Chloroplast Genome Characteristics and Phylogenetic Analysis of Actinidia rubricaulis var. coriacea

doi:10.13560/j.cnki.biotech.bull.1985.2025-1160

Abstract

Abstract:

Objective To elucidate the chloroplast genome characteristics of Actinidia rubricaulis var. coriacea and investigate its phylogenetic relationship within the genus Actinidia, providing a genetic basis for species identification, genetic diversity analysis, and resource conservation of Actinidia species. Method The complete chloroplast genome of A. rubricaulis var. coriacea was sequenced using the Illumina NovaSeq platform, assembled and annotated with bioinformatics software, and compared with chloroplast genome sequences of representative Actinidia species downloaded from GenBank. Result The chloroplast genome of A. rubricaulis var. coriacea is 156 547 bp in length, with a GC content of 37.24%. It is composed of a large single-copy region (88 649 bp), a small single-copy region (20 484 bp), and two inverted repeat regions (23 707 bp each), exhibiting a typical quadripartite structure. For this species, the chloroplast genome contains a total of 133 annotated genes, including 85 protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Among these, 21 genes contain introns. Codon usage analysis revealed that among the 30 preferred codons with a relative synonymous codon usage value >1, 28 end with A or U. Repeat sequence analysis detected 312 long repeat sequences and 207 simple sequence repeats, with 128 single nucleotide repeats, accounting for 61.84%. Phylogenetic analysis showed that Actinidia rubricaulis var. coriacea is most closely related to Actinidia hubeiensis, with bootstrap support of 100%. Conclusion The chloroplast genome of A. rubricaulis var. coriacea is relatively conserved in structural characteristics and gene composition, but shows some variation in genomic boundaries and nucleotide polymorphism compared with other species in the same genus. It exhibits a higher preference for codons ending with A or U. Actinidia rubricaulis var. coriacea is closely related to Actinidia hubeiensis and highlights the need for further refinement of the taxonomic system within the genus Actinidia.

Key words: Actinidia rubricaulis var. coriacea, chloroplast genome, structural characteristics, repeat sequences, codon usage bias, nucleotide polymorphisms, phylogeny, kiwifruit

WANG Zhi, HU Guang-ming, LUO Xuan, GAO Lei, YE Li-xia, HUANG Qiong, XIAO Tao, ZHANG Lei. Chloroplast Genome Characteristics and Phylogenetic Analysis of Actinidia rubricaulis var. coriacea[J]. Biotechnology Bulletin, 2026, 42(8): 173-187.

Figures/Tables 11

References 48

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区域 Region	T （%）	A （%）	C （%）	G （%）	长度 Length （bp）	GC （%）
LSC	33.02	31.48	18.18	17.33	88 649	35.50
SSC	34.93	33.89	16.70	14.47	20 484	31.18
IRa	28.73	28.15	22.43	20.69	23 707	43.12
IRb	28.15	28.73	20.69	22.43	23 707	43.12
合计 Total	31.88	30.87	19.01	18.24	156 547	37.24

区域 Region	T （%）	A （%）	C （%）	G （%）	长度 Length （bp）	GC （%）
LSC	33.02	31.48	18.18	17.33	88 649	35.50
SSC	34.93	33.89	16.70	14.47	20 484	31.18
IRa	28.73	28.15	22.43	20.69	23 707	43.12
IRb	28.15	28.73	20.69	22.43	23 707	43.12
合计 Total	31.88	30.87	19.01	18.24	156 547	37.24

基因类别 Gene category	基因功能 Gene function	基因名称 Gene name	数量 Number
光合作用基因 Photosynthesis genes	光系统Ⅰ亚基 Subunits of photosystem I	psaA， psaB， psaC， psaI， psaJ	5
	光系统Ⅱ亚基 Subunits of photosystem II	psbA， psbB， psbC， psbD， psbE， psbF， psbH， psbI， psbJ， psbK， psbL， psbM， psbN， psbT， psbZ	15
	NADH-脱氢酶亚基 Subunits of NADH dehydrogenase	ndhA， ndhB（2）， ndhC， ndhD， ndhE， ndhF， ndhG， ndhH， ndhI， ndhJ， ndhK	12
	细胞色素复合物b/f亚基 Subunits of cytochrome b/f complex	petA， petB， petD， petG， petL， petN	6
	ATP合成酶亚基 Subunits of ATP synthase	atpA， atpB， atpE， atpF， atpH， atpI*	6
	二磷酸核酮糖羧化酶大亚基 Large subunit of Rubisco	rbcL	1
自我复制基因 Self-replication genes	核糖体大亚基 Proteins of the large ribosomal subunit	rpl14， rpl16， rpl2， rpl20， rpl22， rpl23（2）， rpl32， rpl33， rpl36	10
	核糖体小亚基 Proteins of the small ribosomal subunit	rps11， rps12（2）， rps14， rps15， rps16， rps18， rps19， rps2， rps3， rps4， rps7（2）， rps8*	14
	RNA聚合酶亚基 Subunits of RNA polymerase	rpoA， rpoB， rpoC1， rpoC2*	4
	核糖体RNA Ribosomal RNAs	rrn16（2）， rrn23（2）， rrn4.5（2）， rrn5（2）	8
	转运RNA Transfer RNAs	trnA-UGC（2）， trnC-GCA， trnD-GUC， trnE-UUC， trnF-GAA， trnG-GCC， trnG-UCC， trnH-GUG（2）， trnI-CAU（2）， trnI-GAU（2）， trnK-UUU， trnL-CAA（2）， trnL-UAA， trnL-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， trnfM-CAU（2）	39
其他基因 Other genes	成熟酶 Maturase	matK	1
	包裹膜蛋白 Envelope membrane protein	cemA	1
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD	1
	c型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA	1
	转录起始因子 Translation initiation factor	infA	1
功能未知基因 Genes of unknown function	保守假想叶绿体开放阅读框 Conserved hypothetical chloroplast ORF	#ycf1， ycf1， ycf15（2）， ycf2（2）， ycf3， ycf4	8

