| Relationships |
|---|
| The mRNA, DCAR_003139, is a part of gene, DCAR_003139. |
| The genetic_marker, MK005514 K2958, is located in gene, DCAR_003139. |
| The genetic_marker, MK016764 1_36161337, is located in gene, DCAR_003139. |
| The genetic_marker, MK010711 1_36161359, is located in gene, DCAR_003139. |
| The genetic_marker, MK016735 SSR0425, is located in gene, DCAR_003139. |
| 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_003139 | DCAR_003139.mRNA | mRNA | DCARv2_Chr1:36160125..36168425 |
ATGGCAGATTCCCAACACTCGGCCAGATCTTCGACGGTAACAGTTAATGA
CGGAGATGATGAAGTTTCCGGTGGCTTTCTCCCTCTCGCCTCCGGTCCTC
AGCAACCTTATGTCTCCGAACTCCTCTCTTTCACTCTCGATCGCCTCCAC
AAGGTCAATTACTCCCCCTCCCCATTCTCTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTCCCTCTCCCTCTCCCTCTCTCTCTCTCTCACCCGTTTTCG
ACAGCACATATGTAAATTTAATATGTGTTTTGGTGATGTGATTGAATAAC
CGATTATTCCAAAATGAGCATGAGCTTCTAGTAGTGACTACTTAGACAAT
ACCAATTATATTATGTATGTCTTAGTATGTGTTTCTATACCGATGTGATG
GAATTTGTAATGTCTTGTGTGTGTTAATAATGTGTGGCTCGATTGATGTG
ATCAAGTAAATGATGTAAATGTGAGCTGGAGCCACTGACGGTGTCTTGTA
TATTTCTTTGTTGATATGTGCTTCTATATTGATGTCTTTAAATTGAATAG
GAGCCGGAGCTTTTACGAGTAGATGCCGAGAGAATTGAGAAGCAGATGCA
GGAGGTAGCTGTTAGTAATTACCGCGCTTTTATTTCTGCTGCCGATGCAT
TGCTTGCTGTTCGTCAAGAAGTTTCTTCCATTGACAAACATCTCACTTCT
ATGGTAGTACTCTCAGCTCTTTTACTATATATTGGCTATATAATTTGTTT
TTCTAACTGGATTGTAATTTCCACTAATTTTCATGTGATTCATGACTTCA
GTGTTTGATCTAAACTTGTTACCTTTTGTGAACTATTTGGAAACTATATG
CAGTGATGATGTAACTTTTGGCTTGTATTTGTAGCAACTGATTAGGGAGG
AAACTGTTTTCTTACCATGCAATTAAAATCTAAATAATTGAAACGAAATT
TTTACTTGAGAATATGTTTTGAAACTTCAAAGCAGAGCCTAAAGCATTCC
TATTACAGTGAACACGTCCAATTTTATCTTCAGTGCATCGACATGATTCC
ATATTTCCATCTTTCGTTTCTTTAGTGTTGGTCATTCTAGTGATATAATG
CTCTATTGGTCTACGATATTTTAATTTGCACTTACATATATTTTCATTAT
GCAGATTGCCGAGATCCCCAAGCTAACATCAGGCTGCACAGAGTTCATCG
ACTCGGCAGAACAGATTTTAGAGAAGCGGAAGTTGAACCAAACTTTGCTA
TCTAATCATAGTACTTTGCTTGACTTGCTTGAAATTCCTCAGCTTATGGA
CACGTATGTGTTATTAATTTCCTAACAATCGCATGCAAATGTTAATTAAT
GCGGAAAATTTATATTGTGGGTTTATTGTTTAATCTTCTATCATTTACGC
AATGATTAGTAGGATAAAAGTTATCTGCCTTAAACAAATGGCCAGTACTT
CACTGCTTATATTCTTCTCTACTGTTTCATATTATGGCAACACAATCATT
CTGGTCTAGGTCTTCTAAAGAAGTCTTTTTCAACTTCTCATATATCTATA
ATTTTCAAGTTCCCCTGGAGTTATTGTAGCAACTGCTGTCATTGCTTAGA
GACATACATCTTCTTACATTGATGTAGGTGTGTGAGAAACGGAAACTATG
ATGAAGCTCTTGATCTTGAGACTTTTGTTGGCAAGCTTTCAACAATGCAC
