Identification and Evolution of LRR VIII-2 Subfamily Genes in Four Model Plant Species

doi:10.11983/CBB19157

Abstract

Abstract: Whole-genome duplication and tandem duplication are two important mechanisms for gene duplication, which play important roles in promoting the genomic and genetic diversity. In Arabidopsis, AtLRR-RLK encodes receptor-like kinases rich in leucine repeats, which is a multi-gene family arising from large-scale gene expansion during angiosperm evolution. It is composed of 15 subfamilies, among which, AtLRR VIII-2 is the subfamily with the highest proportion of tandem repeats. In this study, we use the genes in LRR VIII-2 as an example to analyze the gene expansion and differential retention in four model plants (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Carica papaya). Results showed that paralogous gene pairs were identified in the LRR VIII-2 subfamily in Arabidopsis, poplar and grape, while no such pair was found in papaya. The LRR VIII-2 subfamily expanded the most significantly in poplar and moderately expanded in Arabidopsis and grape, but some genes of the LRR VIII-2 subfamily in papaya have been lost. In addition, the paralogous and orthologous genes in the LRR VIII-2 subfamily were under strong purifying selection in the four investigated plant species, except for a pair of paralogous genes in poplar. An in-depth phylogenetic analysis of the LRR VIII-2 subfamily helps to understand the role and significance of gene duplication in plant evolution, and provides useful information for predicting the function of homologous gene among different species. This analytical pipeline is also applicable for deciphering the evolution history of other gene families.

Key words: receptor-like protein kinases, leucine-rich repeats, whole-genome duplication, tandem duplication

Chenyang Yan,Yingnan Chen. Identification and Evolution of LRR VIII-2 Subfamily Genes in Four Model Plant Species[J]. Chinese Bulletin of Botany, 2020, 55(4): 442-456.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB19157

https://www.chinbullbotany.com/EN/Y2020/V55/I4/442

Figures/Tables 8

References 52

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Primer name	Primer sequence (5'-3')	Length (bp)
P7-F	GGGTATTTTATGAGAAAGGGGA	128
P7-R	CAACTTTGACACTTCCTGGGT	128
P8-F	CTCCGGCCTTCCATGTCTAC	285
P8-R	TGGGAATTTCTCTCGCGTTG	285
P26-F	CAGAGCTACACAAACCACAGAAG	158
P26-R	TGAGCATTCCCTTGTAAACAGAG	158
P27-F	TACGAGCACCCTTCAACACC	300
P27-R	AAGCGTCATGGTCGTGCTT	300
UBQ-F	GTTGATTTTTGCTGGGAAGC	192
UBQ-R	GATCTTGGCCTTCACGTTGT	192

Primer name	Primer sequence (5'-3')	Length (bp)
P7-F	GGGTATTTTATGAGAAAGGGGA	128
P7-R	CAACTTTGACACTTCCTGGGT	128
P8-F	CTCCGGCCTTCCATGTCTAC	285
P8-R	TGGGAATTTCTCTCGCGTTG	285
P26-F	CAGAGCTACACAAACCACAGAAG	158
P26-R	TGAGCATTCCCTTGTAAACAGAG	158
P27-F	TACGAGCACCCTTCAACACC	300
P27-R	AAGCGTCATGGTCGTGCTT	300
UBQ-F	GTTGATTTTTGCTGGGAAGC	192
UBQ-R	GATCTTGGCCTTCACGTTGT	192

