| Relationships |
|---|
| The mRNA, DCAR_023265, is a part of gene, DCAR_023265. |
| The genetic_marker, MK009646 6_155594, is located in gene, DCAR_023265. |
| The genetic_marker, MK007777 TP82081, is located in gene, DCAR_023265. |
| The genetic_marker, MK008324 6_160096, is located in gene, DCAR_023265. |
| 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_023265 | DCAR_023265.mRNA | mRNA | DCARv2_Chr6:155398..160552 |
ATGTCAAACAATCTTGTTTCTCAGCAACTTTCTATGTCGAATGCGGACAT
GAGCCAGATGGAGCCTACTTATGTGAAAGTAGATTCTTCAGTGAATATGC
AAATGGGTGTGATGGGATCTATCCCAGATGTGTATGCATCACATCAGTTT
GCGATGTCAGATCAGCAGATGCAGTTGGTAGACCCTTTATCCTACATTTC
TGGACCACAGAGCTACACGATGTCTAATACCCATTTAGGAAACATGGAGT
CAATGGTGGACAATGTGGGTTTGCATAAGTCTAAGCCAGACCAGAAAGAT
GTACAAATGGATGCCATGTTTACCAATCCAGGTCCCCAGAAGTTGTTTCA
GCCAAACAAGCGAAAGGCTGCAGTAGAACCGATGTTTAATAGCACTGTCC
CAAGACAGTTATCTATGCCTAACAAGCGTGCAACACATATGGATTCATTA
TCAACCTCACATGAGCTGCCTAACCATTCTGGTACAAATAGGAAAGGTGG
GACCCTGCAATCTGTTTCAGCTGTATCTGGGTCTCAAACACCTGCATCAA
ACAGGAGAACAGTAAAGAATGACTTAAACTCGAATAAACCTGCTAGTCAG
CGGGTACAGACCCCGAAGGGTCGTACTGCTCAGATAGGAACACCGCGTCA
GACAGAGTCATTTGAAGCTGTCAGGTCCAAAATGAGGGAATCGTTAGCTT
CTGCATTGGCCTTGGTCAATCAGAACCAGAGTTCTTCGCCTAAGCAAGAG
AAGAGTCCTCTACACAAAGACGATAACAACCCAGAGGTGATATCGCAGAA
TGTCAAACTTTCTGAATCTACTTCGGTCCCTGTTGATGCTGCTGTTGCAC
ATGAAAACATCAAGGATGACATACAAACAAAAGATATAAGCTTGGTTAAT
AATCCCAGTCATCGCCTAAGCACATTTGCTGAGAACTTGACTCATGAAGG
CATTGAAAATCTTCCAGACACCTGGAAAAACGACGTATCAGATTCCATGT
ACAATGCTGTTTTGCCTGAAGAAGATGTTGCATTTACAGACAGTTTCTTT
GCCAAAGATGAGCTTCTTCAGGGACATGGGCTTTCCTGGGAATGGGAAAT
CGGTATGGAGGTGGAAGCAAAGCAGCAATTACAATCTTCCAGACAGGTTA
ATGTTCCGGGAGATGATGATGAGCAAAAGGTCAAGCATTCTGATAATTTG
ACATTGAAAACTGAAGAAAAAGTGGCTCAGGCTGCCAATCAAGCGGGTGC
TGGAAGGGATGAGAGTTTTTATACTCTTCGGACTCCTGAAAAATTGGCTT
TTGAAATTGAGGCAGAACTTTTCAAATTATTTGGGGGTGTGAATAAGAAG
TACAAAGAAAAGGGTAGATCTCTCATGTTCAATTTGAAAGACAGGAACAA
TCCAGAACTACGCGAGAAAGTTATGTCCGGCGACATTACTCCTGAAAAGT
