Table 1.
Characterization of B. vulgaris genes located within the BR1 locus interval (102,853 bp) on chromosome 9 on scaffold Bvchr9.sca026.
| Gene models based on RefBeet-1.1 (abbreviation) | Pbr (BETA 1773) specific amino acid changes compared to RefBeet-1.1 and Pb (93161P) | GO protein description/putative function | Homologous Arabidopsis gene, annotation according to TAIR database |
|---|---|---|---|
| Bv9_227290_ksuy.t1 (ksuy)a,b,c | No | Curvature thylakoid protein, chloroplastic | AT1G52220, CURVATURE THYLAKOID 1C (CURT1C), protein located in the chloroplast thylakoid membrane |
| Bv9_227300_uapa.t1 (uapa)a | aa51 H D, aa119 TS, aa208 TA, premature STOP codon for Pbr and Pb resulting in a protein with 223 instead of 235aa (RefBeet-1.1) |
DNA-directed RNA polymerase II subunit RPB1-like | No significant hit |
| Bv9_227310_tswg.t1 (tswg)a | aa84 TK, aa128 H-, aa151 PPS, aa182 PL, aa187 FL, aa188 DF, aa189 HSTOP codon resulting in a protein with 188 instead of 202aa |
Hypothetical protein BVRB_9g221070 | No significant hit |
| Bv9_227320_iirc.t1/t2 (iirc)a,b | aa204 EQ, aa255 AE, aa300 EG, aa319 QR, aa332 AV, aa339 RS, aa407/373 KN, aa454/420 VI, aa467/433 FS specific for t1 and t2, aa384 IV specific for t1 |
Serpin-ZX-like protein (F: serine-type endopeptidase inhibitor activity, transferase activity) | AT1G47710, SERPIN, protein involved in the negative regulation of endopeptidase activity in the apoplast |
| Bv9_227330_dgic.t1 (dgic)a,b,c | aa95 EG, aa113 VL, aa152 ED, aa223 TS, aa248 GE, aa252 KN, aa266 VI, aa302 IT, aa309 QL, aa324 AV, aa772 ED, aa787 AS |
Golgin candidate 5 | AT1G79830, GOLGIN CANDIDATE 5 (GC5), structural component of the Golgi apparatus |
| Bv9_227340_kzoy.t1 (kzoy)a,b,c | No | Basic-leucine zipper transcription factor family protein isoform 1 (F:sequence-specific DNA binding transcription factor activity; P:regulation of transcription, DNA-dependent) | AT1G58110, basic-leucine zipper (bZIP) transcription factor, protein involved in DNA-templated transcription in the nucleus |
| Bv9_227350_pgzt.t1 (pgzt)a,b,c | No | Magnesium transporter mrs2-4 (C: membrane; F:magnesium ion transmembrane transporter activity; P:transmembrane transport, magnesium ion transport) | AT3G58970, MAGNESIUM TRANSPORTER 6 (MGT6), integral component of the plasma membrane |
| Bv9_227360_oeyr.t1 (oeyr)a,b,c | aa618 EK, aa629 AV |
Cleavage and polyadenylation specificity factor subunit 3-i-like isoform (F: hydrolase activity) | AT1G61010, CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I (CPSF73-I), protein involved in the mRNA polyadenylation in the nucleus |
| Bv9_227370_yfgr.t1 (yfgr)a,b,c | aa144 TA, from aa191 changed sequence by a frame shift mutation, at aa204STOP codon resulting in a protein with 203 instead of 633aa |
Cleavage and polyadenylation specificity factor subunit 3-i-like isoform (F: hydrolase activity) | AT1G61010, CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I (CPSF73-I), protein involved in the mRNA polyadenylation in the nucleus |
| Bv9_227380_faqz.t1 (faqz)a,b,c | aa31 LI |
Probable plastidic glucose transporter 3 (C: trans-Golgi network, endosome, integral to membrane; P: negative regulation of biological process, carbohydrate transmembrane transport, determination of bilateral symmetry, xylem and phloem pattern formation, flower morphogenesis; F: sugar:hydrogen symporter activity) | AT1G79820, SUPPRESSOR OF G PROTEIN BETA1 (SGB1), protein involved in the carbohydrate transport through membranes |
| Non-coding genes based on RefBeet-1.1 | Pbr specific nucleotide changes compared to RefBeet-1.1 and Pb | Homology to published miRNAs based on mirBase | Number of putative target genes based on RefBeet-1.1 gene models |
| ncRNA_2240/MIR1122 (nc2240)a | No | Brachypodium distachyon miR5181d, involved in cold stress response; Brachypodium distachyon miR5174e stem-loop, involved in reprogramming leaf growth during drought stress | 12 (non-related to flowering) |
a
RNA evidence according to RNAseq and EST data of RefBeet-1.1 (Dohm et al., 2014).
b
RNA evidence according to RNAseq data derived from shoot apices of annual sugar beet accession 001684 during floral transition (Tränkner et al. unpublished).
c
RNA evidence according to SuperSAGE data derived from leaves of non-vernalized and vernalized KWS2320 sugar beets (Vogt et al. unpublished).