| Relationships |
|---|
| The mRNA, DCAR_026772, is a part of gene, DCAR_026772. |
| The genetic_marker, MK018981 8_28843583, is located in gene, DCAR_026772. |
| The genetic_marker, MK004867 K2311, is located in gene, DCAR_026772. |
| 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_026772 | DCAR_026772.mRNA | mRNA | DCARv2_Chr8:28841847..28849078 |
ATGGGAATACCTGATCATTCGATTCTGGATTTGATACATAAAGTTGGATC
TTGGATTTATTGGGGAAGTGGTGATTTGGATTCTTGTTCCAGTGAATACA
AGATGGCTAAAATCTGCTGTGATTGCATGATGCCTGTAGTGGAGTCTTCC
GGTAGTAACCATTGCCAAAGATGTGGCAGGATCTTGTGTGAGAACTGTGT
GCAGTCAAATGGTTGTATTGGTGTTGTTTCATCGGGGAACTCGATTTTAG
ATGGCTCATCTGAAGCTGGTGCTGTAACTAACTATTGCAAGTTCTGCTCT
CATATCAGTAACAAGGAAAAAGTTGGGAAAAAGTTCATTGAAAAAGTTTA
TCCTTCAGACTCACCTAGACAAAGCCCTGAACCACCATCTCCATGTTCTA
CCGGGAGATGTGATGAATGTTGTCATCCAGATTCTGCCAGAAGCATAATT
CATTACTCTCCAAGCAGGTAAAATATCATCTTGTTCTTGAAATTCCAATC
TTTAGTTTCATATTTTAACAAAAAAGTAGTCCATCTTTGATCAAACAGAG
TAAGTTTTGTCTAAACATGCAGCATATGATATACTCCAGTAATTATTTGG
TAGAGTGACTGGAATTAAGTTCTTTTTGTGTGTGTGTGTGTTTATTACCA
AATTCTATCACATATATAAGTTCATTTTATGGTGATCGGTGGTGCCAATG
GGAGAAAGGATTATATAGGCTTCTCCAAATATTCTAAGAAGTTTAGAATT
CAGTTCATAAGATTATCTTAAATGGTTTACTAATGTATATATGATTATAT
ATGACTATATAGCAAATAGTCTTCATATTGTAATTCCTTATAAACAAACA
TATCTAACGAGTAATAGGAGCCTGTTAGATGGTCAGTAATTATTCTTCTT
CGGATGGTTCACTGATTGTTGTGCAGATGTTTATAGTTGTAAGCCTAAGT
GATCTCTTCCTACTACATAACACTTATAATTACTTCAAACATCCTCATCA
CATACCAATTTAATAGCCTGTTTCATTTATCAGAAGTTGCTTATGCTTTG
GTACACTGAATATATCATGCTTATGTTGTAGGAGCGATGATGATGATAAA
GAGGACTCCAACAAAACCTTTTTCAGTTCATTTTTTGATGATACATCGGA
TGTAGATTCAAGTAGTATTAGTGCTAGACATGAATTTTACAGTTCCAAGT
CAGTTGGATCAAGTCCACTGGACAGCCCCTGTAGGATCCAAAATTTTAAT
AGGATAGGGCATCCTGTAGAGCAGGAGCAAGTAGGAACCTCAAGGTTTCA
AAATGGTCCCTCTGATCAAGAAACTTCGGCTGTATTAGAAATGCCTGAGA
TGGGGACTAAGAATCCTGAAAATGCTTGTCAAAAGGAGAATAATTTGTTG
ACATTCCAAGATCGACCTCTAGATTTGGAGAAGAATGGTCTTATCTGGTT
TCCTCCACCTGCTGTTGATGAAAATGATGAGAAAGAAGACAACTTCTTTG
CATATGAAGATGACGAGGATGATATTGGGGAGTCTACTGCAATGTTTTCA
