGGTATGTAATATAGCTGAAGTTATCTGTCGGCTAGCACAATTA
ATAGTAAATGAAAATTTTTGTTTGACTATTCAGACTCTTAGTAATAACAT
ACAGTTGAACTATACCTGTATTAATTTTTTACTAGAAGCAAGAATCTATC
TATTTAAAAAAAATACCATTTTTACTAGACAAAATTAGGGCTTCATCGAC
TCTGTTTTTTTGTGAAAAATCTCTGAATACACTTTTGATAACCAATACTT
TCCAGCTCTTCAGCATAATAGAATCCTAGGGTGATGAATCTCTCAGTTTT
GCATCTGAACTAGTCTTGTGAAGATTCGTTTGCTAGCTAAAACTTAGAAG
GGTCTAATAACCATAGCTTTCCTGTGACACCGGGGAAGTTCCGTTGCTAT
AAATAAGGGAACAATTTAACCTGATAGATTTGCATTTTATGTTTACAAAC
AATGGGTGAGTTCTTCCAGAACAAATGGTGCAAGGGCTGCTATCAAGTAT
GCACGTCATTCCCCATAACTAGCTTTATATGACATCTATCTTAATATGAT
ATTATTGTTATTCTTGTGGTTGTCATCTGTTACCAGAGAAATATGTTCCA
TCTTGCAACCTAAATTCATTTTGTTTTCTTTGCACTGGTTCGTTTGCTAC
AGATGTCAGAGTTACTGAATCAGAAATCTTCAGTACAAGGAAAAGTACCT
TCAGGATACTTCAATGCTATGTTTGATTTAAGTGGTTCTTGGTTAAACGA
CGCTGCAGAAGCAGATCATCTTGCTTTTGATGGGTACTTTATCTCTTTGT
ACTATCTACACCTGATAGCATCTCCACTAGTACTGCATGACAAGGTTAAG
AAGTCTGTTCCTTCCCACTGGAATCCTGCGTCCTTATCAAGGTAATTTTG
GTCATTGTGTTTCGTACATTATTAATACCTCATTTATAAATTATAATTGA
AGTTAGTCGAATGATGTTTAAATTAAAATGCATTGTTTTCTGAGTGTCAT
TGAGGGTAGTTATAAAAGTTTTAGACTAGATTTAGCAAGGGTCATAACGA
ATTTCCAACGCCTTGGCATTCTGAGCGTGTAACAAATTAGCATTCTGAGC
CTTGTAGTGATTTGGGTACATTGGTTCAGTTTTCTTTTCCGTTTGCTTCA
GGTTCATCCGAACTTATGGAACTCACATAATTGTGGGGTTGGCTGTTGGT
GGTCAAGATATAATTTGCATTAAACAGAGACCGTCCTCTGTAATTCCTCC
TGCTGACCTGCGAGGTTATTTGGAGGATCTTGGGGATCATTTCTTTTCAG
ATGGGAGGAGTCCTCTACTAGAGAGGAAGACGAGAGATGGAAAACAGAAG
GTTTATTGTGTGTTCTAGTGTCTTTCTTATGTCCCTTCAATGTGATGCTT
TTAAGTGGATATTTCAAATTGTGTAGGTTCCCGAGGTTTTTAATCGTATG
CTACAGCAGCATACAATGCAATTCACCAGCATCACAGAAACATCAAGCAA
AGATGTAAGCTCTAAACACCTTATGCTTTCTGATAAACTAAAATGTGGGC
CATGAATATATGAAGTAATTTGGGACAGGGCCTCACAATTATTTCATCAA
AAAGAGGAGGGGATGTATTTTCACAAAGCCATTCCAATTGGCTTCAGACA
GTGGCTTCCCACCCTGAAGCAATTTCTTTCAAACTTGTACCTATTACTTC
TCTCCTCTCCGGTGTTCCAGGAAGCGGCTATCTTAGTCATGCTATCAACT
TATATCTACGCTGTAAGTATGCGATCTTGTCTCATTTATTTAATTTTTCA
TATGATTTATTTATTGTTACCATTTTGTCATACATAAAGGGTTTGAATCA
GATGAAATTGGTCTTCATGTTTGAAAAACAGGAACCTCTAAGGTTTGATT
TATAGATACCGAATGTTCAGCATAACTTTGTATATAAGATATAAATTCTA
TTAAGTGACAATGATCCATGTGCGGATCTCTCTTTCAGAATATATGCATC
AAGTATCATATTACAGAACCAAAATGTTCTATAATTCTATCCTCTGATAA
CAGTCCATATTGAACACTTAAAGTTGTACACACATAAAAATAAAGGTTCA
GCACATTATCGTGTTGAACTTTCGTTATAATTATCATGTTGTAGCATATG
GTTCTCATTTTGTTGTTCTTACATGAACCAGATCCCATAAATATGTAAAT
GGGGGATCTGTTGATAGAAGTTAAGACGCTTCTACATGTGTCAGAAATTA
TTGTCAATCCCTAACAGTATGTAAATGCTTTATCGTCGTTTTAATCCTTT
TTGTTTGTTTTATGTTCCTATATTGTACTTCATGCCTGTGGCCCTTAATG
CGATAGCTTTTGTATCAAATTAGCACTTGGGGCCTGTCTATATTTTTCTT
