Comparison of Codon Characteristics and Phylogeny of Chloroplast Genome between Ranunculaceae and Paeoniaceae

doi:10.7525/j.issn.1673-5102.2022.06.006

Abstract

Abstract:

To clarify the codon usage pattern and phylogenetic relationship of the chloroplast genome between Ranunculaceae and Paeoniaceae， 33 species of Ranunculaceae and seven species of Paeoniaceae were used as materials， and the analysis software CodonW， online software CUSP， and R software were used to analyze the codon characteristics of chloroplast genes， while the MAFFT software， MEGA software were used for phylogenetic analysis respectively. The results showed that the chloroplast genomes of Paeoniaceae and Ranunculaceae （except Columbine） had a high consistency of high frequency codons， with 29 high frequency codons， which were basically biased towards ending with A/U， but the optimal codon were different. The codon bias of the chloroplast genome of Ranunculaceae and Paeoniaceae was mainly influenced by natural selection， and the codon bias of the chloroplast genome of Paeoniaceae was more affected by natural selection than that of Ranunculaceae. The phylogenetic relationship based on the complete chloroplast genome sequence and the CDS sequence of the chloroplast genome showed that although the phylogenetic relationship based on the complete chloroplast genome sequence and the chloroplast genome CDS sequence of Paeoniaceae was different， they could be divided into the peony group and the peony group. The phylogenetic relationship of Ranunculaceae based on the entire chloroplast genome sequence did not conform to the classification relationship of Chinese flora， but it supported the division of Ranunculaceae into four subfamilies and 14 families. The analysis results supported that Paeoniaceae were independent from Ranunculaceae and Ranunculus， and were classified into Saxifraga.

Key words: Ranunculaceae, Paeoniaceae, chloroplast genome, codons, phylogenetic

CLC Number:

S682.1+2

Yingtong MU, Dongchang FAN, Lijuan LÜ, Xiajie LI, Jingshi LU, Xiaoming ZHANG. Comparison of Codon Characteristics and Phylogeny of Chloroplast Genome between Ranunculaceae and Paeoniaceae[J]. Bulletin of Botanical Research, 2022, 42(6): 964-975.

Figures/Tables 11

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科 family	编号 Code	物种 Species	大小 Length /bp	GenBank ID
芍药科 Paeoniaceae	1	Paeonia lactiflora	152 872	MN463100.1
	2	Paeonia veitchii voucher PANOSUBP20151011	152 682	NC_032401
	3	Paeonia decomposita	152 601	NC_039425.1
	4	Paeonia delavayi	152 872	MN463100.1
	5	Paeonia jishanensis voucher PJISH20180113	152 628	MG991935.1
	6	Paeonia rockii	152 821	NC_037772.1
	7	Paeonia suffruticosa	152 811	MH793271.1
毛茛科 Ranunculaceae	8	Actaea dahurica voucher ZW12-003	159 370	NC_041533.1
	9	Actaea asiatica voucher ZR11-020	159 638	NC_041525.1
	10	Adonis coerulea	157 033	MK253469.1
	11	Adonis sutchuenensis voucher SL12-053	157 603	NC_041474.1
	12	Anemone henryi	159 276	NC_039465.1
	13	Anemone reflexa voucher LY2019041111	160 910	MW043774.1
	14	Anemone taipaiensis	162 084	MK843819.1
	15	Aquilegia rockii	162 123	NC_046738.1
	16	Aquilegia barnebyi	161 954	MN882557.1
	17	Callianthemun alatavicum	156 538	MK253466.1
	18	Caltha palustris	155 325	MK253465
	19	Clematis guniuensis	159 682	NC_050373.1
	20	Clematis terniflora	159 528	KJ956785.1
	21	Delphinium anthriscifolium	155 077	MK253461.1
	22	Delphinium maackianum	154 484	MN648402.1
	23	Helleborus thibetanus	154 944	MK253456.1
	24	Isopyrum manshuricum voucher ZR11-028	151 243	NC_041541.1
	25	Nigella damascena	155 234	MN648403.1
	26	Oxygraphis glacialis voucher ZR11-016	155 434	MK569489.1
	27	Ranunculus bungei	156 082	MK253468.1
	28	Ranunculus macranthus	155 129	DQ359689.1
	29	Thalictrum foeniculaceum	155 923	MT922012.1
	30	Thalictrum minus	156 201	MK253450.1
	31	Trollius chinensis	160 191	NC_031849.1
	32	Trollius farreri	160 611	NC_050872.1
	33	Dichocarpum fargesii voucher ZR11-017	153 134	MK569485.1
	34	Dichocarpum dalzielii	153 110	MK253459.1
	35	Pulsatilla chinensis	162 052	NC_039452.1
	36	Consolida ajacis voucher DXS11-018	155 900	MK569484.1
	37	Beesia calthifolia	158 117	MK253467.1
	38	Calathodes oxycarpa voucher ZW12-004	160 415	NC_041475.1
	39	Urophysa rockii	158 512	NC_039742.1
	40	Aconitum kusnezoffii	158 122	MK253471.1

