| Relationships |
|---|
| The mRNA, DCAR_002884, is a part of gene, DCAR_002884. |
| The genetic_marker, MK003353 K0797, is adjacent to gene, DCAR_002884. |
| 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_002884 | DCAR_002884.mRNA | mRNA | DCARv2_Chr1:33706488..33713857 |
ATGGACGATTACAACTTCGACGAGTTCTACGACTACAATCGCCACCCTAA
CTCCACGACGTTGTCTTGGTCCTCCGACAATCCCCGTGCTCACCACTATC
ATCACAACCAGAACATGAATTATTACCCGGAACACGACCCCTTTGGCGGC
CCCGGTGGCTTCAATTTCCCTCCCCATCCCCGTAAAAGACCACATTTCAG
TTCCGGTCCGTATCCTCTTTTTTCGATAATAGTTTTAGCACGAGAATCCG
CGAGAACAATTGTTCTGCACTTTTCGTATTAGTTGTTTTGATAATTTGGA
AAAATTGATACTATGTGAGAATTGGTGATTATTATATTTGTGCATATATG
TGTTGTTTATAGTGTTGCTGAATATAGTGTTTGTTTTAAAGGTTGTGGTG
AAGGCGGTTCTGTTGCCAAGCTTTACGTAGGAGGGACACCGAGAAATGCT
ACTGAACACGATGTAAATTAACTCACTGCCTTCCAGATTTCAAGTACTTT
GTAGTCTTTGTTACTACTATTTTGTCTGTAACATTTCTTTAAACATTCGT
TCGTGTTTGAAAACATGAGCAGTTGTGGTTAAATGATAAGTAAAAAAGTG
GAAGTAGTTAGTAATAACGCAATGCCAAAAGAGTTAATAAGGAAGTCTTG
CAGGCGTGATTTGGTCATTACTAATAGTCACTTAATTGACTAATTGTGGA
CTCTTCTGTATGCTTTTTAATTTTAATAATGTACTGCTAATACCCCTGTT
TTTCATTTTAACATCAGATACGCGCCGTGTTTGGAGAACATGGAAATATC
ATTGAGGTTGTTTTTCTCAGGGACAAAAGAACTGGCATGCAACAAGGTTA
GTAGATGTCGTATGTACATTATTATTCTACTCTAGCAGCATCATGTTGCA
TACCATGTCAAGGTATAGCAGCATGGAGATATGATCGTTGATCACCTGGT
CTTACTTAAAGGAGTTTTATAATGCAGGGAAACTTGTTTAACCTGTAAAA
TAGTTTGTCCTGATTCAGGACACAATTCCCACACACCAGGAGTAGGCTCA
ATAAGTTCTTAAATCAGACCTATCAAATATCATGTATATTAGAAATATAT
ATATATGTTTCCAAGGGTCACGCTCAAGAGAGAACCAGTCCTTAAAATAG
AACCATAGAACCACTCCCTAAATTTTTAATAGGTTTTTAGGATCTAAATC
TAAATACATGTTTTTTTCATCGTTGTGTGTGTTCAAAAATAATTTTAAAA
TGTAATACATAGATATTGACATTTTTTGCATGTGAAGTTCTACTGCAAAA
CCCTAACTAATACTTAAGTTCTGCTGCAGAACCCTAACTAATACTAGAAA
TACGGTAAAGGTTCTATGGGTTCTCTCTCTAATGGTTCTCTCTTGAACAT
GACCCTATCTATGTTTCTAAGTGATTGTGAAACTATTTTTATTTCTTTTT
TATACTATTATATATGTGCACTTGTACTCTTTACGTTAAATCTTGTCATG
CTAGAAAGAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
AAAGAGTGTTTTTTTTTTCTACGTGAAATACTGCTGCTCTGATTGTCCAT
