MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILY
DLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAM
IGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEAN
YEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRG
VLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHM
SAPSLLAHELLRALSR*
| Relationships |
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| The polypeptide, DCAR_009882, derives from mRNA, DCAR_009882. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A5J5ACV8 (AB hydrolase-1 domain-containing protein {ECO:0000259|Pfam:PF12697})
HSP 1 Score: 485.723 bits (1249), Expect = 1.270e-173
Identity = 233/266 (87.59%), Postives = 249/266 (93.61%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
MG LL+ALNVRV+GSG ++L LAHGFGTDQSAW RILPYFLP Y+VILYDLVCAGSVNPDYFDFRRYT+LDAYVDDLLSILD LGVDRC YVGHSVSAMIGILA+IRRPELF+KLILIGASPRFLND +YHGGFEQGEI+KVFSAMEANYEAWV+GFAPLAVGADVPAAVREFSRTLFNMRPDI+LFVSRTVFNSD+RGVLGLVKVPCCI+QTAKDVSVP SVA YLKNHLGGRNTV MLN EGHLPH+SAP +LA L RALSR
Sbjct: 1 MGHNLLEALNVRVVGSGEKILVLAHGFGTDQSAWQRILPYFLPYYRVILYDLVCAGSVNPDYFDFRRYTTLDAYVDDLLSILDALGVDRCAYVGHSVSAMIGILASIRRPELFSKLILIGASPRFLNDKDYHGGFEQGEIEKVFSAMEANYEAWVSGFAPLAVGADVPAAVREFSRTLFNMRPDITLFVSRTVFNSDMRGVLGLVKVPCCIVQTAKDVSVPQSVATYLKNHLGGRNTVEMLNTEGHLPHLSAPGMLALVLRRALSR 266
Match: A0A103XWP0 (AB hydrolase-1 domain-containing protein {ECO:0000259|Pfam:PF12697})
HSP 1 Score: 479.559 bits (1233), Expect = 3.410e-171
Identity = 231/266 (86.84%), Postives = 247/266 (92.86%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
MG +LLDALNVRV+GSG++ L LAHG GTDQS W+RILPYF YKVILYDLVCAGSVNPDYFDFRRY SLDAYVDDLL ILD LGVDRCFYVGHS+S+MIGILAAIRRPELF+KLILIGASPRFLND +YHGGFE+GEI+KVF AMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFN+RPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVP SVA YLK HLGGRNTV M+N+EGHLPH+SAP+LLAH L RALSR
Sbjct: 1 MGPSLLDALNVRVVGSGKKFLLLAHGLGTDQSVWSRILPYFRSHYKVILYDLVCAGSVNPDYFDFRRYNSLDAYVDDLLQILDSLGVDRCFYVGHSLSSMIGILAAIRRPELFSKLILIGASPRFLNDKDYHGGFEEGEIEKVFLAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNVRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPTSVAMYLKEHLGGRNTVEMMNVEGHLPHLSAPALLAHHLNRALSR 266
Match: F6H1A2 (AB hydrolase-1 domain-containing protein {ECO:0000259|Pfam:PF00561})
HSP 1 Score: 477.633 bits (1228), Expect = 2.176e-170
Identity = 229/266 (86.09%), Postives = 250/266 (93.98%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
MG TLL+ALNVRV+G+G RVL LAHGFGTDQSAW RILPYFLP +++ILYDLVCAGSVNPDYFDFRRYT+LDA+VDDLL+ILD LGVDRC YVGHSVSAMIGILA+IRRPELF KL+LIGASPRFLND +YHGGFE+GEI+KVFSAMEANY+AWV+GFAPL+VGADVPAAVREFSRTLFNMRPDI+LFVSRT+FNSDLRGVLGLVKVPCCIIQTAKDVSVP SVA YLKNHLGGRNTV MLN+EGHLPH+SAP LLA L RALSR