TCTGCCGACATTGACAACATGCTATCAGAGAAGGATAAAGACAATGATGG
CCAAAAGGATTCATTAAGAGCTGTCGTACAGGGGCATTTTAGAGCCCTTG
TGTTGCAGCTTTTGCTTGGGGAGGGGATACAGGTGAGTAAAGAAAACAAT
GAAGACAATTGGCTAGATGTAGTTACAGAAATATCATGGCAAGCTGCAAA
CTTTGTGAGACCAGATACTAGCAGAGGAGGTAGTATGGATCCTGTCGATT
ACGTAAAAGTTAAGTGTATAGCATCCGGAAATCCCAGTGAAAGGTATACA
TTCATCTTCTCTTTTTGTTATTTCCTTTAATTTCCAGTTCTATATATCCC
TTCTTGTACTAGTCTATACAGTAAACCGTGAAGAGTTTAATGCTACATTT
GTAATATTTTTCATATGCATGCAGCAAATTCATTAAAGGAGTAGTTTGCA
CAAAAAATATAAAACACAAACGCATGATTTCACAGTACAGAAACACTAGA
TTACTCATTTTGGATGGAGCACTCGAGTACCAAAGAGTTCCTAATCAGCT
GGCATCTTTTGATACGCTACTACAACAGGTTTGTTTTTAGAAATCTGGTC
TATTTGGTAAAATTGTGTGAAAGCATGAGCTTATGACCTTTACTTATCTC
AATAGGAAATTGATTATCTGAAGATGATCGTTTCAAGGATAGAGGCTCAT
CATCCAAATGTGTTACTGGTTGAGAAAGGTGTATCTTCATATGCCCAAGA
GTATCTGTTGGCGAAGGAGATCTCCTTGGTGTTGAATGTTAAAAAGCCTT
TACTACAGAGAATAGCTAGGTGCACTGGTGCTTCTATAACTCCTATTGAT
AAGTTGTCTGTAGCTCGTTTAGGGCATTGTGAACTCTTTCGCATAGAAAA
AGTATCTGAAAACCTTGAACAAGTGAATCAGCACCAGAGAAAGCCATCTA
AGACCTTAATGTTCTTTGAAGGATGTCCACGGCGGTTAGGTTGCACGGTA
AAGTTTTCCATCTATGCAAATTCATTTTAAACTTGAATATTTATTATATA
TTTTAAGAAATGATGGGAACTGCAATCACTTTATGAGCTTTAGGCATAGA
CATTGTTTTTCTTTATTAATCAGTTCATAAGAATATGTAAATAGTTATTC
AGCACTGTGTCGTAATAGCTATCTGGTACAGTGTCCCTGACAGCAAGCTG
TACAAAATTTTCACCTAATTAATTTTCCTTGAGCTAAAATCTCTTAGAAG
TACAAAATCTGATAACAAAATGTGTGCATACTTGAATCTCGTTTAACAGC
TACCATTAAAAGTATTTGTTATGTAGATGTGAAATGCTTCATATTTAAAC
CCTTTTTTGCATCCTAAATAATGTTTGGTTCAAAGTTTACATGTAGTCTC
TATGTTGCTTACTATTTTTAGCTTCTAAAACAATTTCCCCTTTTAATTGA
TCATTATTTTTTGATTTAATTAGGTCCTGCTGAAGGGTTCTTGTCGTGAA
GAACTAAAGAAAGTTAAACATGTTGTTCAGTATGCTGTTTTTGCAGCTTA
TCATTTGTCCCTTGAAACTTCATTCCTTGCAGATGAGGGTGCTAGCTTAC
CTAAACCGACCTTGGGATCCTCAATATCACTACTAGAAAGGACAAGTGTC
GATAGTACTATTTCTGTTATTCCTACTTCCGTTGTTCCCACCTCCTACTC
AGAAGTTGCTAATATCACAAGTTTTAATGACGAGTCTACAGGCCTCAATC
TAGAACTCGAGGAAAGCGAGTCAGTACTTGAGCCTCTTAATCCTCAGTTC
ATCTCTTCTCCCAACTCTGTGGAATACAGACTCGGGTCCTCAGATGTCAT
AGACGATCACTTAACAGCTACAGCAGCCTTGGAAGAATACAGGCCAGGTG