编号 Code	Codons	GC1	GC2	GC3	GCall	ENC	编号 Code	Codons	GC1	GC2	GC3	GCall	ENC
1	24 387	0.460 4	0.383 5	0.314 1	0.386 0	51.01	21	24 418	0.460 3	0.384 6	0.308 7	0.384 5	50.48
2	24 219	0.460 9	0.384 2	0.313 0	0.386 0	51.02	22	24 419	0.460 2	0.384 9	0.307 8	0.384 3	50.43
3	24 178	0.461 0	0.383 7	0.311 4	0.385 4	50.87	23	24 661	0.457 0	0.381 2	0.304 2	0.380 8	50.27
4	24 179	0.461 3	0.383 8	0.313 2	0.386 1	51.06	24	23 950	0.473 2	0.383 7	0.333 5	0.396 8	52.26
5	24 471	0.460 7	0.383 2	0.311 9	0.385 3	50.88	25	24 359	0.470 6	0.385 7	0.321 6	0.392 7	51.63
6	24 053	0.433 6	0.400 4	0.322 7	0.385 6	51.67	26	24 431	0.458 4	0.381 4	0.303 8	0.381 2	50.24
7	24 791	0.459 8	0.382 2	0.313 5	0.385 1	50.95	27	24 780	0.459 6	0.382 2	0.303 7	0.381 9	50.22
8	24 807	0.461 0	0.384 9	0.314 3	0.386 7	51.02	28	24 696	0.458 4	0.381 8	0.305 6	0.381 9	50.44
9	24 803	0.461 2	0.385 0	0.314 7	0.386 9	51.05	29	24 810	0.460 1	0.384 2	0.312 7	0.385 7	50.85
10	24 623	0.458 1	0.384 4	0.303 2	0.381 9	50.15	30	24 557	0.461 7	0.384 9	0.314 5	0.387 0	50.99
11	24 498	0.458 5	0.384 3	0.303 9	0.382 3	50.18	31	24 700	0.459 1	0.384 5	0.307 2	0.383 6	50.44
12	25 900	0.458 1	0.381 9	0.307 3	0.382 4	50.49	32	24 708	0.459 4	0.384 2	0.307 1	0.383 6	50.43
13	25 577	0.458 4	0.383 4	0.305 0	0.382 3	50.36	33	24 765	0.460 4	0.385 5	0.311 4	0.385 8	50.83
14	25 010	0.457 9	0.381 7	0.303 2	0.380 9	50.23	34	24 652	0.459 4	0.385 1	0.308 2	0.384 2	50.45
15	23 729	0.471 2	0.386 9	0.323 9	0.394 0	57.56	35	24 507	0.463 5	0.383 4	0.309 2	0.385 3	50.55
16	23 927	0.397 4	0.430 5	0.350 4	0.392 8	53.10	36	24 769	0.459 4	0.383 9	0.310 8	0.384 7	50.75
17	24 747	0.457 9	0.383 7	0.306 0	0.382 5	50.37	37	24 741	0.459 7	0.384 1	0.310 7	0.384 8	50.74
18	24 848	0.459 4	0.383 7	0.306 3	0.383 1	50.50	38	25 328	0.455 5	0.379 9	0.306 6	0.380 7	50.55
19	24 973	0.459 1	0.381 5	0.306 7	0.382 4	50.49	39	24 688	0.464 9	0.388 5	0.326 4	0.393 3	51.92
20	25 537	0.460 1	0.383 1	0.306 7	0.383 3	50.48	40	24 445	0.461 2	0.384 2	0.306 8	0.384 1	50.29

	R						F		L						I			M	V				S						Y		C		Q		E		H		G				N		K		P				T				W	A
	AGA	AGG	CGU	CGC	CGA	CGG	UUU	UUC	UUA	UUG	CUU	CUC	CUA	CUG	AUU	AUC	AUA	AUG	GUU	GUA	GUC	GUG	UCU	UCC	UCA	UCG	AGU	AGC	UAU	UAC	UGU	UGC	CAA	CAG	GAA	GAG	CAU	CAC	GGU	GGC	GGA	GGG	AAU	AAC	AAA	AAG	CCU	CCC	CCA	CCG	ACU	ACA	ACC	ACG	UGG	GCU	GCC	GCA	GCG
1
15
16
17

编号 No.	R						F		L						I			M	V				S						Y		C		Q		E		H		G				N		K		P				T				W	A
编号 No.	AGA	AGG	CGU	CGC	CGA	CGG	UUU	UUC	UUA	UUG	CUU	CUC	CUA	CUG	AUU	AUC	AUA	AUG	GUU	GUA	GUC	GUG	UCU	UCC	UCA	UCG	AGU	AGC	UAU	UAC	UGU	UGC	CAA	CAG	GAA	GAG	CAU	CAC	GGU	GGC	GGA	GGG	AAU	AAC	AAA	AAG	CCU	CCC	CCA	CCG	ACU	ACA	ACC	ACG	UGG	GCU	GCC	GCA	GCG
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40

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