Code			Gene ID	Chr.	Genomic location			No. of exons		Protein length (aa)	Extracellular domain
A1			AT1G07650	At1	2359111-2366736			25		1020	LRR10
A2			AT1G16670	At1	5697216-5699870			6		390	K
A3			AT1G29720	At1	10393659-10399873			25		1019	LRR12
A4			AT1G29730	At1	10400564-10405913			24		969	LRR11
A5			AT1G29740	At1	10407220-10413119			26		1078	LRR5
A6			AT1G29750	At1	10413853-10420774			24		1021	LRR9
A7			AT1G53420	At1	19926626-19931494			23		953	LRR10
A8			AT1G53430	At1	19934987-19941185			23		1030	LRR9
A9			AT1G53440	At1	19945869-19951562			23		1035	LRR11
A10			AT1G56120	At1	20987128-20993572			23		1047	LRR11
A11			AT1G56130	At1	20994746-21001013			24		1032	LRR6
A12			AT1G56140	At1	21001269-21007855			24		1033	LRR6
A13			AT3G09010	At3	2749908-2752390			6		393	K
A14			AT3G14840	At3	4988008-4994109			24		1020	LRR11
P1			Potri.001G308600	Pt01	31227276-31234883			24		1006	LRR10
P2			Potri.001G385200	Pt01	40032658-40043384			24		1007	LRR11
P3			Potri.001G385300	Pt01	40046269-40056753			24		1021	LRR13
P4			Potri.001G385400	Pt01	40060761-40069904			24		1036	LRR10
P5			Potri.001G385900	Pt01	40135506-40145556			22		982	LRR7
P6			Potri.001G386300	Pt01	40164017-40178014			23		989	LRR5
P7			Potri.001G393200	Pt01	41232410-41235419			6		396	K
P8			Potri.001G438400	Pt01	47008564-47013154			6		396	K
P9			Potri.003G025600	Pt03	3062484-3069540			22		944	LRR3
P10			Potri.003G025800	Pt03	3088186-3100889			24		999	LRR3
P11			Potri.003G148000	Pt03	16311568-16319951			21		1041	LRR13
P12			Potri.004G040200	Pt04	3050127-3055020			6		373	K
P13			Potri.004G063200	Pt04	5205009-5216081			23		1092	LRR12
P14			Potri.004G063500	Pt04	5238500-5250295			24		1011	LRR9
P15			Potri.004G063600	Pt04	5255561-5259093			6		468	TK
P16			Potri.004G063900	Pt04	5275636-5279061			6		464	TK
P17			Potri.004G135500	Pt04	15551257-15559647			24		1029	LRR12
Code	Gene ID			Chr.		Genomic location			No. of exons	Protein length (aa)	Extracellular domain
P18	Potri.006G128500			Pt06		10474234-10477075			5	471	K
P19	Potri.007G067900			Pt07		8907797-8916407			24	1036	LRR12
P20	Potri.008G040800			Pt08		2314252-2320106			4	341	K
P21	Potri.010G221400			Pt10		20632758-20635063			6	366	K
P22	Potri.011G049600			Pt11		4238297-4243676			5	374	K
P23	Potri.011G072300			Pt11		6917401-6930365			24	1024	LRR8
P24	Potri.011G075400			Pt11		7247330-7259126			22	1003	LRR9
P25	Potri.011G106400			Pt11		12955841-12965039			22	1015	LRR11
P26	Potri.011G112000			Pt11		13684010-13689252			6	396	K
P27	Potri.011G142100			Pt11		16335090-16338863			6	393	K
P28	Potri.016G114800			Pt16		11913776-11918410			7	385	K
P29	Potri.019G005200			Pt19		554428-564520			24	801	LRR5
P30	Potri.019G005300			Pt19		582783-593615			24	1003	LRR8
P31	Potri.019G005700			Pt19		655851-664479			23	978	LRR6
P32	Potri.019G005900			Pt19		681330-690210			24	990	LRR3
P33	Potri.019G006000			Pt19		699799-708891			24	964	LRR5
P34	Potri.019G007900			Pt19		921639-930444			23	1002	LRR3
P35	Potri.019G008900			Pt19		1038688-1047049			24	972	LRR9
P36	Potri.019G009700			Pt19		1141831-1151301			13	988	LRR3
P37	Potri.019G009800			Pt19		1159163-1167756			24	989	LRR9
P38	Potri.T072700			scaffold_79		11693-18613			22	945	LRR8
V1	GSVIVT01006444001			chrUn		26044571-26050096			8	441	K
V2	GSVIVT01013608001			chrUn		1284866-1301072			24	994	LRR12
V3	GSVIVT01013612001			chrUn		1429686-1453826			21	897	LRR10
V4	GSVIVT01013621001			chrUn		1735676-1793223			24	911	LRR11
V5	GSVIVT01014113001			Vv19		501306-518217			23	1036	LRR9
V6	GSVIVT01014134001			Vv19		669185-677944			24	1021	LRR10
V7	GSVIVT01014138001			Vv19		719037-726465			23	935	LRR10
V8	GSVIVT01014145001			Vv19		793325-800964			21	904	LRR5
V9	GSVIVT01014147001			Vv19		813603-825355			24	1063	LRR5
V10	GSVIVT01014150001			Vv19		846312-864401			30	1181	LRR11
V11	GSVIVT01014221001			Vv19		1629917-1636613			6	385	K
V12	GSVIVT01020456001			Vv19		19137067-19142116			6	385	K
V13	GSVIVT01020786001			Vv12		1992495-2002600			24	1011	LRR10
V14	GSVIVT01021280001			Vv10		3340198-3390494			24	1107	LRR10
V15	GSVIVT01021285001			Vv10		3439036-3462765			29	1144	LRR12
V16	GSVIVT01021289001			Vv10		3527408-3540220			24	1008	LRR10
V17	GSVIVT01021291001			Vv10		3556246-3578182			24	1017	LRR11
V18	GSVIVT01024760001			Vv6		7166910-7169739			6	372	K
V19	GSVIVT01025676001			Vv8		13018070-13020594			7	433	K
V20	GSVIVT01033973001			Vv8		16186419-16192809			6	380	K
V21	GSVIVT01038011001			Vv10		12545889-12562513			24	1003	LRR11
C1	evm.model.supercontig_124.16			supercontig_124		342359-355054			9	651	TK
C2	evm.model.supercontig_124.19			supercontig_124		400979-417373			8	604	TK
C3	evm.model.supercontig_131.56			supercontig_131		437441-440461			6	380	K
C4	evm.model.supercontig_163.18			supercontig_163		423778-427253			6	397	K
Code		Gene ID		Chr.			Genomic location	No. of exons		Protein length (aa)	Extracellular domain
C5		evm.model.supercontig_2076.1		supercontig_2076			157-766	2		173	K
C6		evm.model.supercontig_748.4		supercontig_748			17410-21951	9		583	TK
C7		evm.model.supercontig_77.35		supercontig_77			331417-334856	10		636	LRR1
C8		evm.model.supercontig_77.40		supercontig_77			398441-404475	22		880	LRR10
C9		evm.model.supercontig_77.43		supercontig_77			453480-459449	23		829	LRR9
C10		evm.model.supercontig_864.1		supercontig_864			13501-16944	6		419	K
C11		evm.TU.contig_37590.1		contig_37590			240-2161	6		365	LRR1