ATCTGACTGGAAGTCATGATTCAAGCCTCCGAGATGTCATAGCTGATAAT
TTTTTTGTTGATCCCAATTGATGCATTACTAGAGGGATTATTTCAAACCT
GATTTCGAACGTATTTCACATGGATTATGTTTCCATGATTTCTGGAAGTC
ACACATGTAGGCACGTATAGTATAGAACTAGAGTACTGTAGTACTAGTGT
ACCAACTAAAATTCTGTTTATACTGTGGACCAGGGGTGCCGTATACATAA
TGATACCATATACATAGTAATAAAGCCAAAAATATGTATCCTAATTTTTC
AAACTAAAATTGTATTGCATGACATTTTAACCTTATAAGTAATTGGCAGG
TTTTAGCACGAAAAGGGTTCAAATTTTAGATTTAGCACAATGTCTTCGAA
ATAGCTGGGACAACTTGTAATATAGAGGAGTTAAAAAGAATTCGTTTTAT
GTGTTATTTGAACAGCTTATTGCGAAATTAACTGTTTAGAACTTCCTTTT
ATTTTATTTTTAGTGAGATATTTTCTGACTTACATATTACTTATTAGATG
CTTAACAATCCTTAACTTCTGTATAAATTTGTGGGTGAACTCAATAATTT
ATGGGGGCATGTAGTATAATATACACCTAGTTCAAATTAAAAAAATGCCA
GTAAATTGTTTTATTATGGGGGCACGTGACCGTCCCCATGGGCCTCAATA
TACTCGGCCTCTGGTTATAGATGGTCTACTTGTTACTTGATCTTAAATTA
CAGAGTGAGGATATATGATCTGATTTTCAAGTACAAAATAAATTTACAAT
AATATCAATAATCTCCAGATGATGCACATGCCAAAACATTTTTGGAGCAT
GTCTTACTCCAGTGCTAAATATTTATTAGTGCTTGATCTGCACGTTTGAA
ACCTGCTAAGTCGATGCAAAGATGTCTACTGGCTGTTTAAAATCTGCAGT
TCTGCACGTGTAAGCTATTAAGGCCTATTCTAATATATATATTTGGCTCC
AAAAATTTTTGTTTCTTAATATTTAATTAATAATTATTTGCCACTTTTAT
GTGCTGCTGAACGATGTATATTCAAATGAAGGTTAGGAGCACATACTTTC
TGTCCTTTTATGGTAAAATCAGGCCTTATATTTTTGATGGAATCCACGCC
TGATTCTAAAGTTATGTTTGAAGTGATAAACTACATGTCTAATGATTAAT
TTTCTTCTTTACTATATATCTGGTCAGCCTATCATATCTATAAACCGGTC
CTCGATAGTAAGTGACGTGTGTTATCTTGCAGGATCTTGTTTTGTAAAAT
TTTCAAGGTTTGAGGATGCTGATCGGGCGATAGAAGTTTTAGACAACCAA
TACACGTTTTCAGGGGTAATTTATCTGGACGTTAACAAAGTGTGTTGCCT
CTAATTATGTTGCATTGTGCTCAGTGTCTATATTTGTCTTGTCCAGGAAA
TGGCCCCTATCAAAGTTAGATATGCGGATGATAAAGAACGGAGACGCCCG
GGTAATTGAACTTTTAGGTTAATTGAAAGCCAAAACAATATGTGACTTGT
AATTCTGTAATTGATTGTATAGATTGTACGATATCTCTATTTCATCTGGG
TGTCATGGTTCCTCTGCATGGATTAGTACAATTGCAGTAAATATTGAACA
CTGTGCCCTGCCTCCATGCCTATAGAGTATAGACCAATAATTGGACTGTA
CTTCAAATCAATCTACTTGAGAGCCTTTCGATCTCAAATTCATTTATCTG
GGCTTAACCCGCTCAAACTATCTAATCAACTAAATTTGAATAAAGTTGTT
TGTTTTATGAATTTTGGCCGATCTACGCAACCCTTGCTCCCTCGATAAAA