TGTGCTCCATGACGGCAGAGGAACTTGCCTCTAAGGAGCTTTCTGAGTGG
CGAACAGCAAAGGCTGAAGAGCTCGCACAAATGATAGTCTTGCCTGAAGA
TGGTGATAGAAGACGTTTGGTTAAAAAAACTCACAAGGGGGAATACCAAG
TGGAAGTGGAGCAGGATGATGAAATTTCTGTTGAGGTATCTGTCGGGGCA
ACTACTCTGGGACAGTTCCAAAGGAATGATAAGGAGAAACTACCTCCCTC
CTCATCAGATAAGGATGAACTTAAAGATTCAAAAAAAGTCGAAAGTGAGA
AGGGTAGTATGGAAACTATGGATCCATCATATAGTCTTACTATTCCAGCT
GACGGGACTGATTTGATGCAAGGGTTAATAGAGGACGAATTTAAAGATGC
AGAATTTCTTCCTCCAATTGTCTCATTGGATGAATTTATGGAATCCCTCA
ACTCTGAGCCACCGTTTGACAATTTGGCAGCAGACACTCAAACAAAAACT
CCTTTGGATAAGTTGTCAGCTGAAACTGGTGAGAATTCGGAGTCTTCGAA
ATTAGCTTCCAAAGATGTTGATAACAGGACAGGAAAGGCTACAGATCTTG
ATTCCAAAATGACAAAGCAGGATGCAGAAGAGAAGTCTGGCGACTATGCA
AAGGAGCAAAAACAATTGAATCCTGACATGACATCAATGGCTGAACGTGT
ATGGGAGGGTGCATTACAGCTACATATTTCTGCCCTTATTACAGTTATTG
GCCTGTATAGAAGGTATTTTCTTATTCACGTTATAGTTATGCAGGTTTTG
TTTCTGGAGTTTTCCTTCCTATTGGATAAAAGTTAATGATAGTTTAATTG
TGCTGGATAAATCATCTTGATCTTGAGGTTGTATAAATTGTTCATTGCCC
TTATTTTCTGTTTAACCTGCATTATTTAAATCGACATTATAATATATGTA
ATCTGCTGTTGATCCTAAATTTTGTATATAGTTACTACACTGACTGCCTT
AATGTTGATTGCGGGAAAATCGTCACTTCTTGAAATTCTAGACATGCTTA
TTTTGCAATAAATATTAAAATAGATGATAAAATGCAAAAGATTTTGTAGC
TTCCTTTATTTCCAGCAACCTCAAAAAATTTGAATACCTAGTGAAGCAAT
TTATTTTATTTTGGTTCACCTATATTTTTCTCACTAGTTGACAATTTTTT
CTGCTTTTGACAAATCTAGTTACTTCTTGTCTGAGGAATTTTTTGTATTG
ATTTGTTACTCTTGATAGTACATTGGTGGTCTGTTATGGTTTAACAGTGG
CCAGACACATAAATTGGCATATGCCTCTTGCTATTCACATCTCAAAATTT
GATAACTATCAGAGCTACTGTGTTGTCTTGGTTCATATTTATTCTTTTCA
CCAGCTTACAGTTTCCATTTTTTGAGAAATTTAGTTTTATACTTTTCTGG
CATCTATATGTTCTGTATTAGTTCATTACTTGATTCACTTTCTTGTTTGT
GTTTTAATGATCTGTTACTGCTTTACAGTGGTGAAAAAACGTCTACAAAG
GAGTGGCCAAGTTCTCTTGAAATAAAAGGAAGAGTTAGACTTGATGCATT
TGAAAAATTTCTCCAAGAGCTTCCCATGTCTCGAAGTCGTGCAGTCATGG
TATATCAAGTTTCCTTATATCTCATTGTATTTCAAAGTTGTGCTTAGGTG
TTTTGTTAGTGTGTTGTTTTGAGAATTACAGGGTGCCATTCTGTCATCGG
TGGCAATTTACTTTTGTTCAAGGTCATTGGTCGGAATTGACTTATTTCCC
AGGAGGATTCATCGACTAAATATTTTGGCGCAACGTATATATGGAGCAGA
