MTITATAAAAAVVGGGSPVINNLHHRIRIGIESLTPRLSRTNGTSSSELF
SSQLRPLLNHRKNKLNFISRAADSASTQPAAAPNKSSLVTDEEFSLAKVS
FGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYA
ELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRI
FQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQ
AKFASFFGPDISAEVVEGEGNLYEVRLISDTTL*
| Relationships |
|---|
| The polypeptide, DCAR_009854, derives from mRNA, DCAR_009854. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A2G9GUE7 ((Uncharacterized protein {ECO:0000313|EMBL:PIN08886.1}))
HSP 1 Score: 376.711 bits (966), Expect = 6.064e-130
Identity = 197/288 (68.40%), Postives = 228/288 (79.17%), Query Frame = 0
Query: 7 AAAAAVVGGGSPVINNLHHRIR-----IGIESLTPRLSRTNGTSSSELFSSQLR-PL--LNHRKN---KLNFISRAADSASTQPAAAPNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
AA AA+VGGG V+ + + + ++ L S T G + FS+ R P+ +NH KN + ++ AA+S T P++ S+V DEEFSLAKVSFGVIGL G+SLL YGFGAYFNILPGSEWSA+MLTYGFPLAIIGMALKYAELKPVPC+TY+DAQ +REKCATPILKQVRNDV RYRYGDEQHL+EALKRIFQYG GGGI RRSAPTLQMIREEVTE+GRYCLVLVFEAK L+LSDFE+RQAKFASFFGP I+AE+VEGE NLYEV+LIS+T L
Sbjct: 3 AAVAAMVGGGI-VLCSQSSAVSGCTSLLSLKRLPSASSGTIGPNFPSFFSANNRAPIFPINHLKNSSSRFRLVAGAAES--TPPSSVAADKSIVPDEEFSLAKVSFGVIGLGVGISLLSYGFGAYFNILPGSEWSALMLTYGFPLAIIGMALKYAELKPVPCLTYSDAQMLREKCATPILKQVRNDVTRYRYGDEQHLDEALKRIFQYGQGGGIPRRSAPTLQMIREEVTEDGRYCLVLVFEAKALELSDFEQRQAKFASFFGPGITAEIVEGEKNLYEVKLISNTKL 287
Match: A0A5J5BY22 ((Uncharacterized protein {ECO:0000313|EMBL:KAA8547819.1}))
HSP 1 Score: 372.089 bits (954), Expect = 9.161e-129
Identity = 185/237 (78.06%), Postives = 207/237 (87.34%), Query Frame = 0
Query: 50 FSSQLRPLLNHRKN--KLNFISRAADSASTQPAAAPN-KSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
FSS P L+ + +L FI+RAADS TQP++A S+V+DEEFSLAKVSFGVIGL G++LL YGFGAYFNILPGSEWSAIMLTYGFPLA+IGMALKYAELKPVPC+TY+DA+ +REKCAT ILKQVRNDVIRYRYGDEQHL+EALKRIFQYG GGGI RRSAP LQMIREEVTE+G+YCLVLVFE K LQLSDFEKRQAKFASFFGP I+AEV +GE +LYEVRLIS+TTL
Sbjct: 11 FSSNQEPHLSQPRCHLRLKFITRAADS--TQPSSAVTADKSVVSDEEFSLAKVSFGVIGLGVGITLLSYGFGAYFNILPGSEWSAIMLTYGFPLAVIGMALKYAELKPVPCLTYSDAKMLREKCATSILKQVRNDVIRYRYGDEQHLDEALKRIFQYGQGGGIPRRSAPILQMIREEVTEDGKYCLVLVFEGKALQLSDFEKRQAKFASFFGPGITAEVGKGEKDLYEVRLISNTTL 245
Match: A0A5B7BQC2 ((Uncharacterized protein {ECO:0000313|EMBL:MPA69323.1}) (Fragment))
HSP 1 Score: 374.015 bits (959), Expect = 2.224e-128
Identity = 195/280 (69.64%), Postives = 227/280 (81.07%), Query Frame = 0
Query: 10 AAVVGGGSPVINNLHHRIRIGIESLTPRLSRTNGTSSS---ELFSSQLRPLLNHRKN--KLNFISRAADSASTQPAA-APNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
