Analysis on Chloroplast Genomic Characteristics of Forsythia suspensa

doi:10.16420/j.issn.0513-353x.2020-0781

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (1): 187-199.doi: 10.16420/j.issn.0513-353x.2020-0781

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Analysis on Chloroplast Genomic Characteristics of Forsythia suspensa

SONG Yun, JIA Mengjun, CAO Yaping, LI Zheng, HE Jiaxin, WANG Yongfei, ZHANG Xinrui, QIAO Yonggang()

College of Life Sciences,ShanXi Agricultural University,Taigu,Shanxi 030801,China

Received:2021-04-28 Revised:2021-09-09 Online:2022-01-25 Published:2022-01-24
Contact: QIAO Yonggang E-mail:sxndqyg@126.com

Abstract

Abstract:

In order to explore the chloroplasts genomic characteristics of Forsythia suspensa and the phylogenetic development of this genus,high-throughput sequencing technology was used to sequence and functionally annotate the chloroplast genomes of long and short style type in F. suspensa. PCR was used to confirm the sequencing results. The results showed that the chloroplast genomes of the long and short styles type were 156 386 bp,which was a typical four-segment structure in F. suspensa. A total of 114 unique genes were annotated,including 80 protein-coding genes,30 tRNA,and four rRNA. Analysis of 56 simple sequence repeats（SSRs）showed that it mainly composes of A and T bases. In addition,the coding region of the chloroplast genome of F. suspensa prefers to use A and T bases,but the overall codon preference is weak,which is mainly reflected by the difference of Arg and Ser. Based on the chloroplast genome sequence of the heterostyly and 32 plants’ chloroplast genome sequences（including 14 species of Forsythia）published the phylogenetic relationship is analyzed. And the results showed that the chloroplast genome of heterostyly was highly homologous to F. suspensa in Zezhou,Shanxi. It is possible that heterostyly also evolved from the homostyly flowers in F. suspensa.

Key words: Forsythia suspensa, heterostyly, chloroplast genome, SSR, codon preference, phylogenetic analysis

CLC Number:

S685.24

SONG Yun, JIA Mengjun, CAO Yaping, LI Zheng, HE Jiaxin, WANG Yongfei, ZHANG Xinrui, QIAO Yonggang. Analysis on Chloroplast Genomic Characteristics of Forsythia suspensa[J]. Acta Horticulturae Sinica, 2022, 49(1): 187-199.

Figures/Tables 10

References 24

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类型 Type	大小/bp Size				基因数量 Number of genes				GC/%
类型 Type	LSC	SSC	IR	总数 Total	Protein	tRNA	rRNA	总计 Total	LSC	SSC	IR	平均 Mean
长花柱 Long-styled morph	87 142	17 810	25 717	156 386	80	30	4	114	35.8	31.8	43.2	37.8
短花柱 Short style type	87 595	17 781	25 717	156 810	80	30	4	114	35.8	31.9	43.2	37.8

类型 Type	大小/bp Size				基因数量 Number of genes				GC/%
类型 Type	LSC	SSC	IR	总数 Total	Protein	tRNA	rRNA	总计 Total	LSC	SSC	IR	平均 Mean
长花柱 Long-styled morph	87 142	17 810	25 717	156 386	80	30	4	114	35.8	31.8	43.2	37.8
短花柱 Short style type	87 595	17 781	25 717	156 810	80	30	4	114	35.8	31.9	43.2	37.8

