De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

Okubo, Satoshi; Terauchi, Kaede; Okada, Shinji; Saito, Yoshikazu; Yamaura, Takao; Misaka, Takumi; Nakajima, Ken-ichiro; Abe, Keiko; Asakura, Tomiko

doi:10.1186/s12864-021-07674-3

Table 3 Comparison of the expression profiles of C. latifolia and C. capitulata

From: De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

*C. latifolia*			*C. capitulata*
Transcript ID	RefSeq	TPM	Transcript ID	RefSeq	TPM	Pident^a	E-value^a
L_19492_c6_g1_i1	trans-resveratrol di-O-methyltransferase	36,282	C_19332_c0_g2_i1	trans-resveratrol di-O-methyltransferase	277	99.18	0
L_20774_c6_g2_i5	trans-resveratrol di-O-methyltransferase	31,648	C_20405_c1_g1_i2	trans-resveratrol di-O-methyltransferase	573	99.02	0
*L_22219_c0_g1_i1	mannose-specific lectin-like	7634	*C_16562_c0_g1_i1	mannose-specific lectin-like	80	97.75	0
L_22040_c0_g1_i1	chalcone synthase-like	6483	C_22230_c0_g1_i1	chalcone synthase-like	69	100	0
L_39489_c0_g1_i1	cinnamoyl-CoA reductase 1-like	4584	C_43958_c0_g1_i1	cinnamoyl-CoA reductase 1-like	37	100	0
L_17418_c0_g1_i1	benzyl alcohol O-benzoyltransferase	2848	C_20771_c2_g1_i3	benzyl alcohol O-benzoyltransferase	18	96.27	0
L_18625_c0_g1_i1	glutelin type-A 1-like	2641	C_18515_c0_g1_i1	glutelin type-A 1-like	35	100	0
L_20161_c0_g1_i1	probable polyamine oxidase 5	2333	C_20921_c0_g1_i1	probable polyamine oxidase 5	38	99.17	0
L_20171_c0_g1_i1	pyruvate decarboxylase 1 isoform X1	2140	C_19622_c0_g1_i1	pyruvate decarboxylase 1 isoform X1	30	99.74	0
L_19390_c0_g1_i1	benzyl alcohol O-benzoyltransferase-like	1721	C_20336_c0_g1_i1	benzyl alcohol O-benzoyltransferase-like	25	99.01	0
L_17288_c0_g1_i1	5-methyltetrahydropteroyl-triglutamate--homocysteine methyltransferase 1	1527	C_20491_c0_g1_i4	5-methyltetrahydropteroyl-triglutamate--homocysteine methyltransferase 2-like	19	98.22	0
L_22101_c0_g1_i1	cytochrome P450 71A1-like	1130	C_20591_c0_g1_i1	cytochrome P450 71A1-like	14	100	0
L_9054_c0_g2_i1	uncharacterized protein LOC105052971	891	C_20462_c0_g1_i1	uncharacterized protein LOC105052971	16	99.15	0
L_19899_c1_g1_i5	elongation factor 1-alpha-like	720	C_16211_c0_g1_i1	hypothetical protein CARUB_v100096370mg, partial	11	99.75	0
L_39417_c0_g1_i1	palmitoyl-acyl carrier protein thioesterase, chloroplastic-like	659	C_1125_c0_g1_i1	palmitoyl-acyl carrier protein thioesterase, chloroplastic-like	0.89	99.88	0
L_8999_c0_g1_i1	probable protein Pop3	657	C_3239_c0_g1_i1	probable protein Pop3	10	99.79	0
*L_16562_c0_g1_i1	mannose-specific lectin-like	652	*C_16324_c0_g1_i1	mannose-specific lectin-like	8	98.8	0
L_20784_c0_g1_i1	mannan endo-1,4-beta-mannosidase 5-like	477	C_20300_c0_g1_i1	mannan endo-1,4-beta-mannosidase 5-like	8	99.81	0