Code			Gene ID	Chr.	Genomic location			No. of exons		Protein length (aa)	Extracellular domain
A1			AT1G07650	At1	2359111-2366736			25		1020	LRR10
A2			AT1G16670	At1	5697216-5699870			6		390	K
A3			AT1G29720	At1	10393659-10399873			25		1019	LRR12
A4			AT1G29730	At1	10400564-10405913			24		969	LRR11
A5			AT1G29740	At1	10407220-10413119			26		1078	LRR5
A6			AT1G29750	At1	10413853-10420774			24		1021	LRR9
A7			AT1G53420	At1	19926626-19931494			23		953	LRR10
A8			AT1G53430	At1	19934987-19941185			23		1030	LRR9
A9			AT1G53440	At1	19945869-19951562			23		1035	LRR11
A10			AT1G56120	At1	20987128-20993572			23		1047	LRR11
A11			AT1G56130	At1	20994746-21001013			24		1032	LRR6
A12			AT1G56140	At1	21001269-21007855			24		1033	LRR6
A13			AT3G09010	At3	2749908-2752390			6		393	K
A14			AT3G14840	At3	4988008-4994109			24		1020	LRR11
P1			Potri.001G308600	Pt01	31227276-31234883			24		1006	LRR10
P2			Potri.001G385200	Pt01	40032658-40043384			24		1007	LRR11
P3			Potri.001G385300	Pt01	40046269-40056753			24		1021	LRR13
P4			Potri.001G385400	Pt01	40060761-40069904			24		1036	LRR10
P5			Potri.001G385900	Pt01	40135506-40145556			22		982	LRR7
P6			Potri.001G386300	Pt01	40164017-40178014			23		989	LRR5
P7			Potri.001G393200	Pt01	41232410-41235419			6		396	K
P8			Potri.001G438400	Pt01	47008564-47013154			6		396	K
P9			Potri.003G025600	Pt03	3062484-3069540			22		944	LRR3
P10			Potri.003G025800	Pt03	3088186-3100889			24		999	LRR3
P11			Potri.003G148000	Pt03	16311568-16319951			21		1041	LRR13
P12			Potri.004G040200	Pt04	3050127-3055020			6		373	K
P13			Potri.004G063200	Pt04	5205009-5216081			23		1092	LRR12
P14			Potri.004G063500	Pt04	5238500-5250295			24		1011	LRR9
P15			Potri.004G063600	Pt04	5255561-5259093			6		468	TK
P16			Potri.004G063900	Pt04	5275636-5279061			6		464	TK
P17			Potri.004G135500	Pt04	15551257-15559647			24		1029	LRR12
Code	Gene ID			Chr.		Genomic location			No. of exons	Protein length (aa)	Extracellular domain
P18	Potri.006G128500			Pt06		10474234-10477075			5	471	K
P19	Potri.007G067900			Pt07		8907797-8916407			24	1036	LRR12
P20	Potri.008G040800			Pt08		2314252-2320106			4	341	K
P21	Potri.010G221400			Pt10		20632758-20635063			6	366	K
P22	Potri.011G049600			Pt11		4238297-4243676			5	374	K
P23	Potri.011G072300			Pt11		6917401-6930365			24	1024	LRR8
P24	Potri.011G075400			Pt11		7247330-7259126			22	1003	LRR9
P25	Potri.011G106400			Pt11		12955841-12965039			22	1015	LRR11
P26	Potri.011G112000			Pt11		13684010-13689252			6	396	K
P27	Potri.011G142100			Pt11		16335090-16338863			6	393	K
P28	Potri.016G114800			Pt16		11913776-11918410			7	385	K
P29	Potri.019G005200			Pt19		554428-564520			24	801	LRR5