ATACTTGTAAAAAACTTGAATTTGACTAGAGTTAAATTTGTTCTTGCTTT
GTTAAGTAGAAATTGAGCTCAATTATGGGATAGTGAAAGATTTTGTATTC
AGTAAGGCAGCTCGGCTCATTTAAGAAACTTGAACTCGATCTCATTAATT
ATGTGCTTAACGTGACCTTAAGTACAGATTTGTGTCTACAGTACTGCATC
TTTTGGAACACTGTTGATATCTATATCAAGTGCTTAAAACTAACAAATGT
ATTAAATTTCTTTTATGCACTATGGGTTCTATCAAAAGCAAAGTTTATGC
ACTTGGTTTAGAACTATGTTTAGTAGTTTTGGCTTGAATTTATTTGGCAA
ATCTTATTCAAAACTGGAATTTGTGATTTTTTGTCTTTGATCATAAAAAG
TACTTGTTTAGTTCCCATTGTGAAACGAGTGGATGGAATTGTTATCTCCT
GGTACAAGTTTAATGGCATGCCTATGAGTATAGAAGTCAATTAAAGAAGC
ACTTGTATGTGAGAATGTGGTATAGATTTAATGAATTTACAAACTCAAAA
TACAGGAAGTGAATATGAAGAAAAAGAGTAGTAACTAGTAAGATTATATT
AATTAATTATTATGTAGGATATAAGAAGTCTAGCTTCCTTGATACAAGAC
CACTAGGCCAGTAGGCCTTTGAGTCACCCAGAAAAGTCCCAGACCCAAAA
TGGGTTTACAAAACACAATACTGATATCCTTTTCTCCTCCCTGCCAAGTG
CCATCTATCTGTATTTATACCTATTTTTCTTACCCCGTCCTTTACTACCA
CTTATTTTTACATTTTATTGTTCTAACAATAGTGCATTCGGCATTCCCCG
TTTTGCCCTTGGGGTGACGCCTAGCATAAGTTAAAAGTGACTGGGGACCT
TGTCCCTGTAGTCTTTGCAGAAAGTGTCACCTAGAAGTTTTGTCTGAAGA
TGTAATATTGATTAACTAGAACTCGATCGATATGAAAATAAATCATTTAT
GCTGCTTCTTTTTGCATGCATATATGATAATGGGGTCATGGCGTCATGCT
TTGGCAAGGGTCAAACACTCTCGTCTAACATGCCTATTTTGTAGCTTGCA
ATGTTGGGAGTAACATAATTTTCTGCATGGATATTAATAATATTACATGT
TACTGGAATTAAATGCTTTATATATGACTAAGCTTTAATTTTTCTTTTTC
TTATATGTTTCTGACAAGTCTCTCTTTCGCAGCCTCTAACTTTGGGACAT
ATACATTCAAACTGTATGTTGGTGGTTTGAACAAGCAAGCATGCAAAAGG
GAAATTGGAGAAGTATGCTTTCCACTGTGTTCACACTTAGTCATACAGAA
ACTGAATATAGTACTAGTTTTTTCTTGTCATATCATGTTTTAGATGTGTG
TACAGGTGTACTTGCTTTATGCTTACCACTTCTTTGCTGCTTTCCTGCAC
AACCTGCTGGTCTAAGTGCACTTGTCTGTAGGTCCTTGCTGGAACAGTTT
GAACCTAAATTTTTTGTGTTTTGTTAAATAACTAGCATTGCAACTAGCAT
TGCAACTGGTTTGTCACAATTTGTCATATCCATCAAGAACGGGAAATTGA
TATGTGTGATCAAAGCACTTATTCATCTGTCCAGATAACTATATATTTTG
CATTAAAAAATATGGCGTATATATTAGTGTGTTTGGACATACAAAATCCA
AGCATGAGACGGTTGAGTGAACAATAAAAATGGAGTAGGAATAGGTAATC
TGCAAATCAACTAAATGGCACCACATCCTTTCACTAATACCCTATGTTTA
GCAACAAAAAAAGGGTTCATATTCAACAAATAACATAAATTCGCAAAAAT
