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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 | |
This analysis was part of the carrot genome assembly publication In population 97837, root tissue was collected from plants with yellow (yyY2Y2) and white (YYY2Y2) genotypes, with two biological replications per genotype, at 80 days after planting (DAP). In population 70796, root tissue was collected from plants with dark orange (yyy2y2) and pale orange (YYy2y2) genotypes, with three biological replications per genotype, at 100 DAP. Total RNA was extracted from whole root tissue using the TRIzol® Plus RNA Purification Kit (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s protocol. RNA was treated for DNA contamination with the TurboDNA-free kit (Life Technologies, Carlsbad, CA). RNA quantity and integrity was confirmed with an Experion RNA StdSens Analysis kit (Bio-Rad, Hercules, CA). All samples had RQI values above 8.0. For each biological replicate, a 133 nt insert size paired-end library was prepared at the Biotechnology Center, UW-Madison (WI, USA). Libraries were sequenced on Illumina HiSeq2000 lanes using 2 × 100 nt reads. Reads were filtered using Trimmomatic version 0.32 with adapter trimming and using a sliding window of length ≥50 and quality ≥28, i.e. “ILLUMINACLIP:adapterfna:2:40:15 LEADING:28 TRAILING:28 SLIDINGWINDOW:10:28 MINLEN:50”. Filtered reads were aligned to the Daucus carota v2.0 genome assembly using the program TopHat v2.0.12 (ref. 30). Non-default parameters used were “--mate-inner-dist -67 --mate-std-dev 50 --min-intron-length 20 --max-intron-length 10000 --library-type fr-unstranded --num-threads 14”. The aligned read files were processed by Cufflinks v2.2.1 (ref. 61). Reads were assembled into transcripts with “cufflinks” using the carrot annotation v1.0 gene predictions as the reference gtf guide. Samples were combined with “cuffmerge”, and then differential expression analyzed with “cuffdiff”, using non-default parameters of “--multi-read-correct --min-alignment-count=5”. Using the abundance estimations, this performs tests for differential expression and regulation between the samples. Normalized counts of the mapped RNA sequences were used to calculate the relative abundances of transcripts expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM). When testing for differential expression, biological replicates were included as a term in the mixed model analysis to account for experimental error. Testing for differential expression was done at the level of genes, isoforms, and promoters. Some of the data from this analysis were published in | |
This analysis was part of the carrot genome assembly publication In population 97837, root tissue was collected from plants with yellow (yyY2Y2) and white (YYY2Y2) genotypes, with two biological replications per genotype, at 80 days after planting (DAP). In population 70796, root tissue was collected from plants with dark orange (yyy2y2) and pale orange (YYy2y2) genotypes, with three biological replications per genotype, at 100 DAP. Total RNA was extracted from whole root tissue using the TRIzol® Plus RNA Purification