L_17063_c0_g1_i1	uncharacterized protein LOC103705182	457	C_15604_c0_g1_i1		7	99.51	0
L_9763_c0_g1_i1	4-hydroxyphenyl-pyruvate dioxygenase	441	C_17419_c0_g1_i2	4-hydroxyphenyl-pyruvate dioxygenase	6	97.85	0
L_15645_c0_g1_i1	hypothetical protein PHAVU_005G042200g	378	C_19503_c0_g1_i2	uncharacterized protein LOC103713005	4	98.6	0
L_39500_c0_g1_i1	uncharacterized protein C24B11.05-like isoform X2	323	C_15665_c0_g1_i2	uncharacterized protein C24B11.05-like isoform X2	6	96.74	0
L_16206_c0_g1_i1	cytochrome P450 71A1-like	295	C_18399_c0_g1_i1	cytochrome P450 71A1-like	5	99.88	0
L_9770_c0_g1_i1	Os09g0480700, partial	278	C_11365_c0_g1_i1	Os09g0480700, partial	3	99.52	0
L_20943_c2_g1_i1	LOW QUALITY PROTEIN: ATP-citrate synthase beta chain protein 1-like	276	C_20189_c1_g1_i6	LOW QUALITY PROTEIN: ATP-citrate synthase beta chain protein 1-like	5	99.74	0
L_5031_c0_g1_i1		265	C_26197_c0_g1_i1		3	99.53	2E-108
L_19581_c0_g1_i1	peroxidase 43	244	C_20763_c0_g1_i7	peroxidase 43	3	99.32	0
L_22200_c0_g1_i1		237	C_21279_c0_g3_i1		0	92.42	0
L_16082_c0_g1_i1	uncharacterized protein LOC105035694	230	C_20815_c0_g1_i2	uncharacterized protein LOC105035694	4	97.73	0
L_1821_c0_g1_i1	protein EARLY RESPONSIVE TO DEHYDRATION 15-like	213	C_5863_c0_g3_i1	protein EARLY RESPONSIVE TO DEHYDRATION 15-like	1	94.17	0
L_21840_c4_g7_i1		197	C_46444_c0_g1_i1		2	100	0
L_11489_c0_g1_i1		189	C_51079_c0_g1_i1		3	95.13	4E-114
L_21813_c0_g1_i1	protein kinase APK1B, chloroplastic-like	184	C_20869_c0_g1_i9	protein kinase APK1B, chloroplastic-like	0.97	95.04	0
L_16611_c0_g1_i1		163	C_8161_c0_g1_i1		2	100	0
L_12355_c0_g1_i1	myb-related protein 306-like	160	C_7266_c0_g1_i1	myb-related protein 306-like	3	99.89	0
L_18378_c0_g1_i1	probable L-ascorbate peroxidase 4	158	C_17994_c1_2_i1	probable L-ascorbate peroxidase 4	2	96.39	0
L_21677_c0_g1_i1	S-adenosylmethionine decarboxylase proenzyme-like	149	C_15562_c0_g2_i1	S-adenosylmethionine decarboxylase proenzyme-like	0.92	96.67	0
L_14830_c0_g1_i1	NAC transcription factor 29-like	135	C_20428_c0_g1_i1	NAC transcription factor 29-like	0	97.61	0
L_14165_c0_g2_i1	probable peroxygenase 4	131	C_17339_c0_g1_i2	probable peroxygenase 4	2	95.32	0
L_21840_c4_g4_i2		130	C_11729_c0_g1_i1		2	100	0
L_39737_c0_g1_i1	Glutathione peroxidase 2	127	C_8347_c0_g1_i1	Glutathione peroxidase 2	2	96.26	0
L_4928_c0_g1_i1		124	C_44794_c0_g1_i1		1	100	3E-101
L_20250_c0_g1_i1	protein NRT1/ PTR FAMILY 5.6-like	114	C_29979_c0_g1_i1	protein NRT1/ PTR FAMILY 5.6-like	2	97.44	0
L_15628_c0_g1_i1	formin-A-like	103	C_20575_c0_g1_i5	formin-A-like	0	90.44	0
L_21235_c2_g9_i1		101	C_9877_c0_g1_i1		1	92.77	3E-98
*L_19752_c0_g1_i1	mannose-specific lectin 3-like	33	*C_18595_c0_g1_i1	mannose-specific lectin 3-like	2301	97.6	0