TAGTTGACAATTACGAAAGAAGAAATCTTGACGAGGAGAATACCCAGATG
ACCTCAGGCCATATGCAACTACAGGATCTCTACTGTCAGAAAAAGCTTGA
CGAGGTGCTTGCTATTGATGCCTCCAGTGAATACCATTCAGCAGGTGATA
GTCACCAGAGCATACTGGTATCCTTTTCAAGTCGTTGTGTGCTTAATGGA
ACTGTCTGTGAGCGTTCTCGACTCCTGCGCATTAAATTTTATGGTTGTTT
TGATAAACCACTTGGCAGGTATCTTCAAGATGATCTATTTGATCAGGTAA
CTGTTCTGTGTTTATCTGTACTATAATTGTTTGTCGCAAATTCATATGGC
ATGGGATTATTGAACTGCTTCACTTTTAATGCTAGACATCCTGCTGTAAA
TCATGCAAAGAACCAGCTGATTCCCATGTAGTCTGCTACACTCACCAGCA
GGGTAATCTTACAATAAATGTTAGAAGGCTTCCCACAGTAAAGCTACCTG
GAGAACGTGATGGAAAAATTTGGATGTGGCACCGGTGCCTGAGGTGTACA
CATATAGATGGAGTTCCACCAGCAACCCGCAGGGTGGTTATGTCTGATGC
TGCTTGGGGCCTTTCTTTTGGGAAGTTCTTAGAACTTAGTTTCTCGAATC
ATGCAACTGCTAATCGTGTCGCAAGCTGTGGTCATTCTCTGCAAAGGGAC
TGTCTTCGGTACTATGGGTAATGTTATTTTGTTACTAGGACTTTTGTTTT
TTAATTCCACTGTTGTGTTTTTTTGATACATGTCGGTTTATTTATATTTC
TTTATTTTGTTTATAAAATTATGAAATGTTGTCTTTTGTATAACAGCTTT
GGGAGTATGGTAGCATTCTTCCGGTACTCTCCTATTGATATTCTCTCTGT
CCGTTTGCCCCCATCAGTTCTTGAATTCATTCCTCATTCTCAACAGGACT
GGCTAAAGAAAGAGACAGCCGAGGTAATTTAGACACATATTATGCGATAT
CATGTAACAATTAGACTGCATGTTATCTGTCACATTTTTAATAATCTAAT
TCCTTTACTCTGCTACAGCTTTTAAGCAAGCAAACCACTTTGTACGAGGA
AATATTGGGAGTGCTTCATAGGATTGAACAAAAAAGTACCTCTCTTGGAC
TTGAATCATCTGATAGAATTGAGTTACATAGTCACATCATTGAATTGAAG
GACCAGCTAATAAAAGAGAGAGATGATTCTAATGTAAGCTCCAAGCAGAT
AACATATGTTTCTACATTGATATTGTCCACTGTTATTTGAGATAAATCTA
TGCTTTGAAATAATGTATTGAAAAAAGTATACTAATTTTTGCCTGCTTTA
ATGTTTTTTATGCAGTGTATACTCCAACCACCTAGCAAAGAGAGTTTAGA
ACTAGCTACAGTGACGATGGACATTTTTGAACTTAATCGCTTGAGACAAT
CGCTCCTGATCGTTTCACATGACTGGGATCAACGGCTTTGTTCATTGGAT
TCTCGCCTTAACTCTGAGACACGGCTTGGTCCCTCAGATCATGCTGGCCT
AAAGAATTCAAGAAGTGTTTCATCTCTCAGCGATGTCACCCTTTCTCTTG
ACCATAATAATGTCGGTGTGTCTGAACAGATTTTAAATATACCAGATTTT
CCCCAGGAAGATTTACCGTGCACGCATGACAAAGATCCTGAAGCTTCAGC
AGTAAATTTTGGCGTTCGTGGAGTTTACATGTCGACATCATGTGAGATTA
AGGATGAGTTGAAGACACATTCAGATGGAGAATCTACAGATAACAAGACA
TTATTAGAGCGTGCTCCCTCAGCGGCATCTGAATTGTCGGATAAAATTGA
CTCTGTGTGGAATGGTACAGCGGACTATAGTCCGCTGAAATTACCTTCGA
