Table 1.
Positional candidate genes for Mt-FTQTL6
| Gene ID [reference] | BAC clone and/or WGS sequence | EST (1) | cDNA (1) | Number of splicing isoforms | Number of intron(s) in the coding sequence [intron size(s) in bp] | Putative gene product | Amino acid length [length of the acidic C-terminal domain] (2) | Theoretical molecular weight (KDa) | Theoretical pI [pI of the C-terminal domain] (2) |
|---|---|---|---|---|---|---|---|---|---|
| MtBAG - 1[40] | - | AW299190; BG646253; AW257319; AW256371; BI308136; AL369679; AW329645; AL373067; BF006595; AW694037; BF650244; AL373068; CA919955; AL373067; CA917144; BE325495; EX533119; BG588510; BE322176 | - | 1 | - | Bcl-2-associated athanogene | 355 | 39.9 | 9.37 |
| MtCBF14 | Scaffold065bis | - | - | - | - | CBF/DREB1 protein | 230 [103] | 25.74 | 5.55 [4.02] |
| MtCBF13 | Scaffold065bis | - | - | - | - | CBF/DREB1 protein | - | - | - |
| MtCBF3[32]/MtDREB1C[14] | Scaffold065bis | CA920049; CF069650; BG581707; BF005835; BQ138271; BG582534 | DQ267620; EU139868 | 1 | - | CBF/DREB1 protein | 227 [109] | 25.99 | 5.64 [4.11] |
| MtCBF12 | Scaffold065bis | GT136747; GT141343 | BT134401 | 1 | - | CBF/DREB1 protein | - | - | - |
| MtCBF11 | Scaffold065bis | - | - | - | - | CBF/DREB1 protein | 281 [103] | 31.21 | 5.66 [4.07] |
| MtCBF2[32] | Scaffold065bis; mth2-221P20; mte1-60A22 | BF520341 | EU139867 | 1 | - | CBF/DREB1 protein | 230 [106] | 26.07 | 5.8 [4.12] |
| MtCBF10 | Scaffold065bis; mth2-221P20; mte1-60A22 | - | - | - | - | CBF/DREB1 protein | 198 [104] | 22.58 | 5.39 [4.03] |
| MtCBF9 | Scaffold065bis; mte1-60A22 | CX528143 | - | 1 | - | CBF/DREB1 protein | 208 [114] | 24.04 | 4.99 [3.94] |
| MtCBF8 (a) | Scaffold065bis; mte1-60A22 | EY477920; BQ165478; CA921976; BF005540; AW573630; BQ165479; EY476564; BE999274; BE998545;BE999273; CB893700 | DQ778006; BT146058 | 2 | no intron/1 intron [316] | CBF/DREB1 protein | 215 [100]/271 [156] | 24.87/31.11 | 6.1 [4.27]/8.37 [4.92] |
| MtCBF7 | Scaffold065bis; mte1-60A22 | BF005905 | - | 1 | 1 intron [279] | CBF/DREB1 protein | 245 [130] | 27.88 | 6.66 [4.60] |
| MtCBF6 | Scaffold065bis; mth2-92O15 | CF069139; AW775188; BF006671;CA919708 | - | 2 | no intron/1 intron [352] | CBF/DREB1 protein | 216 [101]/248 [133] | 24.67/28.23 | 6.31 [4.22]/8.41 [4.84] |
| MtCBF5 | Scaffold065bis; mth2-92O15 | BG648933; BF005756; CA920720 | - | 1 | 1 intron [380] | CBF/DREB1 protein | 267 [152] | 30.54 | 8.87 [5.04] |
| MtPERLD | Scaffold065bis; mth2-92O15 | BF631847; EV255869; AL373022; CB892925; EY476043; BG449960; BG648146; BF639371; BG648635; CX527766; CX527793; CX527254; BI267056; BF521243; BF642637; CX523947; BE319009; AL373021; BF635170; BM779066; BQ152673; AW736243; BG646840 | BT051744; BT139597 | 2 | 4 introns [2807;93;1008;2220]/ 5 introns [123; 2663; 93;1008;2220] | Per1-like family protein | 342 | 39.48 | 7.6 |
| MTR_050s0020[23] | Scaffold065bis; mth2-92O15; mth2-53l24 (GB acc AC229695) (b) | BF635955; GT141039; GT136423 | - | 1 | 15 introns [2336; 137; 162; 266; 470; 89; 86; 126; 80; 626; 88; 84; 86; 80; 450] (c) | ABC transporter B family member | 715 | 78.37 | 9.07 |
| MTR_050s0019[23] | Scaffold065bis; mth2-92O15; mth2-53l24 (GB acc AC229695) | EV258193; CX522284 | BT147320 | 1 | 1 intron [721] | Conserved uncharacterized protein | 242 | 26.45 | 8.56 |