L_16463_c0_g2_i2	LOW QUALITY PROTEIN: S-norcoclaurine synthase-like	16	C_6989_c0_g1_i1	LOW QUALITY PROTEIN: S-norcoclaurine synthase-like	8393	91.39	0
L_32395_c0_g1_i1		14	C_4973_c0_g1_i1		8765	86.17	4E-92
L_19456_c0_g1_i1	polyphenol oxidase, chloroplastic-like	13	C_20237_c3_g1_i1	polyphenol oxidase, chloroplastic-like	1496	83.82	0
L_14333_c0_g1_i1		12	C_13197_c0_g1_i1		42,047	94.54	7E-75
L_55067_c0_g1_i1	defensin Ec-AMP-D1 {ECO:0000303\| PubMed:18625284}-like	9	C_39416_c0_g1_i1	defensin Ec-AMP-D1 {ECO:0000303\| PubMed:18625284}-like	2475	95.1	0
L_5253_c0_g1_i1	Disease resistance-responsive (dirigent-like protein) family protein, putative	9	C_16870_c0_g2_i1	Disease resistance-responsive (dirigent-like protein) family protein, putative	547	94.54	0
L_1586_c0_g1_i1	glycine-rich protein-like isoform X1	8	C_39384_c0_g1_i1		2895	94.72	0
L_23556_c0_g1_i1	basic blue protein-like	5	C_14117_c0_g1_i1	basic blue protein-like	606	94.75	0
L_13618_c0_g1_i1	non-specific lipid-transfer protein 1-like	5	C_13976_c0_g1_i1	lipid transfer protein precursor	655	96.6	0
L_465_c0_g2_i1	microsomal glutathione S-transferase 3-like	5	C_4959_c0_g1_i1	microsomal glutathione S-transferase 3-like	246	93.89	0
L_21384_c3_g4_i1		5	C_17484_c0_g1_i1		424	86.76	1E-56
L_9003_c0_g1_i1	dirigent protein 22-like isoform X1	5	C_19511_c0_g1_i1	dirigent protein 22-like	834	96.09	0
L_4015_c0_g1_i1	CASP-like protein 2A1	4	C_4840_c0_g1_i1	CASP-like protein 2A1	241	98.25	0
L_16618_c0_g1_i1	hypothetical protein SORBIDRAFT_05g026700	3	C_4999_c0_g1_i1	Bowman-Birk type trypsin inhibitor-like isoform X2	5459	86.06	1E-135
L_4834_c0_g2_i1	xylem serine proteinase 1-like	3	C_9966_c0_g1_i1	subtilisin-like protease	232	96.91	0
L_6907_c0_g1_i1	serine/threonine-protein kinase CDL1-like	3	C_11871_c1_g1_i1	serine/threonine-protein kinase CDL1-like	183	96.44	0
L_17444_c0_g1_i1	cytochrome P450 CYP82D47-like	3	C_20684_c0_g1_i1	cytochrome P450 CYP82D47-like	182	94.92	0
L_40485_c0_g3_i1	non-specific lipid-transfer protein 1-like	3	C_39065_c0_g1_i1	non-specific lipid-transfer protein 1-like	1455	90.92	0
L_18380_c0_g1_i2	conserved hypothetical protein	3	C_39186_c0_g1_i1	conserved hypothetical protein	654	93.2	4E-127
L_31252_c0_g1_i1		3	C_12650_c0_g1_i1	non-specific lipid-transfer protein-like	283	94.9	4E-65
L_42464_c0_g2_i1	alpha carbonic anhydrase 8-like, partial	3	C_40148_c0_g1_i1	alpha carbonic anhydrase 7-like	235	93.1	0
L_13852_c0_g1_i1	endoglucanase 6	3	C_18579_c0_g1_i1	endoglucanase 19-like	707	97.65	0
L_39898_c0_g1_i1	oxygen-evolving enhancer protein 3–1, chloroplastic-like	2	C_12932_c0_g1_i1	oxygen-evolving enhancer protein 3–1, chloroplastic-like	160	96.93	0