基因类别 Gene category	基因功能 Gene function	基因名称 Gene name	数量 Number
光合作用基因 Photosynthesis genes	光系统Ⅰ亚基 Subunits of photosystem I	psaA， psaB， psaC， psaI， psaJ	5
	光系统Ⅱ亚基 Subunits of photosystem II	psbA， psbB， psbC， psbD， psbE， psbF， psbH， psbI， psbJ， psbK， psbL， psbM， psbN， psbT， psbZ	15
	NADH-脱氢酶亚基 Subunits of NADH dehydrogenase	ndhA， ndhB（2）， ndhC， ndhD， ndhE， ndhF， ndhG， ndhH， ndhI， ndhJ， ndhK	12
	细胞色素复合物b/f亚基 Subunits of cytochrome b/f complex	petA， petB， petD， petG， petL， petN	6
	ATP合成酶亚基 Subunits of ATP synthase	atpA， atpB， atpE， atpF， atpH， atpI*	6
	二磷酸核酮糖羧化酶大亚基 Large subunit of Rubisco	rbcL	1
自我复制基因 Self-replication genes	核糖体大亚基 Proteins of the large ribosomal subunit	rpl14， rpl16， rpl2， rpl20， rpl22， rpl23（2）， rpl32， rpl33， rpl36	10
	核糖体小亚基 Proteins of the small ribosomal subunit	rps11， rps12（2）， rps14， rps15， rps16， rps18， rps19， rps2， rps3， rps4， rps7（2）， rps8*	14
	RNA聚合酶亚基 Subunits of RNA polymerase	rpoA， rpoB， rpoC1， rpoC2*	4
	核糖体RNA Ribosomal RNAs	rrn16（2）， rrn23（2）， rrn4.5（2）， rrn5（2）	8
	转运RNA Transfer RNAs	trnA-UGC（2）， trnC-GCA， trnD-GUC， trnE-UUC， trnF-GAA， trnG-GCC， trnG-UCC， trnH-GUG（2）， trnI-CAU（2）， trnI-GAU（2）， trnK-UUU， trnL-CAA（2）， trnL-UAA， trnL-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， trnfM-CAU（2）	39
其他基因 Other genes	成熟酶 Maturase	matK	1
	包裹膜蛋白 Envelope membrane protein	cemA	1
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD	1
	c型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA	1
	转录起始因子 Translation initiation factor	infA	1
功能未知基因 Genes of unknown function	保守假想叶绿体开放阅读框 Conserved hypothetical chloroplast ORF	#ycf1， ycf1， ycf15（2）， ycf2（2）， ycf3， ycf4	8

基因 Gene	位置 Location	序列长度Length of sequence （bp）
基因 Gene	位置 Location	外显子Ⅰ Exon I	内含子Ⅰ Intron I	外显子Ⅱ Exon II	内含子Ⅱ Intron II	外显子Ⅲ Exon III
trnK-UUU	LSC	37	2 492	39
rps16	LSC	42	872	225
trnG-UCC	LSC	23	689	48
atpF	LSC	144	723	411
rpoC1	LSC	435	736	1 614
ycf3	LSC	126	743	228	718	153
trnL-UAA	LSC	37	504	50
trnV-UAC	LSC	38	589	37
rps12	IRa+LSC	114	*	232	*
petB	LSC	6	711	642
petD	LSC	6	799	477
rpl16	LSC	9	1 037	402
rpl2	LSC	405	664	441
ndhB	IRb	777	679	756
rps12	IRb+LSC	232	*	26	*
trnI-GAU	IRb	42	942	35
trnA-UGC	IRb	38	798	35
ndhA	SSC	552	1 095	540
trnA-UGC	IRa	38	798	35
trnI-GAU	IRa	42	942	35
ndhB	IRa	777	679	756