AGCTTGGTATTCAAGAATATAGATAGGGTTCTGCTTATTTGTTAGGCATG
TATTGGAGGAAGCTTTAGCACCTCGTACATTATCAGTTTCATTTACTTAT
ATGATATTGTATTAGTTGATGATAGTAAGTACAACTTATTCTTCAGATAA
GCCTGCTCTGGAGGATTTACATTGTTTCTTGGAGTTCCAAGTCCCCAGAC
AATGGGCCCCCTTGTTTTGTGAACTGCCTCTTAGGCATCAAAGGAAAAAG
TCTTCTTGCCCTTCACTGCAATTTGCTTTCTTTGGTCCCAAGATTAGCGT
GAGCTCCACCCAGGTAATGTATTAGTCCATGCACAATTTTATTATTATTA
TTATTTGGGGAAGGTCATCTCTGTGAGAGTTGATATATATATATAGAGTT
TTACTCCAATAGAAACCTTCTTAGTCTAGAAACTAAAAACCAAGTTGAAA
TATCACTAAATCCTAAAGCAAATACCACTAAATTCTTAAACAACCTCATC
TCCACCTCCATCTTCACCAACCCCACCTCCATCTTCACCAACCCCACCTC
CACATCCGCCACTGCCACCACCTCCGTCTCACCTCCTCCATAACCACCAC
CACCTCTATGCCGCCCGCCTCCTCCATCTCCACCTCCATTATTTCTCTAA
CAACACAATCTCCACCTCCATCTTCACCAACCCCATCTTGGTCGCTGCTT
CAACCTTTTATCTTCACCAACCCCATCTTGGTCGCTGCTTCAACCTTTTT
CAGCCCTGTTCATACTTCTTTCTCCACCTCGGCTCAACTTCAAAACGCCG
CGGAGCCGCCACTATTCCGGCAACGCTCTGATATATATATATATTCTGCC
TTTTGTCTAGGCATTTTGGGGAGGTATCTTGTACTATATCATTATTACTA
GTTCTTACTGTAGAGTACTCAGATTTAGAGATCATCTAGAACTTAGTTTT
GAGGTTAATAACATGGTCTGCTTCAACTATGTTTAAAGTTGTAGATGTTA
TTGGCAAGCCTGTGCCTTCTGGAATCTGTTTACAAAGTTTAGCTGATCCT
ATTGGCCAAAAATTGGTTTTCAATATTGTGAATTCTGAAGGATTGTATTT
TTTTTTTTAATTCAAGTGGTGGAGCATTTTATATATGATCAGCATGATAT
TGAATGTGGCAAATGATATGAATTAATTTTGTTTCAAACATAGTATTGCA
GTTGGCTCATGAAATACTTGGTCAATATTGTGAACACTCGCTTGTGAAGT
GATACACATGTTTGTATTAATTATAACTGTTATCATTAGTTTACTGTCTT
TTAAGTAACTTGCGCATTTTTTTGTGGTTCAGTTTCATGAACAGTCCTAG
GTTACAGGTTCAATTAATGTAGATACCTCCTATCTTTACTTTTACCATGT
TGATGGAAAATCTTTTTTATTTGATATAAGAAAGAGGTGAAGTGAGGTTA
TATGTTCTGCTCTTATTAAGTCGTGGTTCGTAGCTAGGTGCTATATCCAT
CCACTATTTCTTTTTGCAAATTTTCCTTGCATCTGAAACACTGTGGTTTA
CTTTAGTTTTTGACCGATGATAAGTCGAAATAAATTGCGCTGACATTATG
AATTAACTTTATAAATGTTAGCGATGAAGTAAGTGCCATTCCAATATATT
AGAAGATTGTTGCTTTTTGTGGTATGTGTTGGACACTTTAAATATTTCAT
ATTGTTAATTTATCAGGTTGGTAGTGGTAAAAAACCAGTGGTTGGCCTCC
GTTTGTTCCTAGAAGGTAAGAAATGCAACCAGTTGGCAATACATGTGCAG
CATCTTTCTAGCCTTCCAAACATGATGGAGCTTGCTTCAGTTAACTCTTC
TGTAGCATGTCAATGGCGTGGGTCAGATGATTATGAATCAAATGAGCAAT
TCTTGGAACCAGTGAGATGGAAAAAATTTTCAAATGTGTGCTCATCAGTG
GTTAGGCATGATCCCAACTGGCTGCAAGGCCAAGAATCAGGTGGTGCATT
TGTTGTGACTGGTGCTCAGCTTGTCAGCAAGGGGCAATGGCCAAAGACAA
TACTTCATCTCCGTTTGCTCTTCACTTACCTACCCAACTGTACTATTAGG
AAGACCGAGTGGGCAGCTGCACAACAATCTTCTCGAAAGTCAGGTTTCCT
GACAAATATAAGTACAACCTTCTCATTTACCCAGAGAGCTGTGACTGATG
CACCAAAGCAGCTGCCGGCTGCACTGAATTCTGGAGTATACCCTGAAGGA
CCACCTGTGCCGCTTCGTTCTAAGAAACTGCTTAGATACGTAGATGTGAA
TGAGGTTGTGCGGGGTCCACATGACACTCCAGGTCATTGGTTAGTTACTG
CTGCTAAGCTGGTTTCTGATGGTGGTAAAATTGGCATGCATGTGAAGTTT
GCATTATTAGATTATACACCGGCATAG