L_6056_c0_g1_i1	Calvin cycle protein CP12–1, chloroplastic-like	2	C_12691_c0_g1_i1	calvin cycle protein CP12–1, chloroplastic	215	92.42	3E-128
L_6093_c0_g1_i1		2	C_41578_c0_g1_i1		170	93.87	2E-135
L_17773_c0_g1_i1	uncharacterized protein LOC105056845	2	C_12165_c0_g1_i1	uncharacterized protein LOC105056845	249	92.36	0
L_24151_c0_g1_i1	ribonuclease 3-like	2	C_39292_c0_g1_i1	ribonuclease 3-like	389	98.07	0
L_8678_c0_g1_i1	uncharacterized protein LOC105056672	2	C_4730_c0_g1_i1	uncharacterized protein LOC105056672	116	98.71	0
L_19431_c2_g4_i1	polyubiquitin 4-like, partial	2	C_20039_c0_g8_i1	hypothetical protein PHAVU_003G1236000g, partial	2116	94.38	6E-106
L_250_c1_g1_i1	probable glutathione S-transferase parA	2	C_16559_c0_g1_i1	probable glutathione S-transferase parA	419	98.26	0
L_10676_c0_g1_i1	probable linoleate 9S-lipoxygenase 5	2	C_17658_c0_g1_i1	probable linoleate 9S-lipoxygenase 5	1644	98.82	0
L_8975_c0_g1_i1	chitinase-like protein 1	2	C_16475_c1_g1_i1	chitinase-like protein 1	183	97.92	0
L_44393_c0_g1_i1	hypothetical protein POPTR_0004s03650g	2	C_18495_c2_g1_i1	conserved hypothetical protein	2751	92.78	3E-66
L_759_c0_g1_i1	CAS1 domain-containing protein 1-like	2	C_21365_c0_g1_i1	CAS1 domain-containing protein 1-like isoform X2	183	99.26	0
L_30327_c0_g1_i1	conserved hypothetical protein	2	C_23037_c0_g1_i1	conserved hypothetical protein	134	96.47	2E-116
L_5572_c0_g1_i1	short-chain type dehydrogenase/reductase-like	2	C_14194_c0_g1_i1	short-chain type dehydrogenase/reductase-like	205	96.22	0
L_45139_c0_g1_i1	putative germin-like protein 2–1	2	C_21890_c0_g1_i1	putative germin-like protein 2–1	111	96.2	1E-146
L_22251_c0_g1_i1	xyloglucan endotransglucosylase/ hydrolase protein 9-like	2	C_40495_c0_g2_i1	LOW QUALITY PROTEIN: xyloglucan endotransglucosylase/hydrolase protein 9-like	131	98.37	0
L_56341_c0_g1_i1	peroxidase 4-like	1	C_10149_c0_g1_i1	peptide-N4-(N-acetyl-beta-glucosaminyl) asparagine amidase A-like	1301	93.81	2E-93
L_56680_c0_g1_i1	peptide-N4-(N-acetyl-beta-glucosaminyl) asparagine amidase A-like	1	C_19920_c0_g1_i1	peroxidase 4-like	583	98.68	7E-113
*L_307_c0_g2_i1	mannose-specific lectin-like	1	*C_9931_c0_g1_i1	mannose-specific lectin-like	14,867	99.35	0
L_48085_c0_g1_i1	probable indole-3-acetic acid-amido synthetase GH3.1	1	C_19080_c1_g1_i1	probable indole-3-acetic acid-amido synthetase GH3.1	107	84.39	2E-70
L_46946_c0_g1_i1	chlorophyll a-b binding protein 7, chloroplastic-like	1	C_41884_c0_g1_i1	chlorophyll a-b binding protein, chloroplastic	141	98.41	0
L_4845_c0_g1_i1	chlorophyll a-b binding protein CP26, chloroplastic-like	1	C_10575_c0_g1_i1	chlorophyll a-b binding protein CP26, chloroplastic-like	353	98.25	0
L_23363_c0_g1_i1	uncharacterized protein LOC105056050	1	C_21609_c0_g1_i1	uncharacterized protein LOC105056050	1612	98.84	0
