Chloroplast Genome Characteristics and Phylogenetic Analysis of Cucurbita ficifolia

doi:10.7668/hbnxb.20195785

Abstract

Abstract:

The chloroplast genome of Cucurbita ficifolia was assembled,annotated and analyzed to reveal the phylogenetic relationship between C.ficifolia and other Cucurbitaceae plants.The Illumina NovaSeq 6000 platform was used to sequence C.ficifolia,and its sequence characteristics,gene type,gene repeat sequence,codon preference and species evolution were analyzed.The chloroplast genome of C.ficifolia was 157 631 bp in length with a GC content of 37.15%.A total of 141 genes were annotated,comprising 60.99% protein-coding genes,33.33% tRNA genes,and 5.67% rRNA genes.These genes were categorized into four groups:photosynthesis-related genes,self-replication genes,other genes,and genes of unknown function.Simple sequence repeat analysis was performed on the chloroplasts of C.ficifolia,and a total of 192 SSR loci were detected.Codon preference analysis showed that there were 31 codons with RSCU values greater than 1.00,and 29 codons ended with A or U.The boundary genes of C.ficifolia were different from those of 8 other Cucurbitaceae species,and the expansion and contraction phenomena were obvious in the IR region and LSC region.The results of evolutionary analysis showed that C.ficifolia was in the same branch with C.moschata,C.maxima,C.pepo,C.argyrosperma var. palmeri,C.foetidissima,C.okeechobeensis subsp. martinezii and C.lundelliana.C.ficifolia was distant in relationship with other species of Cucurbitaceae.The chloroplast genome of C.ficifolia was assembled,and annotated with 141 genes and 192 SSR loci.Its evolutionary relationship is relatively distant with the selected Cucurbitaceae species.This study provides a theoretical basis for phyletic evolution and molecular breeding strategies in C.ficifolia.

Key words: Cucurbita ficifolia, Chloroplast genome, Structural characteristics, Phyletic evolution

CLC Number:

KANG Jiaxiang, PENG Conggui, ANG Haiyan, JING Zange, YANG Zhengan, XIE Xiufeng, WANG Yuxin, PEI Xuli. Chloroplast Genome Characteristics and Phylogenetic Analysis of Cucurbita ficifolia[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(3): 48-56. doi: 10.7668/hbnxb.20195785.

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References 41

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基因功能分类 Gene functional category	基因组 Genome	基因名 Gene name		基因数量 Gene number
自我复制相关基因	核糖体大亚基	rpl14、rpl16^、rpl2^、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36		10
Self-replication related genes	核糖体小亚基	rps11、rps12^*(2)、rps14、rps15、rps16^、rps18、rps19、rps2、rps3、rps4、rps7(2)、rps8		14
	DNA 依赖核酸聚合酶	rpoA、rpoB、rpoC1^、rpoC2*		4
	核糖体RNA	rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2)		8
	转运RNA	trnA-UGC^(2)、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnG-GCC、trnG-UCC^、trnH-GUG、trnI-CAU(4)、trnI-GAU^(2)、trnK-UUU^、trnL-CAA(4)、trnL-UAA^、trnL-UAG、trnM-CAU、trnN-GUU(4)、trnP-UGG、trnQ-UUG、trnR-ACG(4)、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC(4)、trnV-UAC^、trnW-CCA、trnY-GUA、trnfM-CAU		47
光合作用有关基因	亚光系统Ⅰ		psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis related genes	亚光系统Ⅱ		psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ	15
	NADH 脱氢酶亚基		ndhA^、ndhB^(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK	12
	细胞色素复合物b/f亚基		petA、petB^、petD^、petG、petL、petN	6
	ATP 合酶亚基		atpA、atpB、atpE、atpF^、atpH、atpI*	6
	Rubisco 酶大亚基		rbcL	1
其他基因	成熟酶		matK	1
Other genes	蛋白酶		clpP^**	1
	包裹膜蛋白		cemA	1
	乙酰辅酶A羧化酶亚基		accD	1
	c型细胞色素合成		ccsA	1
	转录起始因子		infA	1
未知功能基因	假定叶绿体阅读框		ycf1、ycf15(2)、ycf2(2)、ycf3^*、ycf4*	7
Genes of unknown function
总计Total				141