P30	Potri.019G005300			Pt19		582783-593615			24	1003	LRR8
P31	Potri.019G005700			Pt19		655851-664479			23	978	LRR6
P32	Potri.019G005900			Pt19		681330-690210			24	990	LRR3
P33	Potri.019G006000			Pt19		699799-708891			24	964	LRR5
P34	Potri.019G007900			Pt19		921639-930444			23	1002	LRR3
P35	Potri.019G008900			Pt19		1038688-1047049			24	972	LRR9
P36	Potri.019G009700			Pt19		1141831-1151301			13	988	LRR3
P37	Potri.019G009800			Pt19		1159163-1167756			24	989	LRR9
P38	Potri.T072700			scaffold_79		11693-18613			22	945	LRR8
V1	GSVIVT01006444001			chrUn		26044571-26050096			8	441	K
V2	GSVIVT01013608001			chrUn		1284866-1301072			24	994	LRR12
V3	GSVIVT01013612001			chrUn		1429686-1453826			21	897	LRR10
V4	GSVIVT01013621001			chrUn		1735676-1793223			24	911	LRR11
V5	GSVIVT01014113001			Vv19		501306-518217			23	1036	LRR9
V6	GSVIVT01014134001			Vv19		669185-677944			24	1021	LRR10
V7	GSVIVT01014138001			Vv19		719037-726465			23	935	LRR10
V8	GSVIVT01014145001			Vv19		793325-800964			21	904	LRR5
V9	GSVIVT01014147001			Vv19		813603-825355			24	1063	LRR5
V10	GSVIVT01014150001			Vv19		846312-864401			30	1181	LRR11
V11	GSVIVT01014221001			Vv19		1629917-1636613			6	385	K
V12	GSVIVT01020456001			Vv19		19137067-19142116			6	385	K
V13	GSVIVT01020786001			Vv12		1992495-2002600			24	1011	LRR10
V14	GSVIVT01021280001			Vv10		3340198-3390494			24	1107	LRR10
V15	GSVIVT01021285001			Vv10		3439036-3462765			29	1144	LRR12
V16	GSVIVT01021289001			Vv10		3527408-3540220			24	1008	LRR10
V17	GSVIVT01021291001			Vv10		3556246-3578182			24	1017	LRR11
V18	GSVIVT01024760001			Vv6		7166910-7169739			6	372	K
V19	GSVIVT01025676001			Vv8		13018070-13020594			7	433	K
V20	GSVIVT01033973001			Vv8		16186419-16192809			6	380	K
V21	GSVIVT01038011001			Vv10		12545889-12562513			24	1003	LRR11
C1	evm.model.supercontig_124.16			supercontig_124		342359-355054			9	651	TK
C2	evm.model.supercontig_124.19			supercontig_124		400979-417373			8	604	TK
C3	evm.model.supercontig_131.56			supercontig_131		437441-440461			6	380	K
C4	evm.model.supercontig_163.18			supercontig_163		423778-427253			6	397	K
Code		Gene ID		Chr.			Genomic location	No. of exons		Protein length (aa)	Extracellular domain
C5		evm.model.supercontig_2076.1		supercontig_2076			157-766	2		173	K
C6		evm.model.supercontig_748.4		supercontig_748			17410-21951	9		583	TK
C7		evm.model.supercontig_77.35		supercontig_77			331417-334856	10		636	LRR1
C8		evm.model.supercontig_77.40		supercontig_77			398441-404475	22		880	LRR10
C9		evm.model.supercontig_77.43		supercontig_77			453480-459449	23		829	LRR9
C10		evm.model.supercontig_864.1		supercontig_864			13501-16944	6		419	K
C11		evm.TU.contig_37590.1		contig_37590			240-2161	6		365	LRR1