Kit (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s protocol. RNA was treated for DNA contamination with the TurboDNA-free kit (Life Technologies, Carlsbad, CA). RNA quantity and integrity was confirmed with an Experion RNA StdSens Analysis kit (Bio-Rad, Hercules, CA). All samples had RQI values above 8.0. For each biological replicate, a 133 nt insert size paired-end library was prepared at the Biotechnology Center, UW-Madison (WI, USA). Libraries were sequenced on Illumina HiSeq2000 lanes using 2 × 100 nt reads. Reads were filtered using Trimmomatic version 0.32 with adapter trimming and using a sliding window of length ≥50 and quality ≥28, i.e. “ILLUMINACLIP:adapterfna:2:40:15 LEADING:28 TRAILING:28 SLIDINGWINDOW:10:28 MINLEN:50”. Filtered reads were aligned to the Daucus carota v2.0 genome assembly using the program TopHat v2.0.12 (ref. 30). Non-default parameters used were “--mate-inner-dist -67 --mate-std-dev 50 --min-intron-length 20 --max-intron-length 10000 --library-type fr-unstranded --num-threads 14”. The aligned read files were processed by Cufflinks v2.2.1 (ref. 61). Reads were assembled into transcripts with “cufflinks” using the carrot annotation v1.0 gene predictions as the reference gtf guide. Samples were combined with “cuffmerge”, and then differential expression analyzed with “cuffdiff”, using non-default parameters of “--multi-read-correct --min-alignment-count=5”. Using the abundance estimations, this performs tests for differential expression and regulation between the samples. Normalized counts of the mapped RNA sequences were used to calculate the relative abundances of transcripts expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM). When testing for differential expression, biological replicates were included as a term in the mixed model analysis to account for experimental error. Testing for differential expression was done at the level of genes, isoforms, and promoters. Some of the data from this analysis were published in | |
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. |
ATGAACAACCTTAAGCTTGGAGTTGATGTAGCTAGTGCCCACAACCTTCT
GCCAAAAGATGGGCAAGGCTCATCCAATGCCTATGTGGAACTCTACTTTG
ATGGCCAAAGGCACCGCACAACCATCAAAGAGAAAGACCTGAGCCCAGTC
TGGGATGAAAGCTTCTACTTTAACATCTCCGATCCATCCAACCTTCACAA
TCTAACTCTTGAAGCATACATTTACAATAATATCAAAATCGCCCAATCAA
ATTCTTTTCTTGGAAAGGTTTCCATCAACGGGACATCCTTTGTTCCCCAC
TCTGATGCTGTAGTCCTGCACTATCCTTTGGAAAAGCGTGGAATTTTCTC
ACGTGTGAGAGGAGAACTCGGTCTGAGGGTTTATATTACTGATGATGCAT
CCTTGAAGGCCTCTAAATCACAACATGCAGCTGAAGAGACTGAAATGCAT
TCCCACGCAGCTGAAGCTCAAGTATCTAGGGCATTTTCTAATATCAAATC
TGAATCGAGGCACAGTTTCCATCATCTTCCAAATCCTAGTCATCACATGC
AGCAGCAGCATTCCCCTTCTATGTCAGTTTATGAATCAACAAAATATGGG
GTTGATAATATGAAAGCTGAACCACAACCCCCAAAACTTGTCCGCATGTA
TTCTGCTGCATCAGTGCAACCAGTTGACTATGCACTTAAAGAGACGAGCC
CATTTCTTGGAGGAGGACGAGTTGTAGGGGGGCGAATACTTCATACAGAC
AAGGCTGCTTGTACTTATGATCTTGTAGAAAAAATGCACTTTCTTTTTGT
ACGTGTTGTTAAGGCTCGTGAACTTCCTGCCATGGATATTACTGGAAGTC
TTGATCCTTTTGTTGAGGTGAGAATAGGTAATTACAGAGGAGTCACAAAG
CATATGGAGAAACAGCAGAACCCAATGTGGAATGTTGTTTTTGCATTCTC
AAGGGAGCGAATGCAGGCATCGGTCCTGGAAGTTGTAGTTAAAGACAAAG
ATCTGCTGAAAGATGACTTTGTTGGCCTTGTAAGGTTTGACCTGAATGAA