Sbjct: 1 MGNTLLEALNVRVVGNGERVLVLAHGFGTDQSAWQRILPYFLPHFRIILYDLVCAGSVNPDYFDFRRYTTLDAFVDDLLNILDALGVDRCAYVGHSVSAMIGILASIRRPELFTKLVLIGASPRFLNDHDYHGGFEEGEIEKVFSAMEANYDAWVHGFAPLSVGADVPAAVREFSRTLFNMRPDITLFVSRTIFNSDLRGVLGLVKVPCCIIQTAKDVSVPTSVALYLKNHLGGRNTVEMLNVEGHLPHLSAPMLLAPVLRRALSR 266
Match: A0A438KN83 ((Putative strigolactone esterase DAD2 {ECO:0000313|EMBL:RVX22661.1}))
HSP 1 Score: 477.633 bits (1228), Expect = 2.176e-170
Identity = 229/266 (86.09%), Postives = 250/266 (93.98%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
MG TLL+ALNVRV+G+G RVL LAHGFGTDQSAW RILPYFLP +++ILYDLVCAGSVNPDYFDFRRYT+LDA+VDDLL+ILD LGVDRC YVGHSVSAMIGILA+IRRPELF KL+LIGASPRFLND +YHGGFE+GEI+KVFSAMEANY+AWV+GFAPL+VGADVPAAVREFSRTLFNMRPDI+LFVSRT+FNSDLRGVLGLVKVPCCIIQTAKDVSVP SVA YLKNHLGGRNTV MLN+EGHLPH+SAP LLA L RALSR
Sbjct: 1 MGNTLLEALNVRVVGNGERVLVLAHGFGTDQSAWQRILPYFLPHFRIILYDLVCAGSVNPDYFDFRRYTTLDAFVDDLLNILDALGVDRCAYVGHSVSAMIGILASIRRPELFTKLVLIGASPRFLNDHDYHGGFEEGEIEKVFSAMEANYDAWVHGFAPLSVGADVPAAVREFSRTLFNMRPDITLFVSRTIFNSDLRGVLGLVKVPCCIIQTAKDVSVPTSVALYLKNHLGGRNTVEMLNVEGHLPHLSAPMLLAPVLRRALSR 266
Match: A0A1U7W4L0 ((probable strigolactone esterase DAD2 {ECO:0000313|RefSeq:XP_009773538.1}))
HSP 1 Score: 476.863 bits (1226), Expect = 3.696e-170
Identity = 231/265 (87.17%), Postives = 247/265 (93.21%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALS 265
MGQTLLDALNVRV+GSG R L LAHGFGTDQSAWNRILP+FL Y+V+LYDLVCAGSVNPD+FDFRRYT+LD YVDDLL ILD LG+DRC YVGHSVSAMIGILA+IRRPELF+KLILIGASPRFLND +YHGGFEQGEI+KVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDI+LFVSRTVFNSD+RGVLGLVKVPC I QTA+D SVPASVA YLKNHLGGRNTV LNIEGHLPH+SAP+LLA EL RALS
Sbjct: 1 MGQTLLDALNVRVVGSGERFLVLAHGFGTDQSAWNRILPFFLRDYRVVLYDLVCAGSVNPDFFDFRRYTTLDPYVDDLLHILDTLGIDRCAYVGHSVSAMIGILASIRRPELFSKLILIGASPRFLNDEDYHGGFEQGEIEKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDITLFVSRTVFNSDMRGVLGLVKVPCHIFQTARDHSVPASVATYLKNHLGGRNTVHWLNIEGHLPHLSAPTLLAQELRRALS 265
Match: A0A1S4C8X8 ((probable strigolactone esterase DAD2 {ECO:0000313|RefSeq:XP_016497697.1}))
HSP 1 Score: 476.863 bits (1226), Expect = 3.696e-170
Identity = 231/265 (87.17%), Postives = 247/265 (93.21%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALS 265
MGQTLLDALNVRV+GSG R L LAHGFGTDQSAWNRILP+FL Y+V+LYDLVCAGSVNPD+FDFRRYT+LD YVDDLL ILD LG+DRC YVGHSVSAMIGILA+IRRPELF+KLILIGASPRFLND +YHGGFEQGEI+KVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDI+LFVSRTVFNSD+RGVLGLVKVPC I QTA+D SVPASVA YLKNHLGGRNTV LNIEGHLPH+SAP+LLA EL RALS