+++VGGG+ + ++ + R S T+G +SS +F +Q PL + +L F +RAADS TQP++ A S+V+DEEFSLAKVSFGVIGL G++LL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TY+DAQ +REKCATPILKQVRNDVIRYRYGDEQHL+EALKRIFQYG GGGI RRSAP LQMIREEVTE+G+YCLVLVFEAK LQLSDFE+RQAKFASFFGP I+AEV +GE +LYEVR IS+TTL
Sbjct: 41 SSLVGGGTVLCSHRYELCNRQFFLSLNRPSSTHGLNSSARPTIFINQ-EPLFAQPRYHLRLKFTTRAADS--TQPSSTATADKSVVSDEEFSLAKVSFGVIGLGVGITLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYSDAQILREKCATPILKQVRNDVIRYRYGDEQHLDEALKRIFQYGQGGGIPRRSAPILQMIREEVTEDGKYCLVLVFEAKALQLSDFEQRQAKFASFFGPGITAEVGKGEKDLYEVRFISNTTL 317
Match: B9H3P8 ((Uncharacterized protein {ECO:0000313|EMBL:PNT40524.1}))
HSP 1 Score: 370.933 bits (951), Expect = 1.033e-127
Identity = 177/229 (77.29%), Postives = 203/229 (88.65%), Query Frame = 0
Query: 53 QLRPLLNHRKNKLNFISRAADSASTQPAAAPNKS-SLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISD 280
+L P HR KL F+++AADS+ P++ S +++TD+EFSLAKVSFGVIGL G+SLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TY+DA+ +REKCATPILKQVRNDVIRYRYGDEQHL+EALKRIFQYGLGGGI RR+AP LQMIREEVTE+G+YCLVLVFE+K LQLSDFEKRQ KF SFFGPDI+AE+ +GE NLYEVRL+S+
Sbjct: 50 KLSPKQPHRV-KLVFLTKAADSSQASPSSTATASKTIITDDEFSLAKVSFGVIGLGFGISLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYSDAEMLREKCATPILKQVRNDVIRYRYGDEQHLDEALKRIFQYGLGGGIPRRNAPILQMIREEVTEDGKYCLVLVFESKALQLSDFEKRQGKFTSFFGPDITAEIGKGENNLYEVRLVSN 277
Match: A0A4U5QG87 ((Uncharacterized protein {ECO:0000313|EMBL:TKS07515.1}))
HSP 1 Score: 370.933 bits (951), Expect = 1.234e-127
Identity = 179/229 (78.17%), Postives = 202/229 (88.21%), Query Frame = 0
Query: 53 QLRPLLNHRKNKLNFISRAADSASTQPAAAPNKS-SLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISD 280
+L P HR KL F+++AADS+ P++ S ++VTD+EFSLAKVSFGVIGL G+SLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TY++A+ REKCATPILKQVRNDVIRYRYGDEQHL+EALKRIFQYGLGGGI RR+AP LQMIREEVTE+G+YCLVLVFEAK LQLSDFEKRQ KF SFFGPDI+AE+ +GE NLYEVRLIS+
Sbjct: 51 KLSPKQPHRV-KLVFLTKAADSSQASPSSTTTASKTIVTDDEFSLAKVSFGVIGLGFGISLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYSNAEMSREKCATPILKQVRNDVIRYRYGDEQHLDEALKRIFQYGLGGGIPRRNAPILQMIREEVTEDGKYCLVLVFEAKALQLSDFEKRQGKFTSFFGPDITAEIGKGENNLYEVRLISN 278
Match: B9SWM3 ((Uncharacterized protein {ECO:0000313|EMBL:EEF31998.1}))
HSP 1 Score: 369.777 bits (948), Expect = 2.016e-127
Identity = 184/265 (69.43%), Postives = 215/265 (81.13%), Query Frame = 0
Query: 19 VINNLHHRIRIGIESLTPRLSRTNGTSSSELFSSQLRPLLNHRKNKLNFISRAADSASTQPAAAPNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
V N+ + R + + +P L + S L + + HR KL F+++AADS TQP+ A ++V+DEEFSLAKVSFGVIGL G+SLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TY+DAQ +RE ATPILKQVRNDVIRYRYGDEQHL+EALKRIFQYG GGGI RRSAP LQMIREEVTE+G+YCLVLVFEAK L+L DFEKRQAKFASFFGP+I+AEV +G+ +LYEVRLIS+ ++
