Chloroplast Genome Characteristics and Phylogenetic Analysis of Scrophulariaceae

doi:10.13560/j.cnki.biotech.bull.1985.2024-0753

Abstract

Abstract:

Objective To explore the characteristics and phylogenetic relationships of chloroplast genome of the Scrophulariaceae. Method The chloroplast genomes of Hubei Scrophularia ningpoensis were sequenced, assembled, and annotated. Additionally, a total of 46 complete chloroplast genomes of Scrophulariaceae were downloaded from GenBank database for comparative analysis. Result The full length of the chloroplast genome in Scrophulariaceae ranges from 142 336 to 154 710 bp, with a GC content between 37.7% and 38.1%. The genome shows a typical quadripartite structure, comprising a large single copy region of 83 531 to 97 103 bp and a small single copy region of 17 375 to 18 600 bp, as well as an inverted repeat region spanning 13 497 to 25 695 bp. Comparative analysis of chloroplast gene composition within the Scrophulariaceae reveals evolutionary patterns of gene gain and loss. Collinearity analysis indicates that the genomic arrangement of the Scrophulariaceae chloroplast genome is relatively conserved, although instances of genome rearrangement events have also been observed. Analysis of long repeat sequences shows that the majority of the Scrophulariaceae chloroplast genome consists of forward repeats and palindromic repeats. Furthermore, simple repeat sequence analysis identified 117 to 156 SSR sites within the Scrophulariaceae chloroplast genome, with single nucleotides composed of A/T being the most frequent, accounting for 85.50% to 91.50% of the total. Relative synonymous codon usage (RSCU) analysis identified 25 optimal codons, the majority of which ended with A/U. Divergence time analysis suggests that the common ancestor of Scrophulariaceae and closely related species diverged approximately 70.5 million years ago (MYA) and formed a monophyletic branch around 52.4 MYA, with most species of Scrophulariaceae appearing nearly 50 MYA. Conclusion Although the chloroplast genomes of the Scrophulariaceae demonstrate similar structural characteristics, they have also experienced gene acquisition and loss as well as genome rearrangement events during their evolutionary history. A more refined phylogenetic tree of the Scrophulariaceae has been constructed based on the chloroplast genomes. Furthermore, the divergence time analysis indicates that the rapid diversification of Scrophulariaceae species mainly occurre around 50 million years ago.

Key words: Scrophulariaceae, chloroplast genome, sequence features, phylogenetic analysis

LI Bin, SU Xiang-ping, LIU Chang, WANG Yu-bing, ZHANG Yong-hong, ZHOU Chao, XU Qing. Chloroplast Genome Characteristics and Phylogenetic Analysis of Scrophulariaceae[J]. Biotechnology Bulletin, 2025, 41(3): 240-254.

