Study on Intraspecific Variation of Chloroplast Genome in Idesia polycarpa

doi:10.16420/j.issn.0513-353x.2025-0487

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (8): 2345-2362.doi: 10.16420/j.issn.0513-353x.2025-0487

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Study on Intraspecific Variation of Chloroplast Genome in Idesia polycarpa

CAO Yuxiang¹^,², WANG Yanpeng¹, LUO Jing³, XU Yang¹^,⁴^,^*()

¹ Institute of Subtropical Forestry， Chinese Academy of Forestry， Hangzhou 311400， China
² School of Ecology， Technology and Engineering，Shanghai University of Applied Sciences， Shanghai 201400， China
³ Guizhou Forestry Seed and Seedling Station， Guiyang 550001， China
⁴ Key Laboratory of Forest Breeding， Zhejiang， Hangzhou 311400， China

Received:2026-04-01 Revised:2026-06-02 Online:2026-08-25 Published:2026-08-25
Contact: XU Yang

Abstract

Abstract:

The chloroplast genome structure and evolutionary variation mechanisms of Idesia polycarpa remain unclear at present. In this study，41 samples of I. polycarpa were used as materials，and the complete chloroplast genome sequences of I. polycarpa were obtained from the National Genomics Data Center（NGDC）for chloroplast genome structure analysis and intraspecific variation research. The results showed that the full length of the chloroplast genome of I. polycarpa ranged from 155 177 bp to 157 133 bp，with a total of 129 to 130 genes annotated，including 85 protein-coding genes，36 to 37 transfer RNA（tRNA）genes and 8 ribosomal RNA（rRNA）genes. The total GC content was between 36.7% and 36.84%. A total of 3 397 simple sequence repeat（SSR）loci and 2 215 long repeat sequences were identified. The variation degree of non-coding regions in the chloroplast genome of I. polycarpa was higher than that of coding regions，and seven highly variable regions were screened. Phylogenetic analysis indicated the population in northern Sichuan is rich in haplotypes，which may be the center of origin of I. polycarpa.

Key words: Idesia polycarpa, chloroplast genome, intraspecific variation

CAO Yuxiang, WANG Yanpeng, LUO Jing, XU Yang. Study on Intraspecific Variation of Chloroplast Genome in Idesia polycarpa[J]. Acta Horticulturae Sinica, 2026, 53(8): 2345-2362.