GTTCCTATGCGTGTTCCACCTGATAGTCCACTGGCTCCTGAATGGTACCG
ACTCCAGGATAAGAAAGGAGAGAAAATTAAGAGTGAACTGATGCTTGCAG
TGTGGATTGGTACCCAAGCAGATGAAGCTTTTCCTGATGCTTGGCACTCT
GATGCAGCAACGCCTATTGACAGCTCCGGAGCTGCCTCAACACTAATTCG
GTCAAAGGTCTATCATGCACCGCGATTATGGTATGTTCGTGTGAATGTTG
TTGAGGCCCAAGACTTGGTTCCAACAGAGAGAACTCGCTTCCCTGACGTA
TATGTAAAGGCACATATAGGGAGCCAGGTTTTCAAAACAAAGACAGTTCA
AGCAAGGTCTCTGAATCCTCTTTGGAATGAGGATCTCATATTTGTTGCCG
CAGAACCATTTGAAGATCATTTGGTCCTTACTGTTGAGGATCGTGTGGGT
CCTGGAAAAGATGAGATTCTGGGGAGGGTAATCATCCCCTTAAGCATGGT
GGAGAAGCGTGCTGATGATCGTCTCATCCATTCTCGTTGGTTTAATTTGG
AGAAACCTGTCGCTATAGACGTGGATCAGCTAAAAAGAGAGAAGTTCTCT
AGCAGGCTCCATCTTCGAGTCTGTCTAGATGGTGGTTACCATGTTCTTGA
TGAATCTACACATTACAGCAGTGATCTTCGTCCGACAGCAAAACAACTTT
GGAAGCCATCTATTGGGGTTCTGGAACTTGGTATTCTCAATGCAGTTGGA
CTCCACCCTATGAAAACAAGAGATGGCAGGGGCACATCAGACACATATTG
TGTAGCCAAGTATGGTCATAAATGGGTTAGGACGCGCACAATTGTTGATA
ATTTGTGTCCAAAATACAATGAGCAGTACACTTGGGAGGTGTTTGATACT
GCTACAGTTCTAACTATAGGTGTTTTTGACAATAGCCAGCTAGGGGAAAA
AGGGGGCAAGGACCTGCAAATTGGAAAGGTACGAATTCGCCTTTCTACAC
TTGAAGCTGGCCGCGTTTACACACACTCTTATCCTCTACTTGTTCTTCAC
CCTACTGGTGTCAAGAAGATGGGGGAGGTGCATTTGGCAATAAGGTTTTC
ATGCACTTCTTTTGTAAACATGATGTACATATACTCTAAACCTCTGTTGC
CGAAAATGCACTATGCTAGGCCATTTAGCGTAATGCAGCTTGACATGCTG
CGTCACCAGGCTGTGAACATAGTTGCAGCGCGCCTGGGACGTGCAGAGCC
CCCTCTTAGGAAGGAGGTCGTGGAGTATATGTCTGATGTGGACTCACATT
TGTGGAGCATGCGCCGCAGCAAGGCCAATTTCTTCCGTCTCATGTCAATT
TTTTCGGGATTATTTGCTGTTGGAAAATGGTTTGGGGATATATGCATGTG
GAAAAACCCCATCACAACAGTGCTTGTCCATGTCCTATATGTTATGCTTG
TTTGCTTCCCAGAACTAATTTTGCCTACTTGTTTCCTTTACATGTTTCTG
ATTGGAATCTGGAACTTTCGATACCGGGCAAGATACCCTCCTCACATGAA
CACAAAGATCTCACAGGCAGAGGCAGTGCACCCTGATGAACTTGATGAAG
AATTCGACACATTCCCCACAAGTCGTAACCCTGAGATTGTCAGAATGAGG
TATGATCGCCTGAGGAGTGTAGCTGGTAGAATTCAAACAGTGGTAGGTGA
TATTGCTACACAGGGTGAGCGTGTTCAATCATTGTTAAGCTGGAGGGACC
CTCGCGCTACCTCCATCTATGTCACATTCTGCGTAGTAGCTGCTATAGTG
CTGTATGTGACACCATTCCAGGTGATTGCTGCATTGGCAGGGGTATACAT
GATGAGGCATCCCAGATTCCGCTATCGTCTGCCTTCTGTGCCTGTCAATT
TCTTCCGTCGACTTCCTGCAAGGACTGATAGTATGCTCTAA
MNNLKLGVDVASAHNLLPKDGQGSSNAYVELYFDGQRHRTTIKEKDLSPV
WDESFYFNISDPSNLHNLTLEAYIYNNIKIAQSNSFLGKVSINGTSFVPH
SDAVVLHYPLEKRGIFSRVRGELGLRVYITDDASLKASKSQHAAEETEMH
SHAAEAQVSRAFSNIKSESRHSFHHLPNPSHHMQQQHSPSMSVYESTKYG
VDNMKAEPQPPKLVRMYSAASVQPVDYALKETSPFLGGGRVVGGRILHTD
KAACTYDLVEKMHFLFVRVVKARELPAMDITGSLDPFVEVRIGNYRGVTK
HMEKQQNPMWNVVFAFSRERMQASVLEVVVKDKDLLKDDFVGLVRFDLNE
VPMRVPPDSPLAPEWYRLQDKKGEKIKSELMLAVWIGTQADEAFPDAWHS
DAATPIDSSGAASTLIRSKVYHAPRLWYVRVNVVEAQDLVPTERTRFPDV
YVKAHIGSQVFKTKTVQARSLNPLWNEDLIFVAAEPFEDHLVLTVEDRVG
PGKDEILGRVIIPLSMVEKRADDRLIHSRWFNLEKPVAIDVDQLKREKFS
SRLHLRVCLDGGYHVLDESTHYSSDLRPTAKQLWKPSIGVLELGILNAVG
LHPMKTRDGRGTSDTYCVAKYGHKWVRTRTIVDNLCPKYNEQYTWEVFDT
ATVLTIGVFDNSQLGEKGGKDLQIGKVRIRLSTLEAGRVYTHSYPLLVLH
PTGVKKMGEVHLAIRFSCTSFVNMMYIYSKPLLPKMHYARPFSVMQLDML
RHQAVNIVAARLGRAEPPLRKEVVEYMSDVDSHLWSMRRSKANFFRLMSI
FSGLFAVGKWFGDICMWKNPITTVLVHVLYVMLVCFPELILPTCFLYMFL
IGIWNFRYRARYPPHMNTKISQAEAVHPDELDEEFDTFPTSRNPEIVRMR
YDRLRSVAGRIQTVVGDIATQGERVQSLLSWRDPRATSIYVTFCVVAAIV
LYVTPFQVIAALAGVYMMRHPRFRYRLPSVPVNFFRRLPARTDSML*
Relationships |
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The mRNA, DCAR_000606, is a part of gene, DCAR_000606. |
The polypeptide, DCAR_000606, derives from mRNA, DCAR_000606. |