| Relationships |
|---|
| The mRNA, DCAR_020740, is a part of gene, DCAR_020740. |
| The genetic_marker, MK018565 6_28739043, is located in gene, DCAR_020740. |
| The genetic_marker, MK002232 ESSR-127, is adjacent to gene, DCAR_020740. |
| 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_020740 | DCAR_020740.mRNA | mRNA | DCARv2_Chr6:28735889..28742816 |
ATGGAAGCTCTACACATCTCTGCAATTTCACACACTTATAAATCTCATCA
AACCCCAAGCTTCAACTCCGCCAGAACATCAACACCGCATATTTGCAGCG
CCTACTCTTCTTCTACTCATTCTCGATCATTGTTATCGCACTCAACATAT
AACTCATTCACTGTAACTACTTAACCACATCTGCTCTCTCATTATCCACC
TTTGCTTTTCATTCTCTCTTATCTTTTTGTTTTTTTGTTAATCAACAGAG
GCAATTATGGGGATTTGTACATTCTTCTAGTACTGATAGAAAGAGAGACT
TGCGTAGAGGTTTAGTTGTGAGAGCCGAAATGTTCGGACAGCTAACTAGC
GGTCTTGAATCGGCTTGGAACAAGCTCAAAGGCGAAGGTAAGGTCCCTCT
GCGTTACTATCAATCTCTCTTTTGCGTTTCGGTACTAGTTAATTCTTCAA
TTGTAATTTGTGAAATTAAAGCATGACACTATACTGGAATTTTGTGTAAA
AAAGTTAATAATTATGTGTGTGTTGTGTAGAGATATTGACAAAAGAAAAC
ATTGTGGAGCCGATGAGAGACATTAGGCGAGCTCTTCTCGAAGCAGATGT
AAGTTGTTCCAGACTAGTGTAATTGAGAAATAGCTGCTGTATCGTAATAC
GAGCAACTCAACTATGTGATCACCAGGTTAGCCTTCCTGTAGTGCGAAGG
TTCATCCAATCCGTGAGTGAACAAGCTGTTGGTGTTGGTGTGACTCGAGG
AGTAAAACCAGATCAACAATTGGTTAAAGTAAGTGTTCAACTGACTTTAT
TTTGTGCAGAAATAATGCAAGCAAACAGTGTTACATGGCCTTGAATAAGA
ATCTGTGTATAAACAGTGTTACATAGCCATTAATAAGAATCTGTCGTATG
GGCCTGACCTCGCTGGCCTAATACATTGATGTTCATATAGGGTTTCAGTT
TTTCGTATAGGTTTATTAACAGGCGTACTCTGTACCTGTTTAGTAGCTTG
TAAACCTCTCTTAACTATATATACTAGCTGTGTGTTACAACATGTTGTAA
TCTGAATTCCTTATGGTCAACAAAATAAATATTCTGCCTGTGGATGTAGC
TAACACTTTGTTAGTGAACCAAGTTAAAGGTTTGTGCTTTGATCTCTGTT
GATTTTGTGTTAGTCTTTTTCACTTCTGTCATGACACGATACATCCCCTT
TCCTGTAAAGTCAGTTGATATTTTGATTATAATTTTGAAGCTTGAAATGC
TAGTACATAGAGATTGATAGCATTGATGCACATTAATAAATTTACAACAT
TTTTCCTTCTTTACATGATCATTAGTTGTTGGCTATATCGGGCATCATAG
AATGATAGAATCTCTTGTACTATCATTGCACAATATTTTAATCAATTTTT
CAAATCTGTCCAGTCCCTTGTCTTAAAAGGAAAGCAGTTGAAACATGAAC