Figures/Tables 10

References 28

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样品名称 Sample name	样本居群 Sample area	总长度 Total length		LSC区长度 Length of LSC area	SSC区长度 Length of SSC area	IR区长度 Length of IR area	GC含量% GC content
样品名称 Sample name	样本居群 Sample area	样本长度 Sample length	地区长度 Regional length	LSC区长度 Length of LSC area	SSC区长度 Length of SSC area	IR区长度 Length of IR area	GC含量% GC content
CRR634761	北京 Beijing（BJ）	156 269	156 311.5 ± 463.5 bp	84 037	16 530	27 851	36.78
CRR634759		155 848		84 534	16 533	27 854	36.82
CRR634773		156 775		84 534	16 533	27 854	36.71
CRR634755		156 061		83 955	16 500	27 803	36.81
CRR634766	四川广元朝天	156 061	156 826 ± 51 bp	83 954	16 501	27 803	36.82
CRR634768	Chaotian，	156 043		83 936	16 501	27 803	36.82
CRR634779	Guangyuan，	155 852		83 601	16 513	27 869	36.81
CRR634780	Sichuan（CT）	155 850		83 599	16 513	27 869	36.81
CRR634781		155 850		83 599	16 513	27 869	36.81
CRR634787		156 056		83 949	16 501	27 803	36.82
CRR634788		156 043		83 922	16 503	27 809	36.80
CRR634789		155 877		83 728	16 515	27 817	36.84
CRR634790		155 847		83 597	16 512	27 869	36.82
CRR634791		156 877		84 798	16 467	27 806	36.73
CRR634767	四川广元青川	156 455	155 816 ± 639 bp	84 347	16 546	27 781	36.78
CRR634774	Qingchuan	155 177		83 524	16 509	27 572	36.80
CRR634775	Guangyuan，	156 255		84 086	16 493	27 838	36.79
CRR634776	Sichuan（QC）	156 049		83 941	16 502	27 803	36.82
CRR634777		156 058		83 950	16 502	27 803	36.82
CRR634778		156 455		84 346	16 547	27 781	36.78
CRR634792		156 058		83 951	16 501	27 803	36.82
CRR634763	四川广元	156 452	155 979.5 ± 802.5 bp	84 344	16 546	27 781	36.78
CRR634764	Guangyuan，	155 846		83 595	16 513	27 869	36.82
CRR634765	Sichuan（ST）	156 071		83 965	16 500	27 803	36.82
CRR634771		156 782		84 539	16 535	27 854	36.70
CRR634772		155 177		83 524	16 509	27 572	36.81
CRR634782	陕西宁强	156 050	156 145.5 ± 95.5 bp	83 942	16 502	27 803	36.82
CRR634783	Ningqiang，	156 241		84 040	16 567	27 817	36.79
CRR634784	Shaanxi（NQ）	156 077		83 930	16 487	27 830	36.80
CRR634785		156 077		83 930	16 487	27 830	36.80
CRR634786		156 077		83 930	16 487	27 830	36.80
CRR634752	西藏Xizang（XZ）	155 877	155 957.5 ± 80.5 bp	83 728	16 515	27 817	36.84
CRR634753		156 038		83 977	16 500	27 803	36.82
CRR634754		155 877		83 728	16 515	27 817	36.84
CRR634756	四川盐源	157 133	156 592.5 ± 540.5 bp	85 114	16 421	27 799	36.71
CRR634757	Yanyuan，Sichuan	156 087		83 939	16 486	27 831	36.79
CRR634758	（YY）	156 202		84 001	16 567	27 817	36.79
CRR634760		156 954		84 839	16 481	27 817	36.70
CRR634762		156 052		83 903	16 487	27 831	36.80
CRR634769		156 059		83 893	16 500	27 833	36.80
CRR634770		156 088		83 982	16 500	27 803	36.82

样品名称 Sample name	样本居群 Sample area	总长度 Total length		LSC区长度 Length of LSC area	SSC区长度 Length of SSC area	IR区长度 Length of IR area	GC含量% GC content
样品名称 Sample name	样本居群 Sample area	样本长度 Sample length	地区长度 Regional length	LSC区长度 Length of LSC area	SSC区长度 Length of SSC area	IR区长度 Length of IR area	GC含量% GC content
CRR634761	北京 Beijing（BJ）	156 269	156 311.5 ± 463.5 bp	84 037	16 530	27 851	36.78
CRR634759		155 848		84 534	16 533	27 854	36.82
CRR634773		156 775		84 534	16 533	27 854	36.71
CRR634755		156 061		83 955	16 500	27 803	36.81
CRR634766	四川广元朝天	156 061	156 826 ± 51 bp	83 954	16 501	27 803	36.82
CRR634768	Chaotian，	156 043		83 936	16 501	27 803	36.82
CRR634779	Guangyuan，	155 852		83 601	16 513	27 869	36.81
CRR634780	Sichuan（CT）	155 850		83 599	16 513	27 869	36.81
CRR634781		155 850		83 599	16 513	27 869	36.81
CRR634787		156 056		83 949	16 501	27 803	36.82
CRR634788		156 043		83 922	16 503	27 809	36.80
CRR634789		155 877		83 728	16 515	27 817	36.84
CRR634790		155 847		83 597	16 512	27 869	36.82
CRR634791		156 877		84 798	16 467	27 806	36.73
CRR634767	四川广元青川	156 455	155 816 ± 639 bp	84 347	16 546	27 781	36.78
CRR634774	Qingchuan	155 177		83 524	16 509	27 572	36.80
CRR634775	Guangyuan，	156 255		84 086	16 493	27 838	36.79
CRR634776	Sichuan（QC）	156 049		83 941	16 502	27 803	36.82
CRR634777		156 058		83 950	16 502	27 803	36.82
CRR634778		156 455		84 346	16 547	27 781	36.78
CRR634792		156 058		83 951	16 501	27 803	36.82
CRR634763	四川广元	156 452	155 979.5 ± 802.5 bp	84 344	16 546	27 781	36.78
CRR634764	Guangyuan，	155 846		83 595	16 513	27 869	36.82
CRR634765	Sichuan（ST）	156 071		83 965	16 500	27 803	36.82
CRR634771		156 782		84 539	16 535	27 854	36.70
CRR634772		155 177		83 524	16 509	27 572	36.81
CRR634782	陕西宁强	156 050	156 145.5 ± 95.5 bp	83 942	16 502	27 803	36.82
CRR634783	Ningqiang，	156 241		84 040	16 567	27 817	36.79
CRR634784	Shaanxi（NQ）	156 077		83 930	16 487	27 830	36.80
CRR634785		156 077		83 930	16 487	27 830	36.80
CRR634786		156 077		83 930	16 487	27 830	36.80
CRR634752	西藏Xizang（XZ）	155 877	155 957.5 ± 80.5 bp	83 728	16 515	27 817	36.84
CRR634753		156 038		83 977	16 500	27 803	36.82
CRR634754		155 877		83 728	16 515	27 817	36.84
CRR634756	四川盐源	157 133	156 592.5 ± 540.5 bp	85 114	16 421	27 799	36.71
CRR634757	Yanyuan，Sichuan	156 087		83 939	16 486	27 831	36.79
CRR634758	（YY）	156 202		84 001	16 567	27 817	36.79
CRR634760		156 954		84 839	16 481	27 817	36.70
CRR634762		156 052		83 903	16 487	27 831	36.80
CRR634769		156 059		83 893	16 500	27 833	36.80
CRR634770		156 088		83 982	16 500	27 803	36.82