功能 Function	基因家族 Family Name	基因ID Gene ID
光合作用相关基因（45） Photosynthesis related genes	核酮糖-1,5-二磷酸羧化酶 Rubisco	rbcL
	ATP合酶 ATP Synthase	atpA,atpB,atpE,atpF,atpH,atpI*
	NADH脱氢酶 NADH Dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素 Cytochrome	petA,petB,petD,petG,petL,petN,ccsA
	光合系统Ⅰ PhotosystemⅠ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ PhotosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
转录翻译相关基因（60） Transcription and translation related genes	大亚基核糖体 Large Subunit of Ribosome	rpl2,rpl14,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	小亚基核糖体Small Subunit of Ribosome	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	DNA依赖性RNA聚合酶 DNA Dependent RNA Polymerase	rpoA,rpoB,rpoC1,rpoC2*
	核糖体RNA rRNA Genes	rrn5,rrn4.5,rrn16,rrn23
	转运RNA tRNA Genes	trnA-UGC,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
	翻译起始因子 Translation Initiation Factor	infA
其他基因（4） Other genes	乙酰辅酶A羧化酶 Acety1-CoA carboxylase	accD
	包膜蛋白 Envelop membrane protein	cemA
	成熟酶 Maturase	matK
	clpP样蛋白酶 clpP-like protease	clpP*
功能未知基因（5） Unknown	保守开放阅读框Conserved open reading frames	ycf1,ycf2,ycf3,ycf4,ycf15*

功能 Function	基因家族 Family Name	基因ID Gene ID
光合作用相关基因（45） Photosynthesis related genes	核酮糖-1,5-二磷酸羧化酶 Rubisco	rbcL
	ATP合酶 ATP Synthase	atpA,atpB,atpE,atpF,atpH,atpI*
	NADH脱氢酶 NADH Dehydrogenase	ndhA,ndhB,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素 Cytochrome	petA,petB,petD,petG,petL,petN,ccsA
	光合系统Ⅰ PhotosystemⅠ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ PhotosystemⅡ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
转录翻译相关基因（60） Transcription and translation related genes	大亚基核糖体 Large Subunit of Ribosome	rpl2,rpl14,rpl16,rpl20,rpl22,rpl23,rpl32,rpl33,rpl36
	小亚基核糖体Small Subunit of Ribosome	rps2,rps3,rps4,rps7,rps8,rps11,rps12,rps14,rps15,rps16,rps18,rps19
	DNA依赖性RNA聚合酶 DNA Dependent RNA Polymerase	rpoA,rpoB,rpoC1,rpoC2*
	核糖体RNA rRNA Genes	rrn5,rrn4.5,rrn16,rrn23
	转运RNA tRNA Genes	trnA-UGC,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-GCC,trnG-UCC,trnH-GUG,trnI-CAU,trnI-GAU,trnK-UUU,trnL-CAA,trnL-UAA,trnL-UAG,trnM-CAU,trnN-GUU,trnP-UGG,trnQ-UUG,trnR-ACG,trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC,trnV-UAC,trnW-CCA,trnY-GUA
	翻译起始因子 Translation Initiation Factor	infA
其他基因（4） Other genes	乙酰辅酶A羧化酶 Acety1-CoA carboxylase	accD
	包膜蛋白 Envelop membrane protein	cemA
	成熟酶 Maturase	matK
	clpP样蛋白酶 clpP-like protease	clpP*
功能未知基因（5） Unknown	保守开放阅读框Conserved open reading frames	ycf1,ycf2,ycf3,ycf4,ycf15*

差异 Difference	长花柱/bp Long style type site	短花柱/bp Short style type site
SNP₁	-	4 705（A）
SNP₂	6 923（T）	-
SNP₃	-	6 973（T）
SNP₄	21 955（G）	21 956（A）
SNP₅	21 964（A）	21 964（C）
SNP₆	-	31 777（C）
Gap₁	-	31 805 ~ 32 018
SNP₇	32 238（G）	32 454（T）
SNP₈	32 243（G）	32 459（T）
Gap₂	-	32 624 ~ 32 859
SNP₉	-	60 082（C）
SNP₁₀	115 112（A）	-
Gap₃	115 316 ~ 115 343	-
SNP₁₁	115 705（G）	115 528（C）
SNP₁₂	115 919（A）	116 343（G）