Figures/Tables 9

References 54

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属名 Genus	物种名 Organism	登录号 Accession	GC含量 GC/%	Size/bp				基因数量 Gene number				参考文献 Reference
属名 Genus	物种名 Organism	登录号 Accession	GC含量 GC/%	Total	LSC	IR	SSC	Total	PCGs	rRNA	tRNA	参考文献 Reference
Bontia	B. daphnoides	NC_050952.1	37.8	153 946	85 008	25 169	18 600	113	80	4	29	［32］
Buddleja	B. alternifolia	MN395662.1	38.0	154 357	85 405	25 441	18 070	114	80	4	30	［33］
	B. alternifolia	NC_057238.1	38.0	154 280	85 330	25 440	18 070	115	80	4	31	［34］
	B. colvilei	MH411148.1	38.1	154 228	85 203	25 553	17 919	114	80	4	30	［35］
	B. colvilei	NC_042766.1	38.1	154 225	85 200	25 553	17 919	114	80	4	30	［35］
	B. globosa	NC_068052.1	38.1	154 034	84 909	25 524	18 077	114	80	4	30	［36］
	B. sessilifolia	MH411150.1	38.1	154 204	85 181	25 559	17 905	114	80	4	30	［35］
	B. sessilifolia	MH411151.1	38.1	154 710	85 687	25 559	17 905	114	80	4	30	［35］
	B. sessilifolia	NC_042767.1	38.1	154 202	85 179	25 559	17 905	114	80	4	30	［35］
Diocirea	D. violacea	NC_050957.1	37.8	151 900	87 779	22 936	18 250	112	80	4	28	［35］
Eremophila	E. cuneifolia	NC_068053.1	37.8	151 927	87 819	22 925	18 258	114	80	4	30	［32］
	E. gibbifolia	NC_050954.1	37.9	148 717	90 431	20 147	17 992	112	80	4	28	［36］
	E. lanceolata	NC_068054.1	37.9	151 565	87 680	22 812	18 261	114	80	4	30	［32］
	E. latrobei subsp. filiformis	OL977700.1	37.9	151 550	87 692	22 798	18 262	114	80	4	30	［36］
	E. longifolia	NC_068055.1	37.9	151 629	87 699	22 832	18 266	114	80	4	30	［36］
	E. maculata subsp. brevifolia	OL977702.1	37.8	142 336	97 103	13 497	18 239	114	80	4	30	［36］
	E. magnifica subsp. magnifica	OL977703.1	37.8	151 922	87 933	22 971	18 047	114	80	4	30	［36］
	E. magnifica subsp. velutina	OL977704.1	37.8	151 919	87 929	22 971	18 048	114	80	4	30	［36］
	E. oppositifolia	NC_050958.1	37.9	151 715	87 798	22 834	18 277	112	80	4	28	［32］
	E. pilosa	NC_068056.1	37.9	151 541	87 684	22 798	18 261	114	80	4	30	［36］
	E. platycalyx subsp. pardalota	OL977706.1	37.7	151 947	87 902	22 966	18 113	114	80	4	30	［36］
	E. pusilliflora	NC_068057.1	37.9	151 725	87 845	22 803	18 274	114	80	4	30	［36］
	E. spongiocarpa	NC_068058.1	37.9	151 678	87 760	22 820	18 278	114	80	4	30	［36］
Leucophyllum	L. frutescens	NC_050953.1	37.8	154 253	85 003	25 551	18 148	113	80	4	29	［32］
Mimulicalyx	M. rosulatus	NC_068044.1	38.1	153 580	84 572	25 695	17 618	114	80	4	30	［36］
Mimulicalyx	M. rosulatus	OL977687.1	38.1	153 587	84 580	25 695	17 617	114	80	4	30	［36］
Myoporum	M. bontioides	NC_050956.1	37.9	151 742	87 680	23 026	18 010	112	80	4	28	［32］
Myoporum	M. laetum	NC_050955.1	37.9	151 725	87 724	22 997	18 007	112	80	4	28	［32］
Scrophularia	S. buergeriana	NC_031437.1	38.0	153 631	84 454	25 624	17 929	114	80	4	30	［37］
	S. dentata	KT428154.1	38.0	152 553	84 058	25 523	17 449	114	80	4	30	［38］
	S. dentata	OP018677.1	38.0	152 509	84 070	25 532	17 375	114	80	4	30	［39］
	S. incisa	NC_081995.1	38.0	152 481	83 944	25 535	17 467	114	80	4	30	［39］
	S. incisa	OP036429.1	38.0	152 600	84 067	25 534	17 465	113	80	4	29	［39］
	S. integrifolia	NC_081997.1	38.0	152 088	83 588	25 512	17 476	114	80	4	30	［39］
	S. kiriloviana	NC_081996.1	38.0	152 554	84 008	25 512	17 522	115	80	4	31	［39］
	S. kiriloviana	OP036427.1	38.0	152 365	83 891	25 500	17 474	114	80	4	30	［39］
	S. kiriloviana	OP036428.1	38.0	152 528	83 857	25 610	17 454	114	80	4	30	［39］
	S. ningpoensis	NC_053823.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	［40］
	S. ningpoensis	OR664113.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	-
	S. ningpoensis	OR664114.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	-
	S. takesimensis	KP718628.1	38.0	152 436	83 542	25 478	17 938	114	80	4	30	［37］
	S. takesimensis	NC_026202.1	38.1	152 425	83 531	25 478	17 938	113	80	4	29	［41］
Verbascum	V. blattaria	NC_085504.1	38.0	153 014	84 263	25 440	17 871	114	80	4	30	［42］
	V. chaixii	NC_085505.1	38.0	153 495	84 779	25 436	17 844	114	80	4	30	［42］
	V. chinense	NC_051533.1	38.0	153 618	84 834	25 482	17 828	114	80	4	30	［40］
	V. phoeniceum	NC_050920.1	38.0	153 348	84 601	25 430	17 887	114	80	4	30	［43］
	V. phoeniceum	ON121986.1	38.0	153 273	84 571	25 426	17 850	114	80	4	30	［42］
	V. songaricum	NC_085506.1	38.0	153 291	84 534	25 459	17 839	114	80	4	30	［42］