基因功能分类 Gene function	基因分组 Gene group	基因名称 Gene name	数量 Number
光合作用基因 Photosynthesis gene	ATP合成酶亚基 ATP Synthase	atpA，atpB，atpE，atpF^，atpH，atpI*	6
	光系统Ⅱ亚基 Photosystem II	psbA，psbB，psbC，psbD，psbE，psbF，psbI，psbJ，psbK，psbL，psbH，psbM，psbT，psbZ	14
	NADH脱氢酶亚基 NADH Dehydrogenase	nadhA，nadhB(2)，nadhC，nadhD，nadhE，nadhF，nadhG，nadhH，nadhI，nadhJ，nadhK	12
	细胞色素b₆f复合物 Cytochrome b₆f complex	petA，petB，petL，petG，petN，petD	6
	光系统Ⅰ亚基 PhotosystemⅠ	psaA，psaB，psaC，psaI，psaJ	5
	Rubisco大亚基 Large subunit of Rubisco	rbcL	1
	光系统Ⅰ组装因子 Optical systemⅠassembly factor	pafⅠ^，pafⅡ*	2
	光系统生物生成因子 Photosystem biogenic factor	pbf1	1
蛋白质合成和DNA复制基因Protein synthesis and DNA replication genes	核糖体蛋白大亚基 Ribosomal proteins（LSU）gene	rpl2(2)，rpl14，pl16，rpl20，rpl22，rpl23(2)，rpl33，rpl36	10
	核糖体蛋白小亚基 Ribosomal proteins（SSU）gene	rpl2(2)，rpl14，rpl16，rpl20，rpl22，rpl23(2)，rpl33，rpl36	14
	核糖体RNA rRNA Genes	rrn4.5(2)，rrn5(2)，rrn16(2)，rrn23(2)	8
	转运RNA tRNA Genes	TrnA-UGC(2)，trnC-GCA，trnD-GUC，trnE-UUC，trnF-GAA，trnfM-CAU，trnG-GCC，trnG-UCC^，trnH-GUG，trnI-CAU(2)，trnI-GAU(2)，trnK-UUU^，trnL-CAA(2)，trnL-UAA^*，trnlL-UAG，trnM-CAU，trnN-GUU(2)，trnP-UGG，trnQ-UUG，trnR-ACG(2)，trnR-UCU，trnS-GCU，trnS-GGA，trnS-UGA，trnT-GGU，trnT-UGU，trnV-GAC(2)，trnV-UAC，trnW-CCA，trnY-GUA*，	37
	RNA聚合酶 Subunits of RNA polymerase	rpoA，rpoB，rpoC1^，rpoC2*	4
未知功能基因 Unknown	可开放阅读框 Conserved hypothetical chloroplast ORF	ycf1(2)，ycf2(2)	4
其他基因	成熟酶 Maturase	matK	1
Other genes	蛋白酶 Protease	clpP1	1
	被膜蛋白 Envelop membrane protein	cemA	1
	乙酰CoA羧化酶 Acetyl-CoA carboxylase	accD	1
	细胞色素C合成酶 C-type cytochrome synthesis gene	ccsA	1
	翻译起始因子基因 Translation initiation factor	infA	1