ACGACAACCTTTCTCATAATAACTATGATGAGGTGTGTGTGTGTGTGTGT
ATTAGCATCCCAGCTGAGGCCCAACAAATCGTTGGAGCTGAATTATTCTT
TATTAGCAATAGATTCAGTTTAATATATTTTGATCGCCATCTTTCACAAT
CTGCTTATTGTTATTGTCACTAGTGTATATATATGTGTTATTCCAAGCCT
TTGACTCTAACAAGATGTTATATATTTCTTGTATAATACAATCAGATATT
CTCCCCATTTGGTCTTATTGAAGATGTCTTCATAGCGCTCGATGAATTCA
AGCAAAGCCGTGGTTAGTTATTCTCTGAGTTAATCAGTGTCTATTTGTGA
TTAATAGAGTCATATTAGCGAAGCGAAATTGTTTGAGTCAACTCCAATAG
CCTATTTATTCAGCTTTTGCCTGAACCACTTAGCAGCATTTCACAATTGG
CTCCATATGTGTATCTTTTTTTATAGTTAGACTTCCGTTTTCGATATTTT
AACTACTTTGCTTTGGGTCTGCTTTATAGGATATGCATTTGTTCAGTTTT
CACACAGGGATATGGCCGTTGCTGCAATTAATGCATTACATGGAACATAT
ATAATGAGAGTAAGACACTCTGAGTGTTATCGCTCTCATCAATATTCTTC
AAAAATTCATGTTTGCTGATACTATAATATCAAAGCAACAAAACCCTGGG
GAGTACTGTTTTCATGAGATCTGTTTATCTGTTATGCAGGGTTGTGACCA
GCCACTAATTGTTCGATTTGCAGATCCTAAAAGGCCAAAAACTGAAGACT
CAAGGTTAAGCCAGCACCACTTAACTTTAAGAAATTTATTGTGCTGCTTA
ATTTCATTGCAATAAGATCTATGATAAATAAATGATACAGGGGATATTGA
TTTGAAATCTGATAACCATGCTTGCTGATTTTCCAAATCCCCTTAACCTA
CCTGCATGGAAGCGTGACTCATGAAAAGAAACAGCAGAATCTTTTATTTT
GTGCTTCATAATATAATTTGCAAGTGTGTTTAATGCTCACGTAATATTTG
TTCTAGATAATGACCTTCCAATGTCCAATGTTGAAATTTGAATAGATTTT
TGTTCTTTTACTTTTTCTATATTGCTCTAAATATTGATATAAATAGTAGT
TTCGAGCAGGACTTTGTAGTTTCATGAAACAATTCCTTTCACTCTTTTTG
ATAGTGGATATTTTATTGTTTTTTGCTTGTTGCAGGCCGGTACAATCTTT
TAAAGATATTCCAAATCGGTGCAGACAGCCCACTTCATCACCTCAGGTTA
GTCTATATTGGTGTTATCTGTCAAGATAGTTAAGTGCACAGGCAAAAGGG
CTGTTCTTTTAGTTTATTTATAATCTTGCATCACTCTCTTAACTTCTGTG
GGAGTTTAAAGAGGCAATAGTATGAACGTTATATTTAGTACTTGTAGTCT
TCTTGAACCAGAAGGTTGCATGTGATAGGTTTTAGCATCGTACAGGTCTC
AACTTCAATGGGGTATCATGCTTCTCCTGAGCCCTTCAGCAACGACCCAG
AAGATTCTATAGATTGTGATTGGAGTGAGCATGTTTGTCCAGATGGATAC
TTGTACTACTACAATTGTGCAACTTGTGAGAGCCGGGTCAGTTCCTGACA
AAATTATGTATGAACTCTTTCTTATCCTGATTTAGACTGTTTGAATTGCT
AATTATCTATTGGTTTGGTAAATAGTGGGAGAAACCTGAGGAATATTTGT
TTTATGAACAACAATTGCAAAAGGGCCTGGAGCAAGGAAATTCACAGCGT
AAACAACCGTACATGCCATGTTCTCAGATTCATCCAACTGATCAAGGTTT
TCAAATGCAACAGGTTTAG