CCAAAGTAAGTTCATGTTTCTTCTTATTTTGGTTGCATCTCTTTCTTTTT
TACAAATCTTTCTAACTGTCTTCTGATTATGCTCCAATATATTTATTTAT
ATTGTGTCTTTGCCGTAATAAGGTTGCCTGTTATTCAAGCACTTGCTGCA
GAAGTTAAGCACACCACCCAATCTCTACTTACACAGCTTCTCCAGAAACT
CAGATCAAACATTCAGGTATGCTACACATAATACATACTTGGCGNGCTGG
AAAGACTGGGTTCAAAGTCCTTGACAAACCTGCATATTTTATCTTGTATT
GCAGTTGCCAGAATGTCTCCGCATAATTGGATATTTACGTCGAATAGGAG
TATACAGTGAATACGAAATGCGCTTACAGGTGGTTTTTTGTAAGTTAATC
TTGATTTGTATAAACTATTTGCAAGCGTAGAAGATCCATGTAGTTGCTTA
CCTTAACACTTAAGATATTAAGAGAGGTGGTCATCCAGCATCATATCGCA
GCTCAGGCACACCGAGAGGTTTTAAGTTTGGGCCTGGTACCCCACAAATT
AAAAAAAAGTAATCTAGACACTATAATTAATTTCTGGCCAAAAGATGGGC
TTCAAGCGAGGTAGCGCAGTAAAACTATATAGTAACACCTGGTACTTAGC
TTACGAAACTGCAGGTTCTAAATGCTTTTTATATTTGCTTATACATGTGG
TTAGTGACAAATACTTTTTTCAGTTTTTAAGATGCAGAGAAGCATGGTTA
ACTGGAATTCTCGATGACTTGGACCAGAGGAATGCATATGAGTACTTAAA
AGGGATGGTCAATTGTCACAGAATGCATCTTTTTGATGTTGTAAACCAAT
ATCGAGCAATATTCGCTGATGATACATCGGGAAGTGAGGAGAACCATGAT
GGCGGCCTTCTTTTTAGCTGGGCCACCCATCAAATTACCTCTCACCTTAA
AATGCTCAAGGTTATGCTTCCCAAAATAGCAGAAGGCGGGTCATTGTCAA
ATATCCTGGACCAGTGCATGGTAAGAAAATTTTTCTGCGGTGAAGTAGTA
ATAGAAGATTCTTTTTTTAATATTTAATTGGACATATGTAAATATGATTG
ATTTCTTAATTTGTGGTGCCTTCTTATGGAAGAGGCTTGCATACAAATAT
ATCTGTTTAGTTTAGTTTTAGTTCTAAAGTGATAGCCTGAGTCTAAAGAA
GTTTCTTACATCCAATACTCATTAAATATATCACTGTGGTGAATAACTAA
AACATTAAAGGCTCAATTTGGCCTGCAAGCCTCAGTAGCAGAGAAATTTG
AAGTGCAATCTCAGCTCGAATAAATATTCGAGTAGCTCGAACTCGAGCTC
TCCTTGATTATTGTCGATCCGAATTTAAATATTTTACGAGCCGAACTCAA
ATAGCTCATGAACAGTTGACTCATTTACACCCCTAGGTCTTTTTACGTGA
AACCTGCTAAGTGGATGGAATAATGATTAATAGAGCATGGAATGTTGCTA
GATGAACGTTTGACTTGCACAAAAAACGTTTATAAAATTTTCTTAAGTGT
TAGATGCTGTACTAGGATCTGGTAAATGATTGCCAAAGTTGTAAATGAAT
ATTCTTGTCTGATATTGTAGGTAAGCATTTCCCTGCCCCTTTCTTGTTAC
TGCTAGTAGTCAGCTGACTCAGCTCCCTCTTAGATCTGTGTCGTGATGAT
GTTAATTAATGTAATGTATACCTGAGGCTTTAAGTTATTTTGTATATATG
TATTCTCGCGGTGAAATCCAAAGACGGAATTTATGCTCTCTATTTTTGTT
GTTGACAGTATTGTGCCATGGGTCTTGGATGGGTTGGACTAGACTTCCGT
GGCTTGCTTCCACCACTTTTCGAAGAGTAAGTAAAATTTATCATTCTTGC
TCTTCCATGCCAACACTTTTAAAACTTGTTGGTAATATCTGTTTGTTTTA
TGGGGTTTTACAGAGCAGTCCTCAACTTATTTTCAAAGAACATGGGTACA
GCTGTGGAGAATTTTCAGGTATGCTACCATATAGTATTATTTTACACCTG
TGTTATTTGATCTTGAAATTCCTAAATTTTATTGTAAAACACTTATTTGA
CTTGATAATTTTTGGTAAAAAGCCATCTTTTTCTTTAATCCAGTCATCTT
CTCTGATATATAGTATGCAAATATGTTTATTTTCATGCAGTTAGTTTTAG