CATACGTGTCTCTCGTAACTTCTGTATAACTGAATTCAGGAACTTAGGCG
TAATGATCCTATCTTTAGTGAGGTAGGTGTAATGGCTAATTCTTGTTTTC
TTAGTATGATCAATTGACATACCTCACCTGTAAGAAATTAGTGTATCTTG
GGTATATTTGATACATTGATGTACCTTTTCCTAGCATTACTGATAGCATG
TTCATGCCATTCAATGGTGAAAAAATTGGTTTCTAGAGCATTTTTATTGA
CCCTCTCATTTAATTAATTTCTAATCTAGTAGTATTCTACATTAAATGTT
TTTTTCTATTGTTGCAAACTCAAACTTCAGTGACCACAATCTCCGAGCAC
ATATCAATGATCACTAATTTCAGTCAATCATTTTCCACTTTACTTAATCT
GTGGACAAATGCACCTCATTGTATTTGTTGTGTGCTTCTTGCCTTTGCTT
AAGATGCACTTATCTGACTGATCGACCAATAGCAACAGCAAAACTTACCA
ATTAAATAAAATTAGCATAACACTTACTAATTACTAAATAGTCTATACTC
TCTTTGTACTGAGATTCTTTTAATGGATGCAACCACAGTGATGTACTAGT
ATTATAGTTAAGGTGCTAATATGAGGATTCGTGTAATGCAGATTGTAAGT
GAGGAACTTGTTAAATTGATGGGTGGAGAGGTTTCTGAACTGTCTTTTGC
CAAATCCGGGCCCACTGTAATTTTATTGGCAGGTCTACAAGGTGTTGGAA
AGACAACTGTCAGTGCCAAGTTAGCAGTGTACCTTAAGAAGCAGGTGTTA
ATGAAATTTCTTCCTTCACTCACTTCGAGTGCCAAAAAAGACTCGCAAAT
CGTCCATATTTGCAATATCTATTTGCTGCACCGTAAATGTGACTATCAGT
CTGTGTGACCTTTGTTTTTGTAATTAAAATGGATTACAGGGGAAGAGTTG
CATGCTGATTGCTGGAGATGTGTACAGACCTGCTGCAATAGATCAACTTC
TTATCTTGGGAAAACAGGTTGCCAACTCTTATCATCAGTATGTTAATGCA
GTAAAAGATAATATCTGTTTGTTTAATGTAGAGATATGTTGTGGTCCTTT
CCCAGGTAATTTTATACTCAGCCTGATTCCTAATATTCGAAATAACTGCC
TTTACAATTGTCTTTCTTGATTGTTTGTAGTGCCCTTTCTTTTGTTTCTT
ATTTTCTTGAAGTTGGTTGAAAGAGTCTTTCATTGATTTGTACCAACTTA
CTTTGTGTCATGTGTCAGTGAGACCTTTGTACTCCAGCGCAACTATTTAG
TCTTCCTTGTAGCTTCAATAGATCTTTTTTTTTACTTGGCAAGTATCTAT
TTGTATTTTCTTTTAAAACAGCAATTATTTAGATTGAAAATCACTCAAAT
CATTCTCTGAGCCAGTTATCATGTGAACAGGTAGATGTGCCAGTTTATTC
AATGGGCACTGATGTAAAACCAGCAGAAATTGCTAGGAAGGGTCTTCTAG
AGGCTAAAAAGAAAAATGTTGATGTTGTCATAATGGATACAGCTGGAAGA
CTTCAGGTTTTCCACTGCATTAATTAGTACAGAGAGAGTTGAAATGTATC
TTTGTTGTCTACGGACAATATATATGATTTATAGTGTCTATGCCATTACA
TTTTTATATCAGATAGATAAGGATATGATGGATGAATTGAAAGAGGTGAA
ACGGGAACTAAATCCCACAGAAGTTTTGCTTGTAGTTGATGCCATGACAG
GCCAAGAAGCCGCAGGTACTTGCAGCAGTTATCTGATCTAATACATGACA
AATTTTTTACTCTTTTACCATTGCCTCAGAAAAACATCCATGTACCATGC