GAAGATTATCATCGCCAGCAAGAGTTCAATCATTTGATTCTGCTATAAGA
TTCCAAGAAAGGGTTAAGAAGGGATTGCCTCCCTCCTCGATGCATTTATC
AGCAGTCAGATCTTTTCACGCTTCTGGGGAATATGTAAACATGCTTAGAG
ATCCCATACCTGACTTACAAAGGACTTCTACTCAAATTTCACCTCACGAG
GCCCAGAAATTTAACCTTTGGAATGCCTCACCCTCATTTATTTCTTCTGC
ATCTCTTTTGCCTAATGGGGCACGATTGGTACTTTCATCAAATGGCCAGA
CAGATTTGATTATTGTTGTTTATGATAATGAACCAACTAGTGCTATATCT
TATGCGCTCAGTTCCAGAGAGCATAAAGACTGGATAGCCGATAAATCTAG
TGGATTTGAAGAGGCCTGGAATGCTGCTCAACTGAAGCGAGAGGATTCTG
CAGCTTCGACCATTCCAGCCTGGCAGTCTTTTGGGTCTTTAGACTTGGAT
TACATCCACTACGGAAGTTATGGTTCTGAAGATGTTTCGACCACTATTGG
TACCATACTAACGGAGCCTAGTAGTAGTCCCCATTTCAAAATTTCTTTTG
AGGCCGAGTCACCTAATTCTGGAGGAAGGGTAAAGTTTTCAGTTACCTGT
TATTTCCCAAAGCAATTTGATGCTCTCAGAAAGAAATGTGGCTGTAATGA
AGTAGATCTTGTACATTCTCTGAGCCGATGTCAGAGGTGGAATGCACAAG
GTGGGAAAAGCAACGTTTACTTCGCAAAGTCTTTGGATGAAAGGTTTATT
GTGAAGCAAGTCACGAAAACTGAATTAGTATCTTTTGAAGAGTTTGCACC
TGAGTACTTTAAATATATGAAAGCTTCTGTAGACTCTAAAAGTCCCACAT
GTCTTGCGAAAATTCTCGGGATATTTCAGGTTGATTTCATTCTTCGTATA
TGCTCTCTTTATTTCTTAGTATCTTAGTTTCTTACAGCTGTCAGTCAACA
TACGCCCGTTCCTTGGGTTCAGCTGGGGTTGGGCAAATGGGACCGATAAT
GCTCTAGTTACTATTATTCTAATTTCTTTGTGAAAATCTCAGGTGACTGT
TAAACACTTGAAGGGTGGCAAGGAAACTAAAATGGATCTGATGGTGATGG
AGAATCTCTTTTTCAGAAGAAACATTTCGAGAGTCTATGATCTCAAGGGC
TCTGCACGGTCCCGTTACAATTCTGATACTACCGGAGAAAACAAGGTGTT
GCTGGATATGAATCTGTTAGAAGCATTACGAACTAAACCCATGTTTCTTG
GAAGCAAGGCCAAGAGAAGCCTGGAAAGAGCAGTTTGGAATGACACATCA
TTTTTAGCGGTAAGCTAATTTTATCCAACTACCTACATAATTGTGATTTT
ATTTATACATTAGTTTATTTTTGGGACGGTAATGTAGTGCAAGTCATGAT
CAAGACCCTTGGTATGCTTAATGAACAATGCACGTAAAAATTAGTGACAG
GGCTTTAAATAATTAAGTAAACAAAAACAGAAACGGGATATTGATAATCT
TGGTAGTTGTGTGCATACCATGAGCTGGAATGCATCGAAAATATGTTAAG
TTCCAAGTTCGTATTCTGTGTTGCAGTCGGTGGATGTTATGGATTATTCT
TTGCTGGTGGGAGTGGATGAAGAAAGGAAAGAGCTGGTACTAGGGATAAT
CGATTACATGAGACAATATACATGGGACAAGCACTTGGAGACATGGGTGA
AGAGCTCTGGAATACTAGGCGGTGCAAAGAATGCTGCCCCGACTATTGTT
TCTCCGAAACTATACAAGAAACGATTTAGAAAGGCGATGACAACCTATTT
CCTTACAGTGCCTGATCAGTGGTCGGCATAG