ACTCTCATCGCTGGGTACCGCTCCCAGCAGTTGGTTTCTCAGCCAATAGC
TTTGGTGATGAAAACCAGGAAGACGTTACTCCTCCTCCAAATCTAATGGA
TCATCCACCTCTTGCTGTATTTGTAAATGGTAAGTTTTCATGAAGCTGGG
AAATTTACGTGCTACTTCCATTTCTTTTAGTTCTAACAAAAATAGATAGG
GGGTATAAATAATGACTTTAGATTGTTTAGGTGTATATGTCAATTTTTTT
AAGGACTTCAATTGTTGTATAAGAATTAAATCGTTTACATATAGTTTAAT
AAGCAACATGACAAATCCATCTACCTTTTGCGTCTGCCCCACCTTAATGT
GAGTGCACTTGGTAATAGCAGTTCCTATCAGGAAATTTCACATCTTAGTA
GGAGCTTTTAAAGGGAACATAGAGATAAGGGAATGTTGATATTAATGAAA
TTGGAACACTTGCCTCTTACTTATCTTTTCCTGTTCGAGTTTGCTTTCGC
TCCTATTTCATTTTAGAGAATGTGAAAGGGAGGTTCCAGCTATTTCTAGT
CTGTTCCCATTTGTACCTTCCTAGGGATTTTAACACCATTGGTCTCACTT
TTGTTATTTCTATCTTAGATGTTTCATTCACCATAAAATCTGTTGTCCAT
TGACAGTTTTATTGCTATCCTATTTGAACCAGTCTCAATTTCCGGGTTTT
GTAGTTAGTGGTAACTTTTAAAGGCACTTGCAAGGTTCGATCTGAATTAG
CCGTCTTCTACAAAGATCGGTGGAGATATTTGGCTGTTGTTTCCTTTATT
CCATTTTTGACTATGTTGGTAATGGCCTTCGATGAGAGCAAGGCTGAATG
ATGTCGAGAGATAGACTGATGTGTAGATTCAATTTCCATGCACCGCACTT
GTTTTTAAAAAAGTCGTCTAATAATATAAACCTTTTTTATGTATTATTAA
AATGCTTTCGTAATTCCGATCAACAAAATTTGCTTAATTTTAATAAATAC
TCCCTCTGTCTCAACTCTTGCCCAATTCTTTACATTGGGGTTGGGCACAG
AGGTTAAGAAAAATGTATAAAGTAGTGCGAAAAAGTAAGAAAAGTGGGTA
AGTGGTGGGTCCCATTAATATTTAATTAATAGACTGGGAGAGATTGATGA
AAGTGTGGGCGATATTAGCTTTTATATTATAAAAAAATATTATTTTTAGA
AAGTTTTGAAATGTAAAGAATTGAAATGGACATCTCAAAAAGGAAAGAGT
AAAGAAATGGATGTGACGGAGGGAGTAATAAAATGAAACAAAATAACAAA
ATATATCTTAAAAGTAGGTAATAGTTGTAGCTTACTGTTATTATGGAATT
TGGCACTAGAAGCTTTACACCTAGCGACAAACATCACATTGTAGCTTCTG
TATACTGGATAATAGTAGTCTTGACAAAGTACAATGCAACAGAGCATTTA
AAAGGTCCAAGGACGCTTGGTTGGACCAAGACAAGCAGTGTCCAAACCCA
AGAAGTTTCACAGTCCAACCAAGTGTAAGATTCTGGTTAATTAAAATTGT
TTGTTCTATAACTTTTTTCTTTTTATGTTAATAGAATGTAGATCATTGCT
AGGAGATCTAGAATGAAAATCAGTTACAGTTTTGACTGGAAAATTGAAGT
AGTGTATTGGTGATGTGGCTTGTATTAAAACTTAAGATTAGTAATATTGT
AATTCTGAGTTCATTGCATGGTTACTTTCCTCAATCCATATTATGAATTT
ATTCTGGTCCCCACTGTCAATAATACGAGTGTATGGGTTATTCAAGAAAT
CCATTTTCAAATTTTGATGAACAAACGAAGTTCCAAAGGCTAGTAATAGT
ATGCCTTCAATGGCAGTCAAAACTGTTAATAATAGTTAGTTTCCTACAGG
GGATATTGACTATTTTGCTATAGTCTCATACACTTTCAAACTTGACACAG
GAGGAGGCCAGTTGCAACTTTAAAAAGGTAAAAAGCAGATGAAGAGGAAG
TCAAATAACGACTCTAAATTTTTTTTAAGAAGGAAAGCAAGTAAAAATTT
ATATGCTTTCCTCCCAAACTTAATCGAACAATGGGATGAGAGGATAGCAA
GTAGGAGAGGTAAATTAAAAATGACGTGATAGTACCAGTATACCCCTTGC
TACTACATTCTCACTTTTTAAAAGGAAGGATAATATCGTTCTCTGATGTT
