Bioinformatics Analysis of the TPS Gene Family in Coffee canephora

doi:10.11983/CBB15022

Abstract

Abstract: Terpenoids are catalyzed by terpenoid synthase and have important physiological, ecological and medicinal value. By integrating data for the Coffee canephora genome and transcriptome, terpenoid synthase genes from C. canephora were identified. Then, the molecular evolution, structure, duplication and expression pattern of the genes were analyzed. Finally, functional differentiation among the terpenoid synthase subfamilies was investigated. C. canephora contains 43 full-length terpenoid synthase genes, which can be divided into 5 subfamilies (a, b, c, e/f, g), with largely different gene structure. Amplification of the genes is mainly caused by tandem duplication. Also the expression pattern of C. canephora terpenoid synthases differs in different tissues. Functional differentiation between each terpenoid synthase subfamily may have several reasons; cis-regulatory elements in the gene promoter region may be strongly related to functional differentiation and the differentiation is mainly caused by the subfamily-specific amino acid.

Key words: bioinformatics, Coffee canephora, functional differentiation, molecular evolution, terpenoid synthase

Tian Cheng, Qiang Wei, Guanglin Li. Bioinformatics Analysis of the TPS Gene Family in Coffee canephora[J]. Chinese Bulletin of Botany, 2016, 51(2): 235-250.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB15022

https://www.chinbullbotany.com/EN/Y2016/V51/I2/235

Figures/Tables 10

References 45

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ID	Aa	PI	Conserved motifs				Loc^b	Tplen^c	Chr.	Strand	Begin	End
			RR(x)₈W	RXR	DDXXD	NSE/DTE
Cc01_g19400	822	5.69	N^a	N^a	N^a	N^a	C	54	1	-	36232113	36239469
Cc02_g11820	589	5.63	RR(x)₈W	RXR	DDXXD	NDXXTXXXE	C	36	2	+	9762146	9765886
Cc02_g11830	587	5.63	RR(x)₈W	RXR	DDXXD	NDXXTXXXE	C	34	2	+	9775928	9779555
Cc02_g11870	605	6.24	N^a	RXQ	DDXXD	DDXXSXXXE	C	32	2	+	9817486	9821171
Cc02_g12790	843	5.71	N^a	RXK	DDXXD	NDXXSXXXE	S	143	2	-	10962357	10968950
Cc02_g12800	721	5.93	N^a	RXK	DDXXD	NDXXSXXXE	_	-	2	-	10974562	10979896
Cc02_g20930	510	5	N^a	RXR	DDXXD	DDXXTXXXE	C	41	2	-	18646492	18649797
Cc02_g29500	487	5.83	RR(x)₈W	RXR	DDXXD	N^a	C	-	2	+	30876701	30879109
Cc02_g29590	553	5.1	RP(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	2	+	31081548	31090061
Cc02_g35640	599	5.32	RR(x)₈W	RXR	DDXXD	DDXXTXXXE	C	48	2	+	49559875	49563902
Cc03_g14100	569	5.51	RL(x)₈W	RXR	DGXXD	NDXXSXXXE	_	-	3	+	27992091	28002647
Cc04_g16380	567	5.66	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26533839	26536938
Cc04_g16390	470	5.68	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26575942	26580763
Cc04_g16400	568	5.62	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26628007	26631524
Cc04_g16520	545	5.71	RP(x)₈W	RXR	DDXXD	DDXXGXXXG	_	-	4	+	26837450	26841294
Cc04_g16530	571	5.07	RP(x)₈W	RXR	DDXXD	N^a	_	-	4	+	26861073	26866930
Cc05_g05380	612	5.99	N^a	RXR	DDXXD	NDXXSXXXE	_	-	5	+	19945840	19951165
Cc05_g05400	614	5.49	RR(x)₈W	RXR	DDXXD	NDXXSXXXE	C	42	5	+	19959720	19964609
Cc05_g05410	603	5.27	RR(x)₈W	RXR	DDXXD	NDXXSXXXE	C	42	5	+	19970432	19976641
Cc05_g05490	624	6.27	RR(x)₈W	RXR	DDXXD	NEXXTXXXE	M	35	5	+	20061653	20068755
Cc05_g05500	739	6.3	N^a	RXR	DDXXD	NEXXTXXXE	_	-	5	+	20064933	20069377
Cc05_g13060	551	5.44	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	5	-	26746571	26750238
Cc05_g13070	550	5.76	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	5	-	26767977	26770620
Cc08_g06940	553	5.33	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	8	-	18458061	18462018
Cc08_g06960	553	5.37	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	8	-	18474336	18480348
Cc08_g07420	714	5.35	N^a	RXV	DDXXD	NDXXTXXXE	_	-	8	-	19681648	19689451
Cc08_g07480	597	6.64	N^a	N^a	N^a	N^a	_	-	8	+	19801873	19809275
Cc08_g07530	735	6.47	N^a	N^a	N^a	N^a	S	22	8	+	20232648	20240540
Cc08_g07540	536	5.52	N^a	N^a	DDXXD	NDXXTXXXE	S	29	8	+	20247389	20255575
Cc10_g12310	565	5.3	RQ(x)₈S	RXM	DDXXD	NDXXTXXXE	C	40	10	+	21701855	21705459
Cc10_g12320	598	5.35	RQ(x)₈S	RXM	DDXXD	NDXXTXXXE	C	39	10	-	21708529	21712087
Cc10_g12360	544	5.25	KQ(x)₈W	RXI	DDXXD	NDXXTXXXE	_	-	10	+	21847515	21853384
Cc00_g06380	552	5.2	RQ(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	0	+	50283228	50288386
Cc00_g06390	581	5.57	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	M	83	0	-	50369458	50372316
Cc00_g06420	580	4.92	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	M	83	0	+	50428795	50431627
Cc00_g09030	553	5.18	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	0	+	78120342	78123629
Cc00_g13600	426	5.11	N^a	RXR	DDXXD	NDXXTXXXE	S	23	0	-	101152670	101155134
Cc00_g16490	584	5.63	N^a	RXR	DDXXD	DDXXTXXXE	C	44	0	+	112444838	112448504
Cc00_g16500	480	5.17	N^a	RXR	DDXXD	DDXXGXXXE	_	-	0	+	112472815	112475864
Cc00_g17280	693	5.37	N^a	N^a	N^a	N^a	_	-	0	+	115693382	115700157
Cc00_g20580	555	5.02	RQ(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	0	-	131112913	131117645
Cc00_g27830	609	5.25	RR(x)₈W	RXR	DDXXD	DDXXTXXXE	C	40	0	-	174429457	174432386
Cc00_g31970	459	9.03	N^a	N^a	N^a	N^a	_	-	0	-	189453118	189455434