*L_30823_c0_g1_i1	mannose-specific lectin-like	1	*C_17363_c2_g1_i3	mannose-specific lectin-like	317	98.64	0
L_645_c0_g1_i1	putative lipid-transfer protein DIR1	1	C_12082_c0_g1_i1	putative lipid-transfer protein DIR1	108	97.09	0
L_50661_c0_g1_i1	oxygen-evolving enhancer protein 2, chloroplastic-like	1	C_14711_c0_g1_i1	oxygen-evolving enhancer protein 2, chloroplastic-like	133	97.74	0
L_16663_c0_g1_i2		1	C_20564_c0_g1_i1		642	89.54	2E-112
L_41624_c0_g1_i1	isocitrate lyase	1	C_15046_c0_g1_i1	isocitrate lyase	116	98.32	7E-180
L_33923_c0_g1_i1	galactinol synthase 2-like isoform X1	1	C_13705_c0_g1_i1	galactinol synthase 1-like	127	92.82	0
L_36400_c0_g1_i1	putative cell wall protein	0.98	C_26021_c0_g1_i1	putative cell wall protein	117	98.05	2E-98
L_53880_c0_g1_i1	uncharacterized protein LOC105056050	0.93	C_5177_c0_g1_i1	proactivator polypeptide-like 1	644	98.94	0
L_6399_c0_g1_i1	auxin-induced protein 22D-like	0.93	C_10469_c0_g1_i1	auxin-induced protein 22D-like	171	96.71	0
L_10569_c0_g2_i1		0.91	C_16356_c0_g1_i1		1072	93.62	0
L_21646_c1_g1_i3	protein HOTHEAD-like	0.91	C_14207_c0_g1_i1	protein HOTHEAD-like	330	96.12	0
L_22097_c0_g1_i1		0.82	C_9693_c0_g2_i1		155	92.67	0
L_30250_c0_g1_i1	polygalacturonase inhibitor	0.64	C_17486_c1_g1_i2	Polygalacturonase inhibitor	171	93.72	2E-170
L_50985_c0_g1_i1	putative phytosulfokines 6 isoform X1	0.47	C_22933_c0_g1_i1	putative phytosulfokines 6 isoform X2	136	95.71	0
L_39567_c0_g2_i1	profilin-1	0	C_15886_c0_g1_i1	profilin-1	615	97.97	0
L_5103_c0_g1_i1	trans-resveratrol di-O-methyltransferase-like	0	C_39904_c0_g1_i1	trans-resveratrol di-O-methyltransferase-like	430	79.15	0
L_24431_c0_g6_i1	60S ribosomal protein L24	0	C_1942_c0_g1_i1	60S ribosomal protein L24	278	97.76	0
L_3220_c0_g1_i1		0	C_1273_c0_g1_i1	chlorophyll a-b binding protein 6, chloroplastic	264	92.97	3E-47
L_16735_c0_g2_i2	uncharacterized protein LOC105047938	0	C_39063_c0_g1_i1	uncharacterized protein LOC105047938	172	92.49	0
L_256_c0_g1_i2	Os06g0133500	0	C_16734_c1_g2_i1	Os06g0133500	151	92.07	9E-165

Common genes with TPM value ≥50 between the two species, except when the TPM values of both genes is < 100. The genes were sorted based on the TPM value of C. latifolia along with the corresponding genes of C. capitulata. Note that there were no cases of genes that were highly expressed in both species. This pattern strongly suggests changes in the gene expression regulatory system due to divergence of two species
*neoculin-related transcripts (cf. Figure 5 and Additional file 6)
^aPident and E-value are BLASTN results performed with C. latifolia as query against C. capitulata

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