MLRRQVSSLISICKQNGSTYLQKPIVSTSMIPQHPLQFSKWGNSKIGFLG
TRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTH
KFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSEL
ITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVE
AAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIG
RLPAPTKPIPFTAEEKET
| Relationships |
|---|
| The polypeptide, XM_017371916.1, derives from mRNA, XM_017371916.1. |
Analysis Date: 2022-01-09
Analysis Name: NCBI peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 10
Match: A0A4S4DK47 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 426.017 bits (1094), Expect = 7.276e-150
Identity = 222/269 (82.53%), Postives = 234/269 (86.99%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQN-GSTYLQKPIVST-SMIPQHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKE 267
MLRR++SSLI+ N S+ +Q + S S I P F+ N + RAYSLLSLNDLRDNKGA+K KTRKGRGIGSGKGKTAGRGHKGQKARGT KFGFEGGQTPLRRR+PKRGF NPFSLTFQPVGLGKIAKLINAG+IDSSELITMKTLK+AGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAK AVEAAGGSVRRVYYN LGFRALLKPEWFEKKGRLLPRAARPPPKQ DKVDSIGRLPAPTKPI FTAEEKE
Sbjct: 1 MLRRKLSSLIATSIFNTCSSKIQSKLCSIGSPISPSP-SFATPTNFNVQAQSLRAYSLLSLNDLRDNKGAKKQKTRKGRGIGSGKGKTAGRGHKGQKARGTMKFGFEGGQTPLRRRMPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSELITMKTLKDAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKGAVEAAGGSVRRVYYNNLGFRALLKPEWFEKKGRLLPRAARPPPKQRDKVDSIGRLPAPTKPISFTAEEKE 268
Match: A0A7J7FQT8 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 423.32 bits (1087), Expect = 8.377e-149
Identity = 220/269 (81.78%), Postives = 233/269 (86.62%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQN-GSTYLQKPIVST-SMIPQHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKE 267
MLRR++SSLI+ N S+ +Q + S S I P F+ N + RAYSLLSLNDLRDNKGA+K KTRKGRGIGSGKGKTAGRGHKGQKARGT KFGFEGGQTPLRRR+PKRGF NPFSLTFQPVGLGKIAKLINAG+IDSSELITMKTLK+AGAIGKQIRDGVRLMGRG+EHIEWPIHLEVSRVTVRAK AVE AGGSVRRVYYN LGFRALLKPEWFEKKGRLLPRAARPPPKQ DKVDSIGRLPAPTKPI FTAEEKE
Sbjct: 1 MLRRKLSSLIATSIFNTCSSKIQSKLCSIGSPISPSP-SFATPTNFNVQAQSLRAYSLLSLNDLRDNKGAKKQKTRKGRGIGSGKGKTAGRGHKGQKARGTMKFGFEGGQTPLRRRMPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSELITMKTLKDAGAIGKQIRDGVRLMGRGSEHIEWPIHLEVSRVTVRAKGAVETAGGSVRRVYYNNLGFRALLKPEWFEKKGRLLPRAARPPPKQRDKVDSIGRLPAPTKPISFTAEEKE 268
Match: A0A6S7N8H7 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 421.009 bits (1081), Expect = 8.228e-148
Identity = 217/274 (79.20%), Postives = 231/274 (84.31%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQKPIVSTSMIP---------QHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEE 265
MLRR++SSL+S +N S Y + STS P H F K NS G RAYSLLSLNDLRDNKGA K KTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRR+PKRGF NPFSL FQPVGLGKIA+LINAG+IDSSELITMKTLK+ GAIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAK AVEA GGSVR+VYYNKLGFRALLKPEWFEKKGRL+P+AARPPPKQ DKVDSIGRLPAPTKPIPFT E+