AAATTAATCATATTGCTCTGAACTAGAAAATGGGCATGCATTCCTTTTAA
TTTACCAGTTCTCCCAAAACTTCAAGTTGCTAGGAATGGACTTAACTGAA
TCAAATCATTTTACATCTTTAACACTTTCAATCTCATCCCAACCTTAATA
TGTGGAATCATATATGACTACTATGTCTCAGCCTCACAGGCACCCATACT
TCCTTTACTCTGAACCTGGAACCAAGAGTAACTTGTATATAACCTTTCCT
GAATCCCATGCATGCAGTATACTACAAAATAAGGCAACGAGTTTTCGCTC
ATTTATCTGCTTATGTTATCTAATCTGGTTTTACACATAAAATGTCTCTA
ACATGGATATTATTAACCATTATTGCTTGTATTATCTAATCTTCGCACAT
CTATTTGTGAATACAGATACTATTATGCCTCTCTTGATGTCCTTGGTAAT
TGTGCAGCTTTGGTCACCACATTCAATCTTGAAATTGGAATTACTGGTGC
CATTTTGACGAAATTAGATGGGGATTCAAGAGGTGGGGCAGCTTTGAGTG
TGAAGGAGGTCAGCTTTGTTAACTTTGACTTCTGATGGTTATTGTTTAAC
AACAAACTCTCCCATAAATACTTCATATACACTTCAAAGGATTAAAAAGA
CCTAAAGGAGACCGTTGATATTATATATATTTATCTTGTTTGGTTTTTCT
TCAGCACTGTTCAAATCAAGTAAGTATGAGTTTGTCATGAATCCCCAACA
GAGAGATGGTGAACTTACCTACAATCAAAACAAAAATAAAAAAATCTACA
CTTTATTATGCATATCATCTCTAATTAGGTAGAATATCAAGAAATCAAGT
GGATTGGGTGTTTTTAGATGAATTTTTTTAATATTCTGTTGTTGGACTTT
GTAAAGAGTGAAAAGTAGCACCTTAAATTAATTGCTAATGACTGGCTATG
ACAGGTATCGGGAAAGCCAATCAAGCTTGTAGGACGCGGAGAAAGAATGG
AGGATCTTGAGCCTTTTTACCCTGATCGTATGGCAGGGCGCATACTGGGA
ATGGGAGATGTTCTATCGTTTGTGGAAAAAGCACAAGAAGTTGTGAGTGT
CACGGATTAATCTTTTCACTTTCCTTGGCTTATTAAATTCTGATAGCTTC
GTATTTACACTTGGATAGATGCGCCAAGAGGATGCTGAAGATATACAAAA
GAAAATAATGAGTGCAAAGTTTGACTTCAATGACTTCCTGAAGCAAACTC
GTGCAGTTGCACAAATGGGATCCATGTCTCGTGTTCTCGGAATGATTCCT
GGCATGGGGAAGGTACCTTACCTGCATCTGTTAATGAAGTCTATTGAGAA
AACTTTTTAGATTTTTTTTGTTAAAAGTATATTTCGTTAACTAATTTACA
TCTTTTCTTTATCCCGGTGCAAATCACGAGTTCAAATATTGTAAAAAGTT
ATTTATATGACTAGATTGTTCCTAATTTTAATTCATTGAAGTTACTCCTG
TGTTATTTATAATTTTAATAATTTTTCAAATCTTATTTTCGCAGAATCAT
TTTATTGTTAGATTGTACTATAAGAATTCTAATGATTGTTCTTGACAAAA
AAAATCTAATAATTGTAAGAAGAACCGAAATCAAATGCTAACATATATTA
TATGCAGTTGACAGATTTCGAAACTTAAACCTTTGATTTTATCATTAAAA
CTAATGATTTATTTGTTTAATGTTGATATGCTGAAGGCGGGATTCGAACT
TTAGACCTTTGATAGCATTTTATGTATTAAATTATTAAATAATCTTTACT