| MtZFWD | Scaffold065bis | CX520203; BE239869 | - | 1 | 8 introns [939; 162; 143; 306; 104; 78; 598; 759] (d) | Zinc finger CCCH and WD40 domain-containing protein | 438 | 47.29 | 7.85 |
| MTR_054s0001[23] | Scaffold065bis; mth2-12e18 (GB acc AC229727) | BQ138417 | - | 1 | 11 introns [1352; 982; 1537; 116; 110; > 418; 443; 1495; 27; 139; 627] (e) | DNA 3′- phosphoesterase | 338 | 37.66 | 6.56 |
| MTR_054s0019[23] | Scaffold065bis; mth2-12e18 (GB acc AC229727) | CB894631; CF068286; DW018377; BG647692; BE316675; EV256045; BF639952; CB893865; EV261994; BE322046; BI263625; AW691341; CX535182; BI265523; BE998615; CA918979; BI266410; CA858657; BF520558; BF637666; BI267231; AJ503890 | BT051762; BT148189; BT136112 | 2 | 5 introns [938; 202; 1366; 511; 864]/ different translation start site and novel intron of 4532 bp | Sorbitol dehydrogenase-like protein | 362 | 39 | 6.13 |
| MTR_6g089580[23] | Scaffold065bis; mth2-50m10 (GB acc AC174372) | BG648131; AW685633; AW586532; AI974700; CA920607 | - | 1 | no intron | unknown protein | 628 | 71.8 | 8.38 |
(1) Corresponding EST and cDNA were identified through BLAST searches against M. truncatula EST and nr/nt databases in GenBank [36] (January 2013), respectively. In case of alternate splicing, the sequence(s) corresponding to the less represented transcript isoform is(are) in italics; (2) similar to [41], the C-terminal domains of MtCBF2-3;5-11;14 were considered as the amino acid sequences that occur after the signature motif “DSAWR” and that up to the last amino acid of the protein; (a) a cDNA sequence corresponding to MtCBF8 was directly submitted to GenBank [36] by Chen JR, Guo L, Wang H in 2007. The respective locus was referred to as DREB1A; (b) In addition to MTR_050s0019 and MTR_050s0020, 7 other non-transposon genes could be identified on AC229695 but were not considered in this study. In fact, the corresponding genomic region for these latter, spanning 114,402 kb (1-19,425; 23,144-90,266; 147,607-159,557; 185,484-201,386 bp) is completely missing from Scaffold065bis. Because of its size exceeding 200 Kb, AC229695 seems to have resulted from sequencing inserts of at least two BAC clones, one of which did not originate from Mt-FTQTL6-containing region; (c) The intron/exon structure of MTR_050s0020 from M. truncatula Mt3.5 genome assembly has been revised and its corresponding coding sequence found to contain 15 introns instead of 16. M. truncatula EST and close protein sequences together with EST from other Papilionoideae species and notably a Pisum sativum L. sequence generated by RNAseq (Alves Carvalho et al. in preparation) were used for this purpose; (d) As related EST do not fully cover MtZFWD coding sequence, intron positions were predicted after multiple alignment with the coding sequences of Glyma16g32370 and Glyma09g27300 and EST sequences from Lathyrus odoratus L. (GO316201, GO317026, GO319782), L. japonicus (FS347722, FS346164, FS360001) and Phaseolus acutifolius A. Gray (HO781358); (e) As the EST BQ138417 does not cover the entire coding sequence of MTR_054s0001, highly similar EST sequences from L. japonicus (GO014516), Vigna unguiculata (L.) Walp. (FF549909) and G. max (AW184979, FK011826) were used for intron location. The positions and sizes of introns 9 and 10 are different from Mt3.5.