Analysis on Chloroplast Genomic Characteristics of Forsythia suspensa

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名称 Name		验证结果 Validation result
SNP₁	F：TAGACGAAGTAATCAAACAAT	SNP₁长短花柱均有A Both long and short styles at SNP₁ locus have A
SNP₁	R：TATCTAGTGTCAATCCAAGAC	SNP₁长短花柱均有A Both long and short styles at SNP₁ locus have A
SNP₂,SNP₃	F：TTGGACAGTAAGGATCACATT	SNP₂长短花柱均有T Both long and short styles at SNP₂ locus have T
SNP₂,SNP₃	R：TATCCTATCCCTTTTATTCAC	SNP₃长短花柱均无T Both long and short styles at SNP₃ locus have no T
SNP₄,SNP₅	F：TGGCAGTTCCGTCTATCACTTTATT	SNP₄长短花柱均为G Both long and short styles at SNP₄ locus are G
SNP₄,SNP₅	R：TAGTCCTTTGTGGCTCCGGTGGCGA	SNP₅长短花柱均为A Both long and short styles at SNP₅ locus are A
Gap₁,SNP₆	F：TTATCCATACCGAATCCAAAC	Gap₁不存在 Gap₁ does not exist
Gap₁,SNP₆	R：AGAGTAAAAAACAGATCAATCAAAG	SNP₆长短花柱均有C Both long and short styles at SNP₆ locus have C
Gap₂,SNP₇,SNP₈	F：AATTGAGGTTACACAAAACCGGAGC	Gap₂不存在 Gap₂ does not exist
Gap₂,SNP₇,SNP₈	R：TTCCGAAATACCCCATACGAAATAC	SNP₇长短花柱均为G_,SNP₈长短花柱均为G Both long and short styles at SNP₇ locus are G; Both long and short styles at SNP₈ locus are G;
SNP₉	F：CAAAATCTAAGACTAAATCCAAATCG	SNP₉长短花柱均无C Both long and short styles at SNP₉ locus have no C
SNP₉	R：CAGAATAAACATAGAAATGCAATCAC
Gap₃,SNP₁₀, SNP₁₁	F：CTGGAAGTGGAACAAAAGGTA	长短花柱均有Gap₃序列 Both long and short styles have Gap₃sequence
Gap₃,SNP₁₀, SNP₁₁	R：TGTTCAAAATGAATCCGTGCT	SNP₁₀长短花柱均有A, SNP₁₁长短花柱均无该位碱基 Both long and short styles at SNP₁₀ locus have A while SNP₁₁ have no it
SNP₁₂	F：GGAATAATCTGAATCGACTTG	SNP₁₂长短花柱均为G Both long and short styles at SNP₁₂ locus are G
SNP₁₂	R：CAGAAAGTTAGACAAAAGGGT	长花柱115947位、短花柱116371位均缺少T No.115947 long style and No.116371 short style lack T