基因功能分类 Gene function	基因分组 Gene group	基因名称 Gene name	数量 Number
光合作用基因 Photosynthesis gene	ATP合成酶亚基 ATP Synthase	atpA，atpB，atpE，atpF^，atpH，atpI*	6
	光系统Ⅱ亚基 Photosystem II	psbA，psbB，psbC，psbD，psbE，psbF，psbI，psbJ，psbK，psbL，psbH，psbM，psbT，psbZ	14
	NADH脱氢酶亚基 NADH Dehydrogenase	nadhA，nadhB(2)，nadhC，nadhD，nadhE，nadhF，nadhG，nadhH，nadhI，nadhJ，nadhK	12
	细胞色素b₆f复合物 Cytochrome b₆f complex	petA，petB，petL，petG，petN，petD	6
	光系统Ⅰ亚基 PhotosystemⅠ	psaA，psaB，psaC，psaI，psaJ	5
	Rubisco大亚基 Large subunit of Rubisco	rbcL	1
	光系统Ⅰ组装因子 Optical systemⅠassembly factor	pafⅠ^，pafⅡ*	2
	光系统生物生成因子 Photosystem biogenic factor	pbf1	1
蛋白质合成和DNA复制基因Protein synthesis and DNA replication genes	核糖体蛋白大亚基 Ribosomal proteins（LSU）gene	rpl2(2)，rpl14，pl16，rpl20，rpl22，rpl23(2)，rpl33，rpl36	10
	核糖体蛋白小亚基 Ribosomal proteins（SSU）gene	rpl2(2)，rpl14，rpl16，rpl20，rpl22，rpl23(2)，rpl33，rpl36	14
	核糖体RNA rRNA Genes	rrn4.5(2)，rrn5(2)，rrn16(2)，rrn23(2)	8
	转运RNA tRNA Genes	TrnA-UGC(2)，trnC-GCA，trnD-GUC，trnE-UUC，trnF-GAA，trnfM-CAU，trnG-GCC，trnG-UCC^，trnH-GUG，trnI-CAU(2)，trnI-GAU(2)，trnK-UUU^，trnL-CAA(2)，trnL-UAA^*，trnlL-UAG，trnM-CAU，trnN-GUU(2)，trnP-UGG，trnQ-UUG，trnR-ACG(2)，trnR-UCU，trnS-GCU，trnS-GGA，trnS-UGA，trnT-GGU，trnT-UGU，trnV-GAC(2)，trnV-UAC，trnW-CCA，trnY-GUA*，	37
	RNA聚合酶 Subunits of RNA polymerase	rpoA，rpoB，rpoC1^，rpoC2*	4
未知功能基因 Unknown	可开放阅读框 Conserved hypothetical chloroplast ORF	ycf1(2)，ycf2(2)	4
其他基因	成熟酶 Maturase	matK	1
Other genes	蛋白酶 Protease	clpP1	1
	被膜蛋白 Envelop membrane protein	cemA	1
	乙酰CoA羧化酶 Acetyl-CoA carboxylase	accD	1
	细胞色素C合成酶 C-type cytochrome synthesis gene	ccsA	1
	翻译起始因子基因 Translation initiation factor	infA	1

Study on Intraspecific Variation of Chloroplast Genome in Idesia polycarpa

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