XM_017391711.1

Resource Type: 
mRNA
Name: 
XM_017391711.1
Identifier: 
XM_017391711.1
Analysis: 
NameDescription

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
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

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

The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/

Data from this analysis can be viewed in JBrowse here.

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Transcript Id: 
XM_017391711.1
Product: 
ATP-dependent Clp protease ATP-binding subunit CLPT1, chloroplastic, transcript variant X1
Sequence: 
CTAGTAAGTTACTGTAAATCAATTATGAATCTGGTGTTTGACATCCAAAA
GCTTGTTATTACACCAAATTAGAAAGAGGGGCAGATTAGAAAATTAGGGT
TTATCTTTCAATACTTGAAAGTTGAAACCCAATTCCCCATCTATTCTATC
CAATATCCATGGCTGCTCACGCCCTCTCGCTGCTCCCCATTTCGACACCT
TCTCGTAATCATTTTTGCTGTAAACAAGAATCAATTAAATCATCACTCTG
TTATCATCTTAGTCTCGCTAGCTCTTTCGTTGGAGCTAAATTGGCTGTTA
ATTATACAAATTCGCGGCAGTACACTCACACACAGCACTCCTCCACGGTG
GCCACCATCTCCGTCAGTCTTCCCACTGGGACACCTGATAGAATCTCGAG
GCAGAAGTCTCCCAAATGGTCAGCTAGGGCAATAAAGTCGTATGCAATGG
CTGAATTGGAAGCTAGAAAGCTTAAGTATCCTAATACTGGGACGGAAGCT
CTTCTCATGGGAATTTTGGTCGAAGGAACCAGTTTAGCTGCAAAGTTCTT
GAGAGAAAATGGTATCACTCTTTTTAAAGTTCGGGATGAGACTGTCAAAT
TGCTTGGAAAATCAGACATGTACTTTTTCAGTCCTGAGCATCCTCCATTC
ACAGAACCAGCTCAGCGGGCACTTGATTGGGCTATAGCTGAGAAACTGAA
GTCAGGCGAAGATGGGGAAGTAACAGCTGCTCACTTTCTTCTGGGAGTGT
GGTCAGAAAAGGAATCAGCTGGTCACAAGATCATGGCTGCACTTGGTTTT
GATGATGAGAAAGCTAAGGAAGTTGCCAAATTTATGGACAAGGATATAGA
CTTGGGCTTCAAGACGAGAAGTTAGAGCTTTGGAAGTGAGCGTAATTTTT
GCTTATTAATCTTCTTAAGAAATTTCTGGGACATATGCTTGGGGTCCTCT
GCGATACTTATGTCCCATATATTCTTTTAAGGCTTCTTAAAAGTTCATTG
TGTCAATTCCTTGTCCAGTGTGTGCAGTCTCTCTTCACAATTTTACCTTA
CTCCCTTTAGCTATAAGATCTATACCTGGTTTCCGTACCA
Sequence Length: 
1090
Sequence Checksum: 
897edf08b2ba6a7a84283927de6fb29b
View location in JBrowse: 
Protein Sequence: 
MAAHALSLLPISTPSRNHFCCKQESIKSSLCYHLSLASSFVGAKLAVNYT
NSRQYTHTQHSSTVATISVSLPTGTPDRISRQKSPKWSARAIKSYAMAEL
EARKLKYPNTGTEALLMGILVEGTSLAAKFLRENGITLFKVRDETVKLLG
KSDMYFFSPEHPPFTEPAQRALDWAIAEKLKSGEDGEVTAAHFLLGVWSE
KESAGHKIMAALGFDDEKAKEVAKFMDKDIDLGFKTRS
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017391711.1, is a part of gene, LOC108218667.
The polypeptide, XM_017391711.1, derives from mRNA, XM_017391711.1.
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Cross Reference: 
NCBI GeneLoading content
NCBI NuccoreLoading content
Gene: 
LOC108218667
Model Evidence: 
Supporting evidence includes similarity to: 3 ESTs, 8 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 25 samples with support for all annotated introns
Gbkey: 
mRNA