属名 Genus	物种名 Organism	登录号 Accession	GC含量 GC/%	Size/bp				基因数量 Gene number				参考文献 Reference
属名 Genus	物种名 Organism	登录号 Accession	GC含量 GC/%	Total	LSC	IR	SSC	Total	PCGs	rRNA	tRNA	参考文献 Reference
Bontia	B. daphnoides	NC_050952.1	37.8	153 946	85 008	25 169	18 600	113	80	4	29	［32］
Buddleja	B. alternifolia	MN395662.1	38.0	154 357	85 405	25 441	18 070	114	80	4	30	［33］
	B. alternifolia	NC_057238.1	38.0	154 280	85 330	25 440	18 070	115	80	4	31	［34］
	B. colvilei	MH411148.1	38.1	154 228	85 203	25 553	17 919	114	80	4	30	［35］
	B. colvilei	NC_042766.1	38.1	154 225	85 200	25 553	17 919	114	80	4	30	［35］
	B. globosa	NC_068052.1	38.1	154 034	84 909	25 524	18 077	114	80	4	30	［36］
	B. sessilifolia	MH411150.1	38.1	154 204	85 181	25 559	17 905	114	80	4	30	［35］
	B. sessilifolia	MH411151.1	38.1	154 710	85 687	25 559	17 905	114	80	4	30	［35］
	B. sessilifolia	NC_042767.1	38.1	154 202	85 179	25 559	17 905	114	80	4	30	［35］
Diocirea	D. violacea	NC_050957.1	37.8	151 900	87 779	22 936	18 250	112	80	4	28	［35］
Eremophila	E. cuneifolia	NC_068053.1	37.8	151 927	87 819	22 925	18 258	114	80	4	30	［32］
	E. gibbifolia	NC_050954.1	37.9	148 717	90 431	20 147	17 992	112	80	4	28	［36］
	E. lanceolata	NC_068054.1	37.9	151 565	87 680	22 812	18 261	114	80	4	30	［32］
	E. latrobei subsp. filiformis	OL977700.1	37.9	151 550	87 692	22 798	18 262	114	80	4	30	［36］
	E. longifolia	NC_068055.1	37.9	151 629	87 699	22 832	18 266	114	80	4	30	［36］
	E. maculata subsp. brevifolia	OL977702.1	37.8	142 336	97 103	13 497	18 239	114	80	4	30	［36］
	E. magnifica subsp. magnifica	OL977703.1	37.8	151 922	87 933	22 971	18 047	114	80	4	30	［36］
	E. magnifica subsp. velutina	OL977704.1	37.8	151 919	87 929	22 971	18 048	114	80	4	30	［36］
	E. oppositifolia	NC_050958.1	37.9	151 715	87 798	22 834	18 277	112	80	4	28	［32］
	E. pilosa	NC_068056.1	37.9	151 541	87 684	22 798	18 261	114	80	4	30	［36］
	E. platycalyx subsp. pardalota	OL977706.1	37.7	151 947	87 902	22 966	18 113	114	80	4	30	［36］
	E. pusilliflora	NC_068057.1	37.9	151 725	87 845	22 803	18 274	114	80	4	30	［36］
	E. spongiocarpa	NC_068058.1	37.9	151 678	87 760	22 820	18 278	114	80	4	30	［36］
Leucophyllum	L. frutescens	NC_050953.1	37.8	154 253	85 003	25 551	18 148	113	80	4	29	［32］
Mimulicalyx	M. rosulatus	NC_068044.1	38.1	153 580	84 572	25 695	17 618	114	80	4	30	［36］
Mimulicalyx	M. rosulatus	OL977687.1	38.1	153 587	84 580	25 695	17 617	114	80	4	30	［36］
Myoporum	M. bontioides	NC_050956.1	37.9	151 742	87 680	23 026	18 010	112	80	4	28	［32］
Myoporum	M. laetum	NC_050955.1	37.9	151 725	87 724	22 997	18 007	112	80	4	28	［32］
Scrophularia	S. buergeriana	NC_031437.1	38.0	153 631	84 454	25 624	17 929	114	80	4	30	［37］
	S. dentata	KT428154.1	38.0	152 553	84 058	25 523	17 449	114	80	4	30	［38］
	S. dentata	OP018677.1	38.0	152 509	84 070	25 532	17 375	114	80	4	30	［39］
	S. incisa	NC_081995.1	38.0	152 481	83 944	25 535	17 467	114	80	4	30	［39］
	S. incisa	OP036429.1	38.0	152 600	84 067	25 534	17 465	113	80	4	29	［39］
	S. integrifolia	NC_081997.1	38.0	152 088	83 588	25 512	17 476	114	80	4	30	［39］
	S. kiriloviana	NC_081996.1	38.0	152 554	84 008	25 512	17 522	115	80	4	31	［39］
	S. kiriloviana	OP036427.1	38.0	152 365	83 891	25 500	17 474	114	80	4	30	［39］
	S. kiriloviana	OP036428.1	38.0	152 528	83 857	25 610	17 454	114	80	4	30	［39］
	S. ningpoensis	NC_053823.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	［40］
	S. ningpoensis	OR664113.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	-
	S. ningpoensis	OR664114.1	38.0	153 175	84 257	25 490	17 938	114	80	4	30	-
	S. takesimensis	KP718628.1	38.0	152 436	83 542	25 478	17 938	114	80	4	30	［37］
	S. takesimensis	NC_026202.1	38.1	152 425	83 531	25 478	17 938	113	80	4	29	［41］
Verbascum	V. blattaria	NC_085504.1	38.0	153 014	84 263	25 440	17 871	114	80	4	30	［42］
	V. chaixii	NC_085505.1	38.0	153 495	84 779	25 436	17 844	114	80	4	30	［42］
	V. chinense	NC_051533.1	38.0	153 618	84 834	25 482	17 828	114	80	4	30	［40］
	V. phoeniceum	NC_050920.1	38.0	153 348	84 601	25 430	17 887	114	80	4	30	［43］
	V. phoeniceum	ON121986.1	38.0	153 273	84 571	25 426	17 850	114	80	4	30	［42］
	V. songaricum	NC_085506.1	38.0	153 291	84 534	25 459	17 839	114	80	4	30	［42］