CAGCAGATTTTTAACTACTGTCATTAATATCATAATAAGAATACCAAAGT
TCACCTTTCTTTCCATTTTTTACAATCTCCGAAGTGAATATCTGATAGTG
TCATTACTTAGATCGGTGGGCTGTACACCTGTACATCATCCCATTGCAGA
GAAGTGTTCTCAGCGAGTGAATACTTTGATCTCACACCATTGGATGAAAG
AAGCACTGCTATATTCCTCCTTGTAGACATGCCTGATGAGATCTGGAGTC
TCCATAGTTATATATGCAGTTGCTGAGAACCTTGATTTGGATTCTGGAAC
TTCAGAAATGATCATTTTGGTTTTGGATGTGAATTGGATAAATGGATAGA
TTTGTCATCTCATTTGTAAATGAGTATCAAGTAAAATTGGTTTATAAATT
CATTTCACATGATGCTTGGAAAATCTAATTTAGAAGGGTAAACATATTTA
ATGATGACTTGAACCATTTCAAGAAATTTTCAGATATGTGGGAACCACAT
TGTAAATGAACAGGCTCTGGCAGAGAAACACAAAAAGCTCATCATCTTAA
TGAAAGTTCCTGTACAATAACTTGTTAAGATTTCTGGTTTTTGACTGGTA
AAAGTAAACATTCCTGTAGGCATTAAGGAGCAAAATGCTAACTGTTATCT
ATACATCTGCTAATGGTCTCTACTTGCTACAAATTGATATCTGGAGTTAT
CATCTTAAGAACTTTCTTCTTTGCTGCAGGTGATACACTTTGTCTTGAAG
GCAGATTCGTCTGCAGATGACCGAGCAAGTCTTCGTGAGGTGACCTCTAC
ACTTTTCAATTCTTTTGTCATACCATACTATTAGAGCCTTTTTGGTCTAA
AGTTATACGGCTTGGTTTGTTTCTTGGGACAGGCTATAGATTCTTATGTT
CTGGATGAGAGGCTAGGATTTGCAGAACCTGCATCAGGAATGGAGCTTTA
TCTCTGCCCACCACACCCAAAGATACTCGAACTGCTTGGCAAACATCTCT
CCAAGGACCAGACCGAGCTAATTAATTCGACAGATAATGGTTTAATTGGT
GTAGTTGTATGGCGTAAGGCTCATTTAAGTTCTACAATCTCACCTAACTC
AACCTCACACCATAAACATAGCTCAAAAAAGCAACAAAACTTTCGGAGAC
AGGAAAAGAACAATAATGTTAATGCTAATATGACCCCAAGAACTCCTGTA
CCTTCAACTCAAGCTCCCATCAGATCTGGAACTTTACCATCCGGTAATGA
TGATGATGATATTCCACCTGGGTTTGGTCCGGGAAATGCTCGGGATGACG
ATGATTTGCCTGAATTCAGCTTTTCTGGCAGTTCTAACCCAACTCAGTCT
TCAAGGCTGTCCTCAAACCCATCACGGCCCGTAGACCAAATTAGAGAGCT
TATTCAGAAATATGGAAAACCTGCAGAAAGTCAGAGCACTAAGAATTGGC
AGGGTAAAAGAAGTGCTGGCCTTGCAGTGCAAGCATGGGATGATGATGAT
GACGACGACATTCCAGAGTGGCGCCCTGATGCTCCCCTGACCCATGTACA
GACTCGTCCTCCTGCTCGTGGCTTTCACCAAGCAGTGCAGCCTCCCTTGG
TTAATCAAACTGCAACTACACAGCATGTTCTGTCACCACAGGTGGCTATG
CCTCCGATGACCATGATACAAAACAACCCCTCATCTTGGCAGCAAGGTAA
TGGGAGATGGGTGGCACAGCCGCCAGGTTTTCAGCAGAGTAGTTTAGCAA
GTCAGCCTAACATAGGGCAGTTCCAAGGTGGGCCCGTGGCTCAGGCTGGG
CAGCCACCGCCTGGTAACTGGAGGAGAGATGCACCTAGAAGTAGGGGTTT
TTGA