Sbjct: 1 MLRRKLSSLLSNSVRNASVYTK----STSHFPITKLLHNPIHHSNLFQKPVNS-FGVHSIRAYSLLSLNDLRDNKGATKQKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRMPKRGFKNPFSLEFQPVGLGKIARLINAGKIDSSELITMKTLKDTGAIGKQIRDGVRLMGRGAEHIQWPIHLEVSRVTVRAKEAVEAVGGSVRKVYYNKLGFRALLKPEWFEKKGRLIPKAARPPPKQMDKVDSIGRLPAPTKPIPFTEED 269
Match: A0A6I9U0V7 ((uncharacterized protein LOC105173556 {ECO:0000313|RefSeq:XP_011093640.1, ECO:0000313|RefSeq:XP_011093641.1}))
HSP 1 Score: 420.239 bits (1079), Expect = 1.837e-147
Identity = 221/276 (80.07%), Postives = 233/276 (84.42%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQKPIVS------TSMIPQHPLQF-SKWGNSKIGFLGTRAYS-LLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKET 268
MLRR+++SLI++ + T QKP S + H LQ S F G RAYS LL+LNDLRDN GARK KTRKGRGIGSGKGKTAGRGHKGQKARGT KFGFEGGQTPLRRRLPKRGF NPFSLTFQPVGLGKIAKLINAG+IDSSELITMKTLK++GAIGKQI DGVRLMGRGAEHI+WPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLG RALLKPEWFEKKGRLLPRAARPPPKQ DKVDSIGRLPAPTKPIPFT EEKE
Sbjct: 1 MLRRRLASLITVSIRTAQTQYQKPTSSFPPFAGLQLDSVHFLQCRSDISKPSCQFGGLRAYSSLLALNDLRDNPGARKQKTRKGRGIGSGKGKTAGRGHKGQKARGTMKFGFEGGQTPLRRRLPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSELITMKTLKDSGAIGKQIGDGVRLMGRGAEHIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGLRALLKPEWFEKKGRLLPRAARPPPKQKDKVDSIGRLPAPTKPIPFTTEEKEV 276
Match: A0A2J6M115 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 419.853 bits (1078), Expect = 2.434e-147
Identity = 211/269 (78.44%), Postives = 229/269 (85.13%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQK----PIVSTSMIPQHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEE 265
MLRR++SSL+S +N S Y + PI P H + + G RAY+LLSLNDLRDNKGA + KTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRR+PKRGF NPFSL FQPVGLGKIA+LINAG+IDSSELITMKTLK+ GAIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAK AVEAAGGSVR+VYYNKLGFRALLKPEWFEKKGRL+P+AARPPPKQ DKVDSIGRLPAPTKPIPFT E+
Sbjct: 1 MLRRKLSSLLSNSVRNASVYTKSTSHFPITKLLHNPIHHSNLIQKPVNSFGVHSIRAYNLLSLNDLRDNKGATQQKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRMPKRGFKNPFSLEFQPVGLGKIARLINAGKIDSSELITMKTLKDTGAIGKQIRDGVRLMGRGAEHIQWPIHLEVSRVTVRAKEAVEAAGGSVRKVYYNKLGFRALLKPEWFEKKGRLIPKAARPPPKQMDKVDSIGRLPAPTKPIPFTEED 269
Match: A0A5N6P869 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 419.468 bits (1077), Expect = 3.012e-147
Identity = 215/265 (81.13%), Postives = 225/265 (84.91%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQK----PIVSTSMIPQHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPF 261
MLRR + L+S QN S Y + PI P H L S NS G RAYSLLSLNDLRDNKGA K KTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRR+PKRGF NPFSL FQPVGLGKIA+LINAG+IDSSELITMKTLK+ GAIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAK AVEAAGGSVR+VYYNKLGFRALLKPEWFEKKGRLLP+AARPPPKQ DKVDSIGRLPAPTKPIPF