	Gene pair	K_a/K_s	Gene pair	K_a/K_s	Gene pair	K_a/K_s
Paralogous	A4-A5	0.2184	P9-P25	0.3214	P32-P36	0.4003
	A8-A9	0.2680	P10-P17	0.1596	P32-P37	0.6808
	A10-A11	0.2870	P10-P25	0.3488	P32-P38	0.3088
	A10-A12	0.2910	P12-P22	0.2362	P33-P34	0.6734
	A11-A12	0.2498	P13-P23	0.2871	P33-P35	0.5076
	P1-P29	0.3010	P14-P15	0.2140	P33-P36	0.5615
	P1-P30	0.3292	P14-P16	0.1985	P33-P37	0.6011
	P1-P31	0.3020	P15-P16	1.4030	P33-P38	0.3093
	P1-P32	0.3077	P15-P24	0.3642	P34-P35	0.5274
	P1-P33	0.2955	P16-P24	0.3469	P34-P36	0.6011
	P1-P34	0.3075	P20-P21	0.1211	P34-P37	0.7145
	P1-P35	0.3188	P29-P30	0.3678	P34-P38	0.3139
	P1-P36	0.2997	P29-P31	0.3321	P35-P36	0.3943
	P1-P37	0.3122	P29-P32	0.3381	P35-P37	0.5829
	P1-P38	0	P29-P33	0.3334	P35-P38	0.3204
	P3-P4	0.3683	P29-P34	0.3317	P36-P37	0.4718
	P3-P5	0.3731	P29-P35	0.3411	P36-P38	0.2992
	P3-P6	0.4963	P29-P36	0.3215	P37-P38	0.3134
	P3-P9	0.3791	P29-P37	0.3392	V2-V3	0.3479
	P3-P10	0.4125	P29-P38	0.3169	V2-V4	0.2818
	P3-P25	0.3422	P30-P31	0.5422	V2-V21	0.5377
	P4-P5	0.4843	P30-P32	0.6659	V3-V4	0.3152
	P4-P6	0.3907	P30-P33	0.6512	V3-V21	0.3481
	P4-P9	0.7093	P30-P34	0.8013	V4-V21	0.2963
	P4-P10	0.4706	P30-P35	0.5957	V6-V7	0.3152
	P4-P17	0.1770	P30-P36	0.5292	V6-V8	0.2935
	P4-P25	0.3206	P30-P37	0.6763	V6-V9	0.3034
	P5-P6	0.3712	P30-P38	0.3368	V6-V10	0.2833
	P5-P9	0.6021	P31-P32	0.4655	V7-V8	0.7300
	P5-P10	0.8590	P31-P33	0.4989	V7-V9	0.5629
	P5-P17	0.1715	P31-P34	0.5435	V7-V10	0.4047
	P5-P25	0.3456	P31-P35	0.4251	V8-V9	0.4763
	P6-P9	0.4063	P31-P36	0.3099	V8-V10	0.3629
	P6-P10	0.4357	P31-P37	0.5370	V9-V10	0.3855
	P6-P25	0.3556	P31-P38	0.3142	V14-V15	0.4844
	P7-P26	0.5268	P32-P33	0.5711	V14-V16	0.2626
	P8-P27	0.2579	P32-P34	0.6597	V15-V16	0.3233
	P9-P10	0.6507	P32-P35	0.5461	V16-V17	0.2770
	P9-P17	0.1859
Orthologous	P7-C3	0.2223	P28-C4	0.2070	C4-V20	0.1760
Orthologous	P25-V10	0.2441	C3-V11	0.2574	C9-V10	0.2076