SSR类型 SSR Type	SSR重复碱基 SSR Repeat Base	SSR起始位置 SSR Start	SSR区域 SSR Region	SSR位置 SSR Location
单核苷酸（37） Mono-nucleotide	(A)10	4 842	LSC	IGS
	(T)12	9 030	LSC	IGS
	(T)10	11 138	LSC	IGS
	(A)13	12 717	LSC	IGS
	(T)13	14 085	LSC	IGS
	(A)10	15 717	LSC	IGS
	(A)10	16 489	LSC	IGS
	(T)11	19 653	LSC	CDS
	(T)12	20 191	LSC	CDS
	(A)21	29 932	LSC	IGS
	(A)10	31 831	LSC	IGS
	(A)10	31 968	LSC	IGS
	(A)17	33 139	LSC	IGS
	(T)10	33 817	LSC	IGS
	(T)13	34 464	LSC	IGS
	(T)12	37 624	LSC	IGS
	(A)10	38 003	LSC	IGS
	(A)15	44 538	LSC	IGS
	(A)16	46 593	LSC	intron
	(A)11	46 852	LSC	IGS
	(T)14	48 603	LSC	IGS
	(T)10	49 569	LSC	IGS
	(T)12	50 845	LSC	IGS
	(T)10	59 736	LSC	IGS
	(T)10	61 617	LSC	IGS
	(T)10	63 559	LSC	IGS
	(T)10	66 245	LSC	IGS
	(T)10	69 156	LSC	IGS
	(T)11	72 217	LSC	IGS
	(T)10	73 677	LSC	intron
	(A)11	73 841	LSC	intron
	(T)10	74 697	LSC	intron
	(T)12	81 215	LSC	CDS
	(T)13	83 627	LSC	IGS
	(A)10	85 352	LSC	intron
	(T)17	86 822	LSC	IGS
	(T)17	117 894	SSC	IGS
二核苷酸（7） Di-nucleotide	(AT)5	4 622	LSC	IGS
	(AT)5	6 532	LSC	IGS
	(AT)5	21 032	LSC	CDS
	(TA)6	48 745	LSC	IGS
	(TA)6	49 264	LSC	IGS
	(TA)5	69 573	LSC	IGS
	(TA)6	69 885	LSC	IGS
三核苷酸（1）Tri-nucleotide	(CCT)4	69 325	LSC	IGS
四核苷酸（5） Tetra-nucleotide	(AAAT)4	9 260	LSC	IGS
	(TCTT)3	31 167	LSC	IGS
	(TTTA)3	55 057	LSC	IGS
	(GAAA)3	63 543	LSC	IGS
	(AAAG)3	73 367	LSC	intron
五核苷酸（1） Penta-nucleotide	(TCTAT)3	9 434	LSC	IGS
复合型 Compound	-	17 431	LSC	IGS
	-	38 479	LSC	IGS
	-	57 033	LSC	CDS-IGS
	-	71 524	LSC	IGS
	-	78 279	LSC	intron

氨基酸 Amino acid	密码子 Codon	数量 Numer	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Numer	RSCU
Phe	UUU	2 262	1.18	Ser	UCU	1 233	1.52
Phe	UUC	1 582	0.82		UCC	872	1.07
Leu	UUA	947	1.17		UCA	966	1.19
	UUG	1 044	1.29		UCG	622	0.77
	CUU	1 043	1.29		AGU	700	0.86
	CUC	651	0.80		AGC	479	0.59
	CUA	700	0.87	Pro	CCU	703	1.10
	CUG	469	0.58		CCC	619	0.97
Ile	AUU	1 814	1.24		CCA	827	1.30
	AUC	1 173	0.80		CCG	403	0.63
	AUA	1 412	0.96	Thr	ACU	707	1.22
Met	AUG	788	1.00		ACC	606	1.05
Val	GUU	831	1.42		ACA	663	1.15
	GUC	435	0.74		ACG	334	0.58
	GUA	711	1.22	Ala	GCU	513	1.32
	GUG	359	0.61		GCC	347	0.89
Tyr	UAU	1 357	1.33		GCA	436	1.12
Tyr	UAC	676	0.67		GCG	256	0.66
TER	UAA	1 095	1.11	Cys	UGU	686	1.21
	UAG	786	0.80	Cys	UGC	449	0.79
	UGA	1 084	1.10	Arg	CGU	377	0.66
His	CAU	970	1.42		CGC	222	0.39
His	CAC	392	0.58		CGA	597	1.05
Gln	CAA	1 110	1.44		CGG	397	0.70
Gln	CAG	428	0.56		AGA	1 177	2.08
Asn	AAU	1 694	1.38		AGG	632	1.11
Asn	AAC	765	0.62	Gly	GGU	612	1.03
Lys	AAA	2 114	1.34		GGC	346	0.58
Lys	AAG	1 041	0.66		GGA	885	1.49
Asp	GAU	1 089	1.44		GGG	531	0.89
Asp	GAC	426	0.56	Glu	GAA	1 364	1.38
Trp	UGG	706	1.00	Glu	GAG	613	0.62

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