氨基酸 Amino acid	密码子 Codon	B. daphnoides	B. globosa	D. violacea	E. oppositifolia	L. frutescens	M. rosulatus	M. laetum	S. ningpoensis	V. chinense
Ala	GCC		***							**
Ala	GCU				*		***	*
Arg	AGG							**
	CGA	*		*	***	**	*		***	**
	CGU		**
Asn	AAU									*
Asn	GAU	**	**		*		*	**	**	**
Glu	GAA	**	*	*	*		*	*	*
Gly	GGU	**	*		**	**		**	**	**
	GGA	**	*	***				*	*	*
His	CAU					*			*	**
Ile	AUA	*		*	*				*	*
Leu	UUA					*	*		*
	CUA					**			***
	UUG									**
Pro	CCA	**	**	***	**	***	*	**	*	**
	CCU	*	*			*
	CCC						***		***	*
Ser	UCC	*								*
	UCA	*	*	*	*			*	***
	AGU		*			*	***			*
TER	UGA	***	***	***	***	***	***	***	***	***
Thr	ACU	*	*		*	**		*
	ACC						**
Val	GUA	*				*		**

氨基酸 Amino acid	密码子 Codon	B. daphnoides	B. globosa	D. violacea	E. oppositifolia	L. frutescens	M. rosulatus	M. laetum	S. ningpoensis	V. chinense
Ala	GCC		***							**
Ala	GCU				*		***	*
Arg	AGG							**
	CGA	*		*	***	**	*		***	**
	CGU		**
Asn	AAU									*
Asn	GAU	**	**		*		*	**	**	**
Glu	GAA	**	*	*	*		*	*	*
Gly	GGU	**	*		**	**		**	**	**
	GGA	**	*	***				*	*	*
His	CAU					*			*	**
Ile	AUA	*		*	*				*	*
Leu	UUA					*	*		*
	CUA					**			***
	UUG									**
Pro	CCA	**	**	***	**	***	*	**	*	**
	CCU	*	*			*
	CCC						***		***	*
Ser	UCC	*								*
	UCA	*	*	*	*			*	***
	AGU		*			*	***			*
TER	UGA	***	***	***	***	***	***	***	***	***
Thr	ACU	*	*		*	**		*
	ACC						**
Val	GUA	*				*		**

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