ID	Aa	PI	Conserved motifs				Loc^b	Tplen^c	Chr.	Strand	Begin	End
			RR(x)₈W	RXR	DDXXD	NSE/DTE
Cc01_g19400	822	5.69	N^a	N^a	N^a	N^a	C	54	1	-	36232113	36239469
Cc02_g11820	589	5.63	RR(x)₈W	RXR	DDXXD	NDXXTXXXE	C	36	2	+	9762146	9765886
Cc02_g11830	587	5.63	RR(x)₈W	RXR	DDXXD	NDXXTXXXE	C	34	2	+	9775928	9779555
Cc02_g11870	605	6.24	N^a	RXQ	DDXXD	DDXXSXXXE	C	32	2	+	9817486	9821171
Cc02_g12790	843	5.71	N^a	RXK	DDXXD	NDXXSXXXE	S	143	2	-	10962357	10968950
Cc02_g12800	721	5.93	N^a	RXK	DDXXD	NDXXSXXXE	_	-	2	-	10974562	10979896
Cc02_g20930	510	5	N^a	RXR	DDXXD	DDXXTXXXE	C	41	2	-	18646492	18649797
Cc02_g29500	487	5.83	RR(x)₈W	RXR	DDXXD	N^a	C	-	2	+	30876701	30879109
Cc02_g29590	553	5.1	RP(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	2	+	31081548	31090061
Cc02_g35640	599	5.32	RR(x)₈W	RXR	DDXXD	DDXXTXXXE	C	48	2	+	49559875	49563902
Cc03_g14100	569	5.51	RL(x)₈W	RXR	DGXXD	NDXXSXXXE	_	-	3	+	27992091	28002647
Cc04_g16380	567	5.66	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26533839	26536938
Cc04_g16390	470	5.68	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26575942	26580763
Cc04_g16400	568	5.62	RP(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	4	+	26628007	26631524
Cc04_g16520	545	5.71	RP(x)₈W	RXR	DDXXD	DDXXGXXXG	_	-	4	+	26837450	26841294
Cc04_g16530	571	5.07	RP(x)₈W	RXR	DDXXD	N^a	_	-	4	+	26861073	26866930
Cc05_g05380	612	5.99	N^a	RXR	DDXXD	NDXXSXXXE	_	-	5	+	19945840	19951165
Cc05_g05400	614	5.49	RR(x)₈W	RXR	DDXXD	NDXXSXXXE	C	42	5	+	19959720	19964609
Cc05_g05410	603	5.27	RR(x)₈W	RXR	DDXXD	NDXXSXXXE	C	42	5	+	19970432	19976641
Cc05_g05490	624	6.27	RR(x)₈W	RXR	DDXXD	NEXXTXXXE	M	35	5	+	20061653	20068755
Cc05_g05500	739	6.3	N^a	RXR	DDXXD	NEXXTXXXE	_	-	5	+	20064933	20069377
Cc05_g13060	551	5.44	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	5	-	26746571	26750238
Cc05_g13070	550	5.76	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	_	-	5	-	26767977	26770620
Cc08_g06940	553	5.33	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	8	-	18458061	18462018
Cc08_g06960	553	5.37	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	8	-	18474336	18480348
Cc08_g07420	714	5.35	N^a	RXV	DDXXD	NDXXTXXXE	_	-	8	-	19681648	19689451
Cc08_g07480	597	6.64	N^a	N^a	N^a	N^a	_	-	8	+	19801873	19809275
Cc08_g07530	735	6.47	N^a	N^a	N^a	N^a	S	22	8	+	20232648	20240540
Cc08_g07540	536	5.52	N^a	N^a	DDXXD	NDXXTXXXE	S	29	8	+	20247389	20255575
Cc10_g12310	565	5.3	RQ(x)₈S	RXM	DDXXD	NDXXTXXXE	C	40	10	+	21701855	21705459
Cc10_g12320	598	5.35	RQ(x)₈S	RXM	DDXXD	NDXXTXXXE	C	39	10	-	21708529	21712087
Cc10_g12360	544	5.25	KQ(x)₈W	RXI	DDXXD	NDXXTXXXE	_	-	10	+	21847515	21853384
Cc00_g06380	552	5.2	RQ(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	0	+	50283228	50288386
Cc00_g06390	581	5.57	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	M	83	0	-	50369458	50372316
Cc00_g06420	580	4.92	RR(x)₈W	RXR	DDXXD	DDXXGXXXE	M	83	0	+	50428795	50431627
Cc00_g09030	553	5.18	RP(x)₈W	RXR	DDXXD	NDXXGXXXD	_	-	0	+	78120342	78123629
Cc00_g13600	426	5.11	N^a	RXR	DDXXD	NDXXTXXXE	S	23	0	-	101152670	101155134
Cc00_g16490	584	5.63	N^a	RXR	DDXXD	DDXXTXXXE	C	44	0	+	112444838	112448504
Cc00_g16500	480	5.17	N^a	RXR	DDXXD	DDXXGXXXE	_	-	0	+	112472815	112475864
Cc00_g17280	693	5.37	N^a	N^a	N^a	N^a	_	-	0	+	115693382	115700157
Cc00_g20580	555	5.02	RQ(x)₈W	RXR	DDXXD	NDXXSXXXE	_	-	0	-	131112913	131117645
Cc00_g27830	609	5.25	RR(x)₈W	RXR	DDXXD	DDXXTXXXE	C	40	0	-	174429457	174432386
Cc00_g31970	459	9.03	N^a	N^a	N^a	N^a	_	-	0	-	189453118	189455434