Sbjct: 1 MLRRTIPYLLSNSIQNASIYTKPNSYFPITKLLHNPIHHLIPSTKTNSSFGIHSLRAYSLLSLNDLRDNKGATKQKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRMPKRGFKNPFSLEFQPVGLGKIARLINAGKIDSSELITMKTLKDTGAIGKQIRDGVRLMGRGAEHIQWPIHLEVSRVTVRAKEAVEAAGGSVRKVYYNKLGFRALLKPEWFEKKGRLLPKAARPPPKQMDKVDSIGRLPAPTKPIPF 265
Match: A0A2G9H222 ((Mitochondrial/chloroplast ribosomal protein L15/L10 {ECO:0000313|EMBL:PIN11567.1}))
HSP 1 Score: 418.313 bits (1074), Expect = 1.120e-146
Identity = 220/279 (78.85%), Postives = 233/279 (83.51%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQKPIVSTSMIPQ-HPLQFSKW---------GNSKIGFLGTRAYS-LLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKET 268
MLRR+++SLI + + QKP S P PLQF+ F RAYS LL+LNDLRDN GARK KTRKGRGIGSGKGKTAGRGHKGQKARGT KFGFEGGQTPLRRRLPKRGF NPFSLTFQPVGLGKIAKLINAG+IDSSELITMKTLK++GAIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLG RALLKPEWFEKKGRLLP+AARPPPKQ D+VDSIGRLPAPTKPIPFTAEEKE
Sbjct: 1 MLRRRLASLIPPAIRCAQNHCQKP---ASTFPHLAPLQFASLQFQQCPVDISKPSCHFGSVRAYSSLLALNDLRDNPGARKQKTRKGRGIGSGKGKTAGRGHKGQKARGTMKFGFEGGQTPLRRRLPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSELITMKTLKDSGAIGKQIRDGVRLMGRGAEHIKWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGLRALLKPEWFEKKGRLLPKAARPPPKQRDRVDSIGRLPAPTKPIPFTAEEKEA 276
Match: A0A5J5BV24 (Ribosomal_L18e/L15P domain-containing protein {ECO:0000259|Pfam:PF00828})
HSP 1 Score: 417.927 bits (1073), Expect = 1.371e-146
Identity = 215/274 (78.47%), Postives = 234/274 (85.40%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQKPIVSTSMIPQH-PLQFSKWGNSKIGF------LGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKE 267
MLRR++ S+++ +N S+Y + ++ + H L+F + N F G RAYSLLSLNDLRDNKGARK KTRKGRGIGSGKGKTAGRGHKGQKARGT KFGFEGGQTPLRRRLPKRGF NPFSLTFQPVGLGKIAKLINAG+IDSS+LITMKTLK+ AIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAKAAVEA GG+VRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQ DKVDSIGRLPAP KPIPFT EEK+
Sbjct: 1 MLRRRLCSVLATSIRNVSSYTKPSLILQPVSSPHLALRFVQCPNPNPSFNGIFVPQGMRAYSLLSLNDLRDNKGARKQKTRKGRGIGSGKGKTAGRGHKGQKARGTMKFGFEGGQTPLRRRLPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSQLITMKTLKDTRAIGKQIRDGVRLMGRGAEHIKWPIHLEVSRVTVRAKAAVEAMGGTVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQRDKVDSIGRLPAPNKPIPFTQEEKD 274
Match: A0A200QFD0 ((Ribosomal protein L15 {ECO:0000313|EMBL:OVA09142.1}))
HSP 1 Score: 417.157 bits (1071), Expect = 3.489e-146
Identity = 213/275 (77.45%), Postives = 232/275 (84.36%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQKPIVSTSMIPQHPLQFSKWGN-------SKIGF-LGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPFTAEEKE 267
MLRR+++SL++ + S Y + +S ++ P Q + N K+ F G RAYSLLSLNDLRDNKGAR+ K RKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGF NPFSLTFQPVGLGKIAKLINAG+IDSSELITMKTLK+ AIGKQI+DGVRLMGRGAE I+WPIHLEVSRVTVRAK AVEAAGGSVR+VYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQ DKVDSIGRLPAPTKPIPF EE +