基因功能分类 Gene functional category	基因组 Genome	基因名 Gene name		基因数量 Gene number
自我复制相关基因	核糖体大亚基	rpl14、rpl16^、rpl2^、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36		10
Self-replication related genes	核糖体小亚基	rps11、rps12^*(2)、rps14、rps15、rps16^、rps18、rps19、rps2、rps3、rps4、rps7(2)、rps8		14
	DNA 依赖核酸聚合酶	rpoA、rpoB、rpoC1^、rpoC2*		4
	核糖体RNA	rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2)		8
	转运RNA	trnA-UGC^(2)、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnG-GCC、trnG-UCC^、trnH-GUG、trnI-CAU(4)、trnI-GAU^(2)、trnK-UUU^、trnL-CAA(4)、trnL-UAA^、trnL-UAG、trnM-CAU、trnN-GUU(4)、trnP-UGG、trnQ-UUG、trnR-ACG(4)、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC(4)、trnV-UAC^、trnW-CCA、trnY-GUA、trnfM-CAU		47
光合作用有关基因	亚光系统Ⅰ		psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis related genes	亚光系统Ⅱ		psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ	15
	NADH 脱氢酶亚基		ndhA^、ndhB^(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK	12
	细胞色素复合物b/f亚基		petA、petB^、petD^、petG、petL、petN	6
	ATP 合酶亚基		atpA、atpB、atpE、atpF^、atpH、atpI*	6
	Rubisco 酶大亚基		rbcL	1
其他基因	成熟酶		matK	1
Other genes	蛋白酶		clpP^**	1
	包裹膜蛋白		cemA	1
	乙酰辅酶A羧化酶亚基		accD	1
	c型细胞色素合成		ccsA	1
	转录起始因子		infA	1
未知功能基因	假定叶绿体阅读框		ycf1、ycf15(2)、ycf2(2)、ycf3^*、ycf4*	7
Genes of unknown function
总计Total				141

氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU
Ter	UAA	55	1.918 5	Ile	AUA	685	0.917 7	Arg	AGA	466	1.801 8
	UAG	16	0.558 0		AUC	472	0.632 4		AGG	170	0.657 0
	UGA	15	0.523 2		AUU	1 082	1.449 9		CGA	361	1.395 6
Ala	GCA	378	1.093 2	Lys	AAA	1 014	1.498 8		CGU	345	1.333 8
	GCC	225	0.650 8		AAG	339	0.501 2	Ser	AGC	124	0.363 0
	GCG	151	0.436 8	Leu	CUA	383	0.835 2		AGU	414	1.211 4
	GCU	629	1.819 2		CUC	187	0.408 0		UCA	419	1.225 8
Cys	UGC	81	0.540 0		CUG	179	0.390 6		UCC	320	0.936 0
	UGU	219	1.460 0		CUU	580	1.264 8		UCG	195	0.570 6
Asp	GAC	226	0.408 0		UUA	855	1.864 8		UCU	579	1.693 8
	GAU	882	1.592 0		UUG	567	1.236 6	Thr	ACA	388	1.176 8
Glu	GAA	1 045	1.498 2	Met	AUG	622	1.996 8		ACC	242	0.734 0
	GAG	350	0.501 8	Asn	AAC	298	0.465 2		ACG	155	0.470 0
Phe	UUC	528	0.720 4		AAU	983	1.534 8		ACU	534	1.619 6
	UUU	938	1.279 6	Pro	CCA	311	1.147 6	Val	GUA	515	1.456 8
Gly	GGA	718	1.630 8		CCC	199	0.734 4		GUC	188	0.532 0
	GGC	171	0.388 4		CCG	160	0.590 4		GUG	192	0