AAGTGACCAATTCATCGTATAGTATTTTAATATTTCACCTTCACTCAAAA
GCCCATTTTTGGGTCGAGAATGGATCACGGGCGCCCATCTTTGTGGCATA
ACTTTGCCTTTGTGTCCGTAATTAAATATGAGAATATTGGGGGTCGCAGG
TAGTTTGAACCCAATTCCCTAGCGAACCTAAGCTCTGATACCATGTTAAG
TGACCAGTTCTCTCAAAACCTCAAGGTTTTGGGATGGCTTACCATGATCA
TATTGTATTCTAACATCTAACAATTAGTTATATGCTTTCCTTCCAACTAG
GAAGCACAATAATGTAGGTAATTTCATTTCATATCCTATTTAAACTTGGT
AGAAAATGAGTGAAATTCATTCCATTCATTTACATCTGTATATATTACTC
TGTTTTCTGCCCTTCATACACTCAGGAGCAGGCACTAGTCCTATAAAATG
ATTCAGTTTCCTTCATCCTAGTAGGTTCTGCAATAAAGCTTATCTTGACT
GATTTAGCTTTGCAAGTTTTGCTAACCCTGGTATTAGGATGATAACTTAA
AGATTTAGTGAGGGTCGGGAAAGAAAATGATATATATGGGATTGAAGCGC
GTAAAAAAGGTGTGGTCTGTTGCCTGTTCGAGATGTAAACTAACTCAATT
CTAGTGTTTGTGTCAATTATGGGCTTTGCTTGCTTATCAGTGAGTGAGTC
TTAATAATAGTACTATACCTCCCATATCTTTGTAGATATAAGAAGGGATC
TTTTCTTATTTTGCCAACTAGAAGTTATGATCTACATTACTGACAAAAAG
AAAACACGATAACATATTTTCTTTTGGCAGTCCAATCCTTATTATAAACC
GTCTCTTGCCTGCTTCGTTCTGTGAATGTTCCCTGCTGGATAAAACTGTA
ATGTATCTGATCTTTATCATATAGTACTTCAGGTGATCTCTTGCTGCCTG
AATGTATTTGGATTTTTTATTCTTTGGATTTTGTTTCTATGTGTTCTCTG
TTTTTACTTTTAGACTTGCTTGTCTCCTTTGCAGCCTGTGTAACTAGTTC
TTAGAGCATCTGTGACAGAGATAGCTGAACAAGTTGCCAACTATTGACAA
GTCACTATTCACGCTTTTTTTATCATCTCTCATCCACATCACCATTGGGC
CTTGGCGACTTTTGTTTGAAATTAAGTCCTGTTGGCAACCCCAAAAGTTG
TCAATATGGTCCCATAACATGAGACAATACAAAAATAGTTCTACTTAAAT
ATAATTTTGGACAATTATATAGGTTTTTACTAGTTTATGAAGTTGCCATG
GCAATCTCTTGACAACCATACAACTCCATAGTTGGCAACCAAAGTTGTCA
TGCCACATTAGCATTGACAACCTCTTGGCAACCCCCCGGTGGAGATGCTT
TTATAAGACGGCTTGGATTCTATATATTGTAGTCGCTTTTTGTTTTTCTT
CTGTCTCTGTAGATATTGGAGTGTTTTTTTTTGGCAGTATATTTATCTGG
ATGGCGGACTAATACTTTTTGTCCATTACCAAGGTTGTATAAAATCAGAT
TATGAAGTGTTTATGAATGTATAATCTTTTCCTACGTCTCTCTTTGTTGT
AGGTGTATCAGCAGCAATGAACGAATTACGTCCGTGTGCCCCAATACGTT
TGAAGTATATAATTGCGCAAGAATTGATTAAGGGACTGCGTGCCGTTTCA
GATTCTTTGCTCAGGTACAATACTACTAGGATGCTGAGGGAGAATGAGTC
TGTGCTTTTCCTTTCTCTTTGCCGCTCATTCACTGAGGTAAGAACATACT
ACACACTTAAAGTAATGTTGTTTTTATTGCTAGTTATACCTTATAATCTC
CAAGATCTCATGCAAACCTTTTTCTTACTGTGCAGGTTGCTTTTCCACAT
TGCGCTACATGCTTTGGTCGTTGTTATGTAGGTGGAGCTTCTCTTATCAC
AGATTCCAAGGGTTTATTTGATGGAATTAACCGTCTTGTAGCAGCATCAA
TCTCTAGAGACTTGCCTAAACCGGTCAATAACTCAGAGAATAAGAACACA
ACAGAAAATGGGGAAGCACCACCAGCTGAAAATGGGGTTATAGATAATGG
AGGACAAACAGAAAGCCTCGGTGCAGTTGAAAAGGAGGAGCATGACACCA
GTCCACAAACTGAGGAGAAACCTGTCAATGATGATGCTACAAGAGCTTAA