Query: 17 SPSGSPRIGFTVPAH--KPKRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATDLTGNRVDLYIRSSLRNAFAKMLDDGNMSSDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
+P SP I FT+P+ + +RP+TSAEIMRQQM+V+EQSDNRLRKTLMRTLVGQ GRR ETIILPLELLRHLKPSEF + EYHLWQKRQLK+LEAGL+LHPSIP++KSN FAM+L +II ++E KPIDTGKNSE M+TLCNC+ +L+WR+ D SPTD CHWADG+PLNVH+Y LL +IFD +D+T+VLDEVDELVELMKKTWSTLGIN+ +HN+C TWVLFEQY++T +VE +L+ A+LAM++E+A+D K DRE ++VKML L++IKRW EK+LLDYH NFN +G+ME LLPL A TKI EE V G A Q+ G++A D TGNRVD YIRSSLRNAFAK+L++GN++S I+EVQ+VT+ALL++A+ T ELA KE+E +S +LKKWHP+AAG AAVTLH CYGTLLKQYL G S LS E + IL A +LEK LVQM VEDS EC DGGK IVREMVPYEVD+II + LK+WIQERLK+ KE LQ AKE+E
Sbjct: 137 NPGSSPGISFTLPSPHVRSRRPMTSAEIMRQQMRVTEQSDNRLRKTLMRTLVGQMGRRVETIILPLELLRHLKPSEFNSSIEYHLWQKRQLKILEAGLILHPSIPLDKSNSFAMRLRDIIRAAETKPIDTGKNSESMRTLCNCVVSLSWRSPDG-SPTDVCHWADGFPLNVHLYTMLLHSIFDLRDETLVLDEVDELVELMKKTWSTLGINRSIHNLCLTWVLFEQYVVTGKVEENLIVATLAMLAEVANDAKRADREP-IYVKMLSSVLTAIKRWTEKRLLDYHGNFNGVTVGLMENLLPLLFAATKILEEDVTGIAVEGQEKGEVAADSTGNRVDQYIRSSLRNAFAKVLENGNVNSMIVEVQEVTEALLKLAEETKELAMKEKEIFSPVLKKWHPIAAGVAAVTLHNCYGTLLKQYLVGVSS-LSRETVPILQKAAQLEKILVQMVVEDSVECEDGGKTIVREMVPYEVDSIICKLLKEWIQERLKTGKECLQRAKETE 635
BLAST of DCAR_000307 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A5B7A1W9 ((Uncharacterized protein {ECO:0000313|EMBL:MPA49716.1}) (Fragment))
Query: 17 SPSGS-PRIGFTVPAH--KPKRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATDLTGNRVDLYIRSSLRNAFAKMLDDGNMSSDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
+P+GS P I FTVP + +RP+TSAEIMRQQM+V+EQSDNRLRKTLMRTLVGQ GRRAETIILPLELLRHLKPSEF + EYHLWQKRQLK+LEAGL+LHPSIP++KSN FAM+L +II + E KP DTGKNSE M+TLCNC+ +L+WR+ D SPTD CHWADG+PLN+HIY LL +IFD KD+T+VLDEVDELVELMKKTWSTLGIN+ +HN+CFTWVLFEQY++T +VE+DLL A+LAM++E+A+D K DRE ++VKML L++IKRW EK+LLDYH +FN +G+ME LLPL TKI EE V G A ++ G++ D TGNRVD YIRSSLRNAFAK L++G+++ I+EVQ+V++AL+++A+ T ELA KE+E +S +LKKWHP+AAG AAVTLH+CYGTLLKQYL G S LS+E I IL AGKLEK LVQM VEDS EC DGGK IVREMVPYEVD+II LK+W++ERLK KE LQ AKE+E
Sbjct: 189 NPAGSSPGISFTVPGPQVRSRRPMTSAEIMRQQMRVTEQSDNRLRKTLMRTLVGQMGRRAETIILPLELLRHLKPSEFNSSHEYHLWQKRQLKILEAGLILHPSIPLDKSNTFAMRLRDIIRACETKPFDTGKNSESMRTLCNCVVSLSWRSPDG-SPTDVCHWADGFPLNLHIYTVLLHSIFDLKDETLVLDEVDELVELMKKTWSTLGINRSIHNLCFTWVLFEQYVVTGKVEVDLLCATLAMLNEVANDAKRADREP-IYVKMLLSVLTAIKRWIEKRLLDYHGSFNRVTVGLMENLLPLVFEATKILEEDVTGIAAPGEEKGEVTADSTGNRVDHYIRSSLRNAFAKTLENGSVNGMIVEVQEVSEALIKLAEETKELALKEKEIFSPVLKKWHPIAAGVAAVTLHSCYGTLLKQYLAGASS-LSSETISILQRAGKLEKVLVQMVVEDSVECEDGGKTIVREMVPYEVDSIILNLLKEWVEERLKKGKECLQRAKETE 688
Query: 3 NNVNSPRDSPRASPS-PSGSPRIGFTVPAHKPKRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATDLTGNRVDLYIRSSLRNAFAKMLDDGNMSSDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
++ S SP A S P SP + FTVP + +RP+TSAEIMRQQM+V+EQSDNRLRKTLMRTL+G RRAETIILPLELLRHLKPSEF + EYHLWQKR LK+LE GL+LHPSIP++KSN FAM+L E I + E KPIDTGKNSE M+TLCNC+ +L+WR+ D SPTD CHWADG+PLNVHIY LL +IFD KD+T+VLDE+DEL+ELMKKTWSTLGIN+ +HN+CFTWVLFEQY+ T +VE+DLL A+LAMM+E+A+D K DRE ++VKML L+SIKRW EK+LLDYH +FN+ +G+ME LLPL + TKI EE V G + + G+ D TGNRVD YIRSSLRNAFAK L++G ++ I+EV++V++ALL++A T ELA KE+E +S +LKKWHP++AGAAAVTLHTCYGTLLKQYL G+S LSNE I IL AGKLEK LVQM VEDS EC DGGK IVREMVPYEVD+II LKQWIQ+ LK +E LQ AKE+E
Sbjct: 120 SSCGSNPSSPNAHNSNPGSSPGMAFTVPQVRSRRPMTSAEIMRQQMKVTEQSDNRLRKTLMRTLMG---RRAETIILPLELLRHLKPSEFNSSHEYHLWQKRLLKILETGLILHPSIPLDKSNTFAMRLREFIRACETKPIDTGKNSESMRTLCNCVVSLSWRSPDG-SPTDVCHWADGFPLNVHIYNVLLHSIFDLKDETLVLDEIDELIELMKKTWSTLGINRSMHNLCFTWVLFEQYVSTGQVEVDLLCATLAMMAEVANDAKRADREP-IYVKMLASVLTSIKRWIEKRLLDYHGSFNKVTVGLMENLLPLVFSATKILEEDVTGISAAGVERGEERADSTGNRVDHYIRSSLRNAFAKTLENGQVNGMIVEVKEVSEALLKLADETEELAMKEKEIFSPMLKKWHPISAGAAAVTLHTCYGTLLKQYLAGSSS-LSNETISILQRAGKLEKVLVQMVVEDSVECEDGGKTIVREMVPYEVDSIILNLLKQWIQQMLKKGRECLQRAKETE 628
Query: 23 RIGFTVP-AHKPKRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATD--LTGNRVDLYIRSSLRNAFAKMLDDGNM--SSDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
R+GFTVP A + +RPLTSAEIMRQQM+V+EQSDNRLRKTLMRTLVGQ GRRAETIILPLELLRHLKPSEF EYHLWQKRQLK++EAGLLLHPSIP+EKS+ FA KL +II SSE K IDTGK S M+TLCNCI +LAWR+ D + TD CHWADGYPLNVHIY ALL ++FD KD+T+VLDE+DEL+ELMKKTWS LGIN+ +HN+CFTWVLFEQY+LT +VE DLL AS AM++E+A D K VDR+ V++KML LS+IK+WCEK+LLDYH NFN +G+ME +LPL + TKI EE VP Y T Q+ G+ D TGNRVD YIRSSLRNAFAKML+D N+ ++ E Q+V++ L++IA+ T EL KE++ +S +LKKWHP+AAG AAVTLHTCYGTLLKQYLTG S +L NE + +L AGKLEK LVQ+ VEDS EC DGGK IVREMVPYEV++ I R LKQWIQERL+ KE L AK++E
Sbjct: 145 RVGFTVPHAGRMRRPLTSAEIMRQQMRVTEQSDNRLRKTLMRTLVGQMGRRAETIILPLELLRHLKPSEFNDPHEYHLWQKRQLKIIEAGLLLHPSIPLEKSDTFAAKLRDIIDSSETKVIDTGKTSPTMRTLCNCIVSLAWRSPDGGT-TDICHWADGYPLNVHIYTALLSSVFDLKDETLVLDEIDELIELMKKTWSMLGINRSMHNLCFTWVLFEQYVLTGQVEPDLLGASFAMLTEVASDAKKVDRDP-VYLKMLGCCLSAIKKWCEKRLLDYHGNFNRGNIGIMENMLPLLFSATKILEEDVPCYVTSSQEKGEAVVDEHSTGNRVDHYIRSSLRNAFAKMLEDQNVNGTTKYTEAQEVSEVLIKIARKTEELGIKEKDIFSPVLKKWHPIAAGVAAVTLHTCYGTLLKQYLTGKSSIL-NETVLVLQRAGKLEKALVQLVVEDSVECEDGGKTIVREMVPYEVESFIARLLKQWIQERLQKGKEYLLRAKQTE 640
BLAST of DCAR_000307 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6P6WPK2 ((protein unc-13 homolog isoform X2 {ECO:0000313|RefSeq:XP_027116621.1}))
BLAST of DCAR_000307 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6I9STB7 ((uncharacterized protein LOC105158480 {ECO:0000313|RefSeq:XP_011073565.1}))
Query: 23 RIGFTVP-AHKPKRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATDLTGNRVDLYIRSSLRNAFAKMLDDGNMS-SDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
R+GFTVP K +RPLTSAEIMRQQM V+EQSDNRLRKTLMRTLVGQ GRRAETIILPLELLRHLKPSEF EYHLWQKRQ ++LEAGLLLHPSIP+EKS+ A K EII SSE+KPIDTGKNS MKTLCNC+ ALAWR+ D + TD CHWADG PLNV IY ALL +IFD+KD+T+VLDE+DEL+ELMKKTWSTLGIN+ +HN+CFTWVLFEQY++T+EVE DLL AS M++E+A D K DRE +++KML L+ +K+WC+K+LLDYH NFN +G+ME +LPL + TKI EE VP Y Q+ GD + TGNRVDLY+RSSLRNAFA+ML+D N++ + E Q+V++ L+++A+ T EL KER+ +S ILKKWHPVAAG AAVTLHTCYGTLLKQYLT S L NE + +L AGKLEK LVQ+ VEDS EC DGGK IVREMVPYEVDA+I R +KQWIQERL+ KE + AK++E
Sbjct: 151 RVGFTVPQGGKLRRPLTSAEIMRQQMNVTEQSDNRLRKTLMRTLVGQMGRRAETIILPLELLRHLKPSEFNDPHEYHLWQKRQFRILEAGLLLHPSIPLEKSDASAAKFREIIESSEMKPIDTGKNSAVMKTLCNCVVALAWRSPDGGT-TDVCHWADGNPLNVLIYTALLSSIFDSKDETLVLDEIDELLELMKKTWSTLGINRPIHNLCFTWVLFEQYVMTQEVEPDLLGASFVMLTEVATDAKKPDREP-IYMKMLASVLNVMKKWCDKRLLDYHRNFNRETIGLMENMLPLLFSATKILEEDVPYYVNAPQEKGDAGEEPTGNRVDLYVRSSLRNAFAQMLEDLNINGTKTTEPQEVSEVLIKVARKTEELGVKERDIFSPILKKWHPVAAGVAAVTLHTCYGTLLKQYLTSKSSL--NETVLVLQRAGKLEKALVQLVVEDSVECEDGGKMIVREMVPYEVDALIVRLMKQWIQERLQKGKEYILRAKQTE 642
BLAST of DCAR_000307 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6P6WXD9 ((protein unc-13 homolog isoform X2 {ECO:0000313|RefSeq:XP_027120104.1}))
BLAST of DCAR_000307 vs. ExPASy Swiss-Prot and TrEMBL without DCAR Match: A0A6P6WMY2 ((protein unc-13 homolog isoform X1 {ECO:0000313|RefSeq:XP_027116620.1}))
Query: 34 KRPLTSAEIMRQQMQVSEQSDNRLRKTLMRTLVGQTGRRAETIILPLELLRHLKPSEFKTGGEYHLWQKRQLKLLEAGLLLHPSIPVEKSNKFAMKLNEIITSSEIKPIDTGKNSEQMKTLCNCIAALAWRTSDNESPTDACHWADGYPLNVHIYIALLRTIFDTKDQTMVLDEVDELVELMKKTWSTLGINKLVHNMCFTWVLFEQYILTREVEIDLLAASLAMMSEIAHDVKTVDRETVVHVKMLKRALSSIKRWCEKKLLDYHANFNESRLGVMEILLPLASAVTKISEE-VPGYATLVQDDGDIATDLTGNRVDLYIRSSLRNAFAKMLDDGNMS-SDIIEVQDVTDALLQIAQGTHELAAKERETYSSILKKWHPVAAGAAAVTLHTCYGTLLKQYLTGTSHLLSNEAIEILHTAGKLEKFLVQMAVEDSAECSDGGKAIVREMVPYEVDAIITRSLKQWIQERLKSVKEALQTAKESE 515
+RP+TSAEIMRQQM+V+EQSDNRLRKTLMRTLVGQ GRRAETIILPLELLRHLKPSEF EYHLWQKRQLK+LEAGLLLHPSIP +KS+ FA KL +II + +IK IDTGKNS M+TLCNCI +LAWR S N TD CHWADGYPLNVHIY LL ++FD KD+T+VLDE+DEL+ELMKKTWSTLGIN+ +HN+CFTWVLFEQY++T +VE DLL+AS AM+SE+AHD K VDRE +++KML L S+K+WCEK+LLDYH +FN + + VME +LPL + TKI EE VP Y T Q+ G+ D TGNRVD YIRSSLRNAFAKML+D N++ + E +V++ L+++A+ T ELAAKE++ +S ILKKWHPVAAG AAVTLHTCYGTLLKQYLTG S L NE + +L AGKLEK LVQ+ VEDS EC DGGKA+VREM PYEVDA+I R LKQW+QERL+ KE L +K++E
Sbjct: 2 RRPMTSAEIMRQQMRVTEQSDNRLRKTLMRTLVGQMGRRAETIILPLELLRHLKPSEFNDPQEYHLWQKRQLKILEAGLLLHPSIPFDKSDTFAAKLRDIINACDIKAIDTGKNSTTMRTLCNCIVSLAWR-SPNGGTTDVCHWADGYPLNVHIYTTLLSSVFDMKDETLVLDEIDELMELMKKTWSTLGINRSIHNLCFTWVLFEQYVVTGQVEPDLLSASFAMLSEVAHDAKKVDREP-IYLKMLASVLVSLKKWCEKRLLDYHGSFNRATVCVMENMLPLLFSATKILEEDVPCYVTSSQEKGEAGDDSTGNRVDYYIRSSLRNAFAKMLEDQNVNGTKYTEGLEVSELLIKLAKKTEELAAKEKDIFSPILKKWHPVAAGVAAVTLHTCYGTLLKQYLTGKSSFL-NETVLVLQRAGKLEKSLVQLVVEDSVECEDGGKAVVREMAPYEVDAMILRLLKQWLQERLQKGKEYLLRSKQTE 482
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.
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
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.