Sbjct: 1 MGQTLLDALNVRVVGSGERFLVLAHGFGTDQSAWNRILPFFLRDYRVVLYDLVCAGSVNPDFFDFRRYTTLDPYVDDLLHILDTLGIDRCAYVGHSVSAMIGILASIRRPELFSKLILIGASPRFLNDEDYHGGFEQGEIEKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDITLFVSRTVFNSDMRGVLGLVKVPCHIFQTARDHSVPASVATYLKNHLGGRNTVHWLNIEGHLPHLSAPTLLAQELRRALS 265
Match: A0A059BLY8 (AB hydrolase-1 domain-containing protein {ECO:0000259|Pfam:PF12697})
HSP 1 Score: 476.478 bits (1225), Expect = 6.011e-170
Identity = 232/264 (87.88%), Postives = 244/264 (92.42%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRAL 264
MG LL+ALNVRV+GSG R L LAHGFGTDQSAW RILP+F P Y+VILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLL+ILD L VDRC YVGHS SAMIGILA+IRRPELF KLILIGASPRFLND +YHGGFE GEI+KVFSAMEANYEAWVNGFAPLAVGADVPAAV+EFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLV+VPCCI+QTAKDVSVPASVAAYLKNHLGGRNTV MLNIEGHLPH+SAP LLA L RAL
Sbjct: 1 MGNILLEALNVRVVGSGERFLVLAHGFGTDQSAWQRILPFFTPHYRVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLNILDALSVDRCAYVGHSFSAMIGILASIRRPELFTKLILIGASPRFLNDKDYHGGFELGEIEKVFSAMEANYEAWVNGFAPLAVGADVPAAVQEFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVRVPCCIVQTAKDVSVPASVAAYLKNHLGGRNTVEMLNIEGHLPHLSAPGLLAQVLRRAL 264
Match: A0A314LHI7 ((Strigolactone esterase d14 {ECO:0000313|EMBL:OIT40479.1}))
HSP 1 Score: 476.093 bits (1224), Expect = 8.050e-170
Identity = 231/265 (87.17%), Postives = 247/265 (93.21%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALS 265
MGQTLLDALNVRV+GSG R L LAHGFGTDQSAWNRILP+FL Y+V+LYDLVCAGSVNPD+FDFRRYT+LD YVDDLL ILD LG+DRC YVGHSVSAMIGILA+IRRPELF+KLILIGASPRFLND +YHGGFEQGEI+KVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDI+LFVSRTVFNSD+RGVLGLVKVPC I QTA+D SVPASVA YLKNHLGGRNTV LNIEGHLPH+SAP+LLA EL RALS
Sbjct: 1 MGQTLLDALNVRVVGSGERFLVLAHGFGTDQSAWNRILPFFLRDYRVVLYDLVCAGSVNPDFFDFRRYTTLDPYVDDLLHILDNLGIDRCAYVGHSVSAMIGILASIRRPELFSKLILIGASPRFLNDEDYHGGFEQGEIEKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDITLFVSRTVFNSDMRGVLGLVKVPCHIFQTARDHSVPASVATYLKNHLGGRNTVHWLNIEGHLPHLSAPTLLAQELRRALS 265
Match: A0A6P6UQJ3 ((probable strigolactone esterase DAD2 {ECO:0000313|RefSeq:XP_027092768.1}))
HSP 1 Score: 475.322 bits (1222), Expect = 2.090e-169
Identity = 230/266 (86.47%), Postives = 247/266 (92.86%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
M +LL+ALNVRV+GSG R+L LAHG GTDQSAW RILP+FLP+Y+VILYDLVCAGSVNPDYFDFRRYT+LDAYVDDLL ILD LGVDRC YVGHSVSAMIGILA+IRRPELF+KLILIGASPRFLND +YHGGFEQGEIDK+FSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDI+LFVSR VFNSDLRGVLG VKVPC IIQTAKD SVP SVA YLKNHLGGR+TV MLN+EGHLPH+SAP+LLA ELLRAL R
Sbjct: 1 MVPSLLEALNVRVVGSGERILVLAHGIGTDQSAWQRILPFFLPNYRVILYDLVCAGSVNPDYFDFRRYTTLDAYVDDLLHILDALGVDRCAYVGHSVSAMIGILASIRRPELFSKLILIGASPRFLNDNDYHGGFEQGEIDKLFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDITLFVSRQVFNSDLRGVLGFVKVPCSIIQTAKDCSVPTSVATYLKNHLGGRSTVHMLNLEGHLPHLSAPALLAQELLRALPR 266
Match: A0A1R3HKD3 ((Putative sigma factor sigb regulation protein rsbq {ECO:0000313|EMBL:OMO70753.1}))
HSP 1 Score: 474.552 bits (1220), Expect = 3.301e-169
Identity = 226/266 (84.96%), Postives = 245/266 (92.11%), Query Frame = 0
Query: 1 MGQTLLDALNVRVIGSGRRVLFLAHGFGTDQSAWNRILPYFLPSYKVILYDLVCAGSVNPDYFDFRRYTSLDAYVDDLLSILDFLGVDRCFYVGHSVSAMIGILAAIRRPELFAKLILIGASPRFLNDPEYHGGFEQGEIDKVFSAMEANYEAWVNGFAPLAVGADVPAAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVKVPCCIIQTAKDVSVPASVAAYLKNHLGGRNTVVMLNIEGHLPHMSAPSLLAHELLRALSR 266
MG LL+ALNVRVIGSG ++L LAHGFGTDQSAW RI+P F P Y++ILYDLVCAGSVNPDYFDFRRYT+LDAYVDDLL+ILD LGVDRC YVGHSVSAMIGILA+IRRPELF KLILIGASPRFLND +YHGGFEQGEI+KVFSAMEANYEAWVNGFAPLAVGADVP AVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLV+VPCC++QTAKDVSVPASVA YL+NHLGGR T+ +L EGHLPH+SAP+LLA L RALSR
Sbjct: 1 MGNILLEALNVRVIGSGEKILVLAHGFGTDQSAWQRIVPLFTPYYRIILYDLVCAGSVNPDYFDFRRYTTLDAYVDDLLNILDALGVDRCAYVGHSVSAMIGILASIRRPELFTKLILIGASPRFLNDKDYHGGFEQGEIEKVFSAMEANYEAWVNGFAPLAVGADVPTAVREFSRTLFNMRPDISLFVSRTVFNSDLRGVLGLVRVPCCVVQTAKDVSVPASVAEYLRNHLGGRTTIEILKTEGHLPHLSAPALLAQVLRRALSR 266
| Match Name | Stats | Description |
|---|---|---|
| A0A5J5ACV8 | E-Value: 1.270e-173, PID: 87.59 | AB hydrolase-1 domain-containing protein {ECO:0000... [more] |
| A0A103XWP0 | E-Value: 3.410e-171, PID: 86.84 | AB hydrolase-1 domain-containing protein {ECO:0000... [more] |
| F6H1A2 | E-Value: 2.176e-170, PID: 86.09 | AB hydrolase-1 domain-containing protein {ECO:0000... [more] |
| A0A438KN83 | E-Value: 2.176e-170, PID: 86.09 | (Putative strigolactone esterase DAD2 {ECO:0000313... [more] |
| A0A1U7W4L0 | E-Value: 3.696e-170, PID: 87.17 | (probable strigolactone esterase DAD2 {ECO:0000313... [more] |
| A0A1S4C8X8 | E-Value: 3.696e-170, PID: 87.17 | (probable strigolactone esterase DAD2 {ECO:0000313... [more] |
| A0A059BLY8 | E-Value: 6.011e-170, PID: 87.88 | AB hydrolase-1 domain-containing protein {ECO:0000... [more] |
| A0A314LHI7 | E-Value: 8.050e-170, PID: 87.17 | (Strigolactone esterase d14 {ECO:0000313|EMBL:OIT4... [more] |
| A0A6P6UQJ3 | E-Value: 2.090e-169, PID: 86.47 | (probable strigolactone esterase DAD2 {ECO:0000313... [more] |
| A0A1R3HKD3 | E-Value: 3.301e-169, PID: 84.96 | (Putative sigma factor sigb regulation protein rsb... [more] |
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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 is a blastp search of all of the DCAR V1.0 Gene Prediction 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 these same DCAR gene predictions. | |
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. |