Gene duplication	Chromosome	Total pairs	Gene ID
Segmental duplication	2/5	1	Cc02_g11870/Cc05_g13060
Tandem duplication	2	3	Cc02_g11820/Cc02_g11830/Cc02_g11870 Cc02_g12790/Cc02_g12800 Cc02_g29500/Cc02_g29590
	4	2	Cc04_g16380/Cc04_g16390/Cc04_g16400 Cc04_g16520/Cc04_g16530
	5	2	Cc05_g05380/Cc05_g05400/Cc05_g05410/Cc05_g05490/Cc05_g05500 Cc05_g13060/Cc05_g13070
	8	2	Cc08_g06940/Cc08_g06960 Cc08_g07420/Cc08_g07480/Cc08_g07530/Cc08_g07540
	10	1	Cc10_g12310 /Cc10_g12320/Cc10_g12360
	0	2	Cc00_g06380/Cc00_g06390/Cc00_g06420 Cc00_g16490/Cc00_g16500

Gene duplication	Chromosome	Total pairs	Gene ID
Segmental duplication	2/5	1	Cc02_g11870/Cc05_g13060
Tandem duplication	2	3	Cc02_g11820/Cc02_g11830/Cc02_g11870 Cc02_g12790/Cc02_g12800 Cc02_g29500/Cc02_g29590
	4	2	Cc04_g16380/Cc04_g16390/Cc04_g16400 Cc04_g16520/Cc04_g16530
	5	2	Cc05_g05380/Cc05_g05400/Cc05_g05410/Cc05_g05490/Cc05_g05500 Cc05_g13060/Cc05_g13070
	8	2	Cc08_g06940/Cc08_g06960 Cc08_g07420/Cc08_g07480/Cc08_g07530/Cc08_g07540
	10	1	Cc10_g12310 /Cc10_g12320/Cc10_g12360
	0	2	Cc00_g06380/Cc00_g06390/Cc00_g06420 Cc00_g16490/Cc00_g16500

Tissue	Total number	Gene ID
Root	10	Cc02_g35640/Cc05_g05400/Cc04_g16520/Cc04_g16530/Cc00_g06420/ Cc00_g06390/Cc08_g07420/Cc08_g07530/Cc00_g31790/Cc00_g17280
Stamen	1	Cc05_g05410
Pistil	2	Cc05_g05490/Cc05_g05500
Leaf	5	Cc08_g06960/Cc00_g20580/Cc00_g06380/Cc05_g13070/Cc02_g12800
Perisperm	2	Cc02_g29500/Cc05_g13060
Endosperm	0	-