ATTGGATCTGACTGTTATAAATGGTCGTTATTCTTTAACCAACTAACCAA
AGCTCCTGCGTATAGTATCAGTAGTTCAGATTGATTTATAGGTTTTATAA
GCATCCCTGGACAATATAAAGACTAAGCAGATCCGTTTTCCTTTTTTAAT
GCTTTGTTGAAAGAACATAAATTTACTTTCTCCTCTAGGTTACTCCTGCT
CAAATTCGAGAGGCAGAGAAGAGCTTAAAGATAATGGAGGGAATGATTGA
AGCAATGACCCCAGGTTTTCCTTTGACAAACAGCTTCTTTAACTATTTGC
TTCAAATGTTCTGGGTTTTAAGACATTTTTCAGCTTTTGCCAAACATAGA
GCTTGTATGCAGAAATGCAAAGTGAGATTCCAACAATGATTTTATGAAAA
AATAACCTGATCAAAGATCCCACCTTCTTAATACTTGCATGTGTTCTGAT
CATTATGTTTTACTATGAGGAATCAAGTAGTTTTTAACTTTGGTTTACTA
TGGCAAAGCCTACGGTTTCAATAGTTGCTCTACACTTTATTTAGAAGGAA
ATTGTTCTTCAGGATTATGCTGTCATCTGTGTGTGTGTTATGTCAGTATT
TAAAGATTGGTTCATTACGGAAATTATACTGATAGCAAAGCTAGTGATAT
TGTACATCAAAGCTTTCATAAGTGGAACTTGTCTTGTAAAAGCAACTAAC
TTGCCTAGCTTTGTACAGAGGAAAGGGAAAAACCAGAACTTTTGGCTGAA
TCCCCAGCTCGTAGAAAGCGAGTTGCTCAAGATTCGGGGAAAACAGAGCA
GCAGGTACTTAGAAGTAGCAGGATGATTAGAATTTAAATTACTATATGGC
TTTCTGTACTGTACCATAATGGCCTTCTGTACTGTTTACTTCTTCTTTAT
TACTGTATATGTTATTTTAATATCAGAAGTATTTTCTCAGTATTAATTTT
TTGTGGCGGAATTAGGTAAATCAACTTGTTGCTCAATTATTTCAAATGCG
AGTCCGTATGAAAAATTTGATGGGTGTCATGGAAGGTGGATCCGTACCTG
CTCTGAGCAATCTTCAGGAGGCTCTTAAATCTGAGCAGAAGGTACCTCTA
TCTTTTAGTTTTCCATTGCACCTACTGACCTACACATGTCTATGGATATT
GAGTTATTGTCTAATTTGTCATGTTCAGAAAAGCCCTAGAGAGTTTATCA
TTATTATCTAATTTATCATGTTCAGAGAAACCCTAGAGAATTTATCTTGC
AGGTTTGCGAATTAGTTTTGTTATATCTTTATTTTTTGCAAATATACTAC
AATTTATAGTGACAAGAGTTTATAATGCATAGTTGAAAACTTCGGGATCT
GCAGAAAGGGCCTTGTTTATCAATCTTACTTTTCAGGAGTAAAATTGAAT
GGATGAATTTGAGATATACTGTCACCTATAACTTGAGACTTTTGAAAGCC
CAGAATTTGTTTGCTGGGGTTGTAAATTTGAACTTTGGAAATTATATGAT
ATACTATCACCTATAAGTGCTTCCTACTGAGAACTTTCTTCTCTGTTATA
GGCTCCTCCAGGTACTGCCAGGAGGAAAAGGAGATCGCAGTCAAGGAAGC
AATTTGCAGAATCAACATCCTCCATGCCTAGTCCTCGTGGTTTTGGCTCC
AAATAATTATTTTGGTTTCGACTCTCCCTATGTTCATAGATTAGCGAACA
TAATGTGTATTGTGTAATCATATCATGACGTGTAGAGACTGTTGTAGAGA
TTAAGGGGCCGTTTGGTTCGCTTCAGAGAAACGGAATGGAATTCAGAAAG
GGAAACGCGGGGAAAGGAAAAGAATGA