Sbjct: 1 MLRRRLTSLLATSIRQSSIYNKPSFISATISSTSPFQSLQTLNPNPNSNLDKVYFPHGIRAYSLLSLNDLRDNKGARQKKRRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFKNPFSLTFQPVGLGKIAKLINAGKIDSSELITMKTLKDTAAIGKQIKDGVRLMGRGAEQIKWPIHLEVSRVTVRAKQAVEAAGGSVRKVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQRDKVDSIGRLPAPTKPIPFLTEEYD 275
Match: A0A251RQV0 ((Putative ribosomal protein L18e/L15 superfamily protein {ECO:0000313|EMBL:OTF86775.1}))
HSP 1 Score: 414.846 bits (1065), Expect = 1.884e-145
Identity = 210/265 (79.25%), Postives = 227/265 (85.66%), Query Frame = 0
Query: 1 MLRRQVSSLISICKQNGSTYLQ----KPIVSTSMIPQHPLQFSKWGNSKIGFLGTRAYSLLSLNDLRDNKGARKPKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPLRRRLPKRGFHNPFSLTFQPVGLGKIAKLINAGRIDSSELITMKTLKEAGAIGKQIRDGVRLMGRGAEHIEWPIHLEVSRVTVRAKAAVEAAGGSVRRVYYNKLGFRALLKPEWFEKKGRLLPRAARPPPKQADKVDSIGRLPAPTKPIPF 261
MLRR++ SLIS +N S + + P +++ P H +G G RAYSLLSLNDLRDNKGA K KTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTP+RRR+PKRGF NPFSL FQPVGLGKIA+LINAG+IDSSELITMKTLK+ GAIGKQIRDGVRLMGRGAEHI+WPIHLEVSRVTVRAK AVEAAGGSVR+VYYNKLGFRALLKPEWFEKKGRLLP+AARPPPKQ DKVDSIGRLPAPTKPIPF
Sbjct: 1 MLRRRIPSLISNAIRNASVFTKPTSYNPTINSLHNPIHHQSVDSFG-----VQGIRAYSLLSLNDLRDNKGATKQKTRKGRGIGSGKGKTAGRGHKGQKARGTHKFGFEGGQTPMRRRMPKRGFKNPFSLEFQPVGLGKIARLINAGKIDSSELITMKTLKDTGAIGKQIRDGVRLMGRGAEHIQWPIHLEVSRVTVRAKEAVEAAGGSVRKVYYNKLGFRALLKPEWFEKKGRLLPKAARPPPKQMDKVDSIGRLPAPTKPIPF 260
| Match Name | Stats | Description |
|---|---|---|
| A0A4S4DK47 | E-Value: 7.276e-150, PID: 82.53 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A7J7FQT8 | E-Value: 8.377e-149, PID: 81.78 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A6S7N8H7 | E-Value: 8.228e-148, PID: 79.20 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A6I9U0V7 | E-Value: 1.837e-147, PID: 80.07 | (uncharacterized protein LOC105173556 {ECO:0000313... [more] |
| A0A2J6M115 | E-Value: 2.434e-147, PID: 78.44 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A5N6P869 | E-Value: 3.012e-147, PID: 81.13 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A2G9H222 | E-Value: 1.120e-146, PID: 78.85 | (Mitochondrial/chloroplast ribosomal protein L15/L... [more] |
| A0A5J5BV24 | E-Value: 1.371e-146, PID: 78.47 | Ribosomal_L18e/L15P domain-containing protein {ECO... [more] |
| A0A200QFD0 | E-Value: 3.489e-146, PID: 77.45 | (Ribosomal protein L15 {ECO:0000313|EMBL:OVA09142.... [more] |
| A0A251RQV0 | E-Value: 1.884e-145, PID: 79.25 | (Putative ribosomal protein L18e/L15 superfamily p... [more] |
| 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 | |
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. | |
This analysis is a blastp search of all of the NCBI Daucus carota subsp. sativus Annotation Release 100 polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove DCAR gene predictions from DCAR V1.0 Gene Prediction. |