Sbjct: 14 VFNSHNDRFFLSVYPHSPPLLLQSPRLDSRLCAKR------HRNVKLVFVAKAADS--TQPSTASTAKAIVSDEEFSLAKVSFGVIGLGVGISLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYSDAQMLRETSATPILKQVRNDVIRYRYGDEQHLDEALKRIFQYGQGGGIPRRSAPILQMIREEVTEDGKYCLVLVFEAKALELLDFEKRQAKFASFFGPNITAEVGKGDNDLYEVRLISNLSV 270
Match: A0A1Q3C6D9 ((DUF2854 domain-containing protein {ECO:0000313|EMBL:GAV75643.1}))
HSP 1 Score: 370.163 bits (949), Expect = 2.524e-127
Identity = 185/253 (73.12%), Postives = 203/253 (80.24%), Query Frame = 0
Query: 36 PRLSRTNGTSSSELFSSQLRPLLNHR----------KNKLNFISRAADSASTQPAAAPNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLI 278
P++ N S S S LRP +H + KL F++RAADS A+A +LVTD+E SLAKVSFGVIGL GVSLL YGFGAYFNILPGSEWSA+MLTYGFPLAIIGMALKYAELKPVPC+TY+DAQ +RE CATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYG GGGI RRSAP LQMI+EEVTE+G+YCLVLVFEAK LQLSDFEKRQ KF SFFGP I+AEV +GE NLYEVRLI
Sbjct: 23 PQVILLNHHSCS--LSHSLRPPRHHHLITQSLPKRHRLKLEFLTRAADSTQPSTASAATDKTLVTDDEVSLAKVSFGVIGLGLGVSLLSYGFGAYFNILPGSEWSALMLTYGFPLAIIGMALKYAELKPVPCLTYSDAQALRETCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGQGGGIPRRSAPILQMIKEEVTEDGKYCLVLVFEAKALQLSDFEKRQGKFTSFFGPGIAAEVGKGESNLYEVRLI 273
Match: A0A1U8FF94 ((thylakoid membrane protein slr0575 isoform X1 {ECO:0000313|RefSeq:XP_016554415.1}))
HSP 1 Score: 369.777 bits (948), Expect = 2.593e-127
Identity = 181/246 (73.58%), Postives = 204/246 (82.93%), Query Frame = 0
Query: 46 SSELFSSQLRPLLNHR------KNKLNF--ISRAADSASTQPAAAPNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
SS L +L NH +N L F ++RAADS+ + +V D+EFSLAKVSFGVIGL G+SLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TYADAQ +REKCATP+LKQVR+DVIRYRYGDEQHL+EALKRIFQ+G+GGGI RRSAP LQ IREEVTE+G+YCLVLVFEAK LQLSDFEKRQAKF SFFGP IS+E+V+GE +LYEVRLIS+TTL
Sbjct: 30 SSPLLVHKLSSFSNHDLILAKTRNHLRFKDVTRAADSSQPSSVITSSDKDIVPDDEFSLAKVSFGVIGLGLGISLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCITYADAQLLREKCATPVLKQVRSDVIRYRYGDEQHLDEALKRIFQFGMGGGIPRRSAPILQNIREEVTEDGKYCLVLVFEAKALQLSDFEKRQAKFTSFFGPRISSEIVKGENDLYEVRLISNTTL 275
Match: A0A5C7HLD4 ((Uncharacterized protein {ECO:0000313|EMBL:TXG57830.1}))
HSP 1 Score: 369.777 bits (948), Expect = 2.604e-127
Identity = 187/264 (70.83%), Postives = 209/264 (79.17%), Query Frame = 0
Query: 18 PVINNLHHRIRIGI-ESLTPRLSRTNGTSSSELFSSQLRPLLNHRKNKLNFISRAADSASTQPAAAPNKSSLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISD 280
P I HH + G + LS S L SS+ L KL+F++RAADS T A A ++V D+EFSLAKVSFGV+GL G+SLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TY+DAQ +RE CATPILKQVRNDVIR+RYGDEQHLEEALKRIFQYGLGGGI RRSAP LQ IREEVTE+G+YCLVLVFEAK L+LSDFE+RQAKF SFFGP I+AEV +GE +LYEVRLISD
Sbjct: 11 PTITCSHHHHQFGFSDHHRSFLSVHPPLSPPTLLSSKRYRL------KLSFVTRAADSTPTSSAPASADKAIVADDEFSLAKVSFGVVGLGVGISLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYSDAQMLRETCATPILKQVRNDVIRFRYGDEQHLEEALKRIFQYGLGGGIPRRSAPILQNIREEVTEDGKYCLVLVFEAKALKLSDFEQRQAKFTSFFGPGITAEVGKGENDLYEVRLISD 268
Match: A0A6N2BA20 ((Uncharacterized protein {ECO:0000313|EMBL:TMW90079.1}))
HSP 1 Score: 369.777 bits (948), Expect = 2.890e-127
Identity = 179/222 (80.63%), Postives = 201/222 (90.54%), Query Frame = 0
Query: 64 KLNFISRAADSASTQPAAAPNKS--SLVTDEEFSLAKVSFGVIGLYGGVSLLGYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCVTYADAQTIREKCATPILKQVRNDVIRYRYGDEQHLEEALKRIFQYGLGGGIARRSAPTLQMIREEVTENGRYCLVLVFEAKDLQLSDFEKRQAKFASFFGPDISAEVVEGEGNLYEVRLISDTTL 283
+L +++AADS +QPA+A S ++V DEEFSLAKVSFGVIGL GVSLL YGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPC+TYADA+ +REKCATP+LKQVR+DVIRYRYGDEQHL+EALKRIFQ+GLGGGI RRSAP LQ IREEVTE+G+YCLVLVFEAK LQLSDFEKRQAKF SFFGP IS+E+V+GE +LYEVRLIS+TTL
Sbjct: 66 RLKVVTKAADS--SQPASAITSSGKAIVPDEEFSLAKVSFGVIGLGLGVSLLSYGFGAYFNILPGSEWSAIMLTYGFPLAIIGMALKYAELKPVPCLTYADAELLREKCATPVLKQVRSDVIRYRYGDEQHLDEALKRIFQFGLGGGIPRRSAPVLQNIREEVTEDGKYCLVLVFEAKALQLSDFEKRQAKFTSFFGPGISSEIVKGENDLYEVRLISNTTL 285
| Match Name | Stats | Description |
|---|---|---|
| A0A2G9GUE7 | E-Value: 6.064e-130, PID: 68.40 | (Uncharacterized protein {ECO:0000313|EMBL:PIN0888... [more] |
| A0A5J5BY22 | E-Value: 9.161e-129, PID: 78.06 | (Uncharacterized protein {ECO:0000313|EMBL:KAA8547... [more] |
| A0A5B7BQC2 | E-Value: 2.224e-128, PID: 69.64 | (Uncharacterized protein {ECO:0000313|EMBL:MPA6932... [more] |
| B9H3P8 | E-Value: 1.033e-127, PID: 77.29 | (Uncharacterized protein {ECO:0000313|EMBL:PNT4052... [more] |
| A0A4U5QG87 | E-Value: 1.234e-127, PID: 78.17 | (Uncharacterized protein {ECO:0000313|EMBL:TKS0751... [more] |
| B9SWM3 | E-Value: 2.016e-127, PID: 69.43 | (Uncharacterized protein {ECO:0000313|EMBL:EEF3199... [more] |
| A0A1Q3C6D9 | E-Value: 2.524e-127, PID: 73.12 | (DUF2854 domain-containing protein {ECO:0000313|EM... [more] |
| A0A1U8FF94 | E-Value: 2.593e-127, PID: 73.58 | (thylakoid membrane protein slr0575 isoform X1 {EC... [more] |
| A0A5C7HLD4 | E-Value: 2.604e-127, PID: 70.83 | (Uncharacterized protein {ECO:0000313|EMBL:TXG5783... [more] |
| A0A6N2BA20 | E-Value: 2.890e-127, PID: 80.63 | (Uncharacterized protein {ECO:0000313|EMBL:TMW9007... [more] |
Pages
back to top| 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 | |
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. |