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. 2017 Nov 9;8:1930. doi: 10.3389/fpls.2017.01930

Table 3.

List of Daucus carota terpene synthase (TPS) gene models sorted by their physical position on the assembled nine carrot chromosomes according to the whole genome sequence (Iorizzo et al., 2016).

Chromosomea Gene name Genomic coordinatesa Locus namea EST contigb Tied Typed TPS
Strand Start Stop Subfamily
1 DcTPS32 − 24861393 24864140 DCAR_002080 1 cons. TPS-b
1 DcTPS11 + 28343809 28346252 1 cons. TPS-a
1 DcTPS45 + 33280212 33282540 DCAR_002829 0.83 cons. TPS-g
1 DcTPS46 + 33285711 33288129 DCAR_002830 0.83 cons. TPS-g
1 DcTPS19 + 33290944 33295685 DCAR_002831 0.83 cons. TPS-g
1 DcTPS47 − 44626531 44658850 DCAR_004091 0.5 put. TPS-b
1 DcTPS10 − 44680158 44682842 ctg6077 1 cons. TPS-b
1 DcTPS24 + 45337090 45339443 1 cons. TPS-b
1 DcTPS48 + 45340690 45343894 1 cons. TPS-b
1 DcTPS22 + 45348547 45351439 1 cons. TPS-b
1 DcTPS49 + 45355908 45363793 0.71 put. TPS-b
2 DcTPS41 − 1270085 1273204 0.83 cons. TPS-a
2 DcTPS40 − 1279452 1282625 1 cons. TPS-a
2 DcTPS42 + 1678080 1680364 1 cons. TPS-a
2 DcTPS03 + 39586545 39589039 ctg1324c 1 cons. TPS-b
3 DcTPS15 − 2697938 2700973 ctg15365 1 cons. TPS-a
3 DcTPS50 − 34521894 34524751 0.57 put. TPS-a
3 DcTPS37 − 34584910 34587493 1 cons. TPS-a
3 DcTPS08 − 34633086 34638612 0.83 cons. TPS-a
3 DcTPS51 − 45432441 45435235 0 put. TPS-b
3 DcTPS05 − 45438050 45440460 ctg21245c 1 cons. TPS-b
3 DcTPS12 − 45451831 45454062 1 cons. TPS-b
3 DcTPS18 − 45459976 45462408 0.86 cons. TPS-b
3 DcTPS25 + 47468861 47475243 DCAR_012483 1 cons. TPS-c
3 DcTPS31 − 48063948 48068009 1 cons. TPS-b
3 DcTPS52 − 48081099 48084450 DCAR_012537 0.67 put. TPS-b
3 DcTPS30 − 48088855 48092222 DCAR_012538 1 cons. TPS-b
3 DcTPS53 + 48692677 48694890 1 cons. TPS-a
3 DcTPS06 + 48729300 48732085 ctg52846c 1 cons. TPS-a
4 DcTPS38 − 15497126 15500214 1 cons. TPS-a
4 DcTPS13 + 25555496 25558124 1 cons. TPS-a
4 DcTPS26 + 31144998 31147390 DCAR_013310 1 cons. TPS-b
4 DcTPS04 − 31217904 31220266 DCAR_013298 ctg13781 1 cons. TPS-b
4 DcTPS54 − 31227164 31230355 DCAR_013297 0.67 put. TPS-b
4 DcTPS55 − 31244459 31247374 DCAR_013294 0.67 put. TPS-b
4 DcTPS27 − 31249549 31251992 DCAR_013293 0.86 cons. TPS-b
4 DcTPS09 − 33893353 33896161 DCAR_012965 ctg260 1 cons. TPS-b
4 DcTPS02c + 33914246 33916610 DCAR_012963 ctg43814c 1 cons. TPS-b
5 DcTPS56 + 8252207 8257662 DCAR_016843 0.77 put. TPS-e
5 DcTPS28 + 8266628 8275147 DCAR_016844 0.92 cons. TPS-e
5 DcTPS14 − 20668670 20672094 DCAR_017536 ctg23518 1 cons. TPS-b
5 DcTPS17 + 27521963 27524389 DCAR_018214 1 cons. TPS-b
5 DcTPS57 + 29664194 29669533 DCAR_018422 0.77 put. TPS-c
5 DcTPS58 − 37087498 37090480 DCAR_019208 0.67 put. TPS-b
5 DcTPS33 − 37091126 37102038 DCAR_019208 1 cons. TPS-b
5 DcTPS59 + 39496367 39502226 DCAR_019490 0 put. TPS-c
6 DcTPS01c + 1181665 1185241 DCAR_023152 ctg4929c 1 cons. TPS-a
7 DcTPS23 + 18910630 18913238 DCAR_024752 1 cons. TPS-g
7 DcTPS60 + 18916711 18919574 DCAR_024753 0.17 put. TPS-g
7 DcTPS61 − 29317415 29321559 0.33 put. TPS-a
8 DcTPS62 − 14626722 14629935 DCAR_028138 0.67 put. TPS-b
8 DcTPS21 + 14744248 14746910 1 cons. TPS-b
8 DcTPS29 − 17430080 17434674 DCAR_027915 1 cons. TPS-f
8 DcTPS44 − 27097599 27100761 DCAR_026972 1 cons. TPS-b
8 DcTPS43 − 27108437 27111829 DCAR_026971 1 cons. TPS-b
9 DcTPS36 + 8799300 8801682 1 cons. TPS-a
9 DcTPS35 + 8908269 8912243 0.83 cons. TPS-a
9 DcTPS63 + 8935068 8937899 0 put. TPS-a
9 DcTPS64 − 8953248 8958027 0 put. TPS-a
9 DcTPS07 + 8977442 8981304 ctg58617c 1 cons. TPS-a
9 DcTPS34 + 8999311 9003484 1 cons. TPS-a
9 DcTPS65 + 23073510 23076811 1 cons. TPS-a
9 DcTPS20 − 31868960 31872669 0.83 cons. TPS-b
9 DcTPS39 − 32232277 32234933 DCAR_031040 0.86 cons. TPS-a
S3773e DcTPS16 + 14141 17230 DCAR_032119 1 cons. TPS-b

Transcript intron evidence (tie) was calculated with the GeMoMa software (Keilwagen et al., 2016) using RNA-seq data from Iorizzo et al. (2016). Predictions were split in conservative genes with tie ≥ 0.8 and putative genes with tie < 0.8 and compared with the annotation of Iorizzo et al. (2016) and EST contigs identified previously in the carrot transcriptome (Iorizzo et al., 2011).

a

Chromosomes (pseudomolecules), genomic coordinates, orientation and locus names according the carrot whole genome sequence assembly (Iorizzo et al., 2016).

b

EST contig no. according the assembled carrot transcriptome (Iorizzo et al., 2011).

c

Known carrot TPS genes (DcTPS01, DcTPS02) or predicted full-length carrot TPS cDNA according Yahyaa et al. (2015).

d

Tie (transcription intron evidence) according GeMoMa analysis; Type classification: conservative/putative according to tie values (conservative ≥ 0.8).

e

Scaffold number according the carrot whole genome sequence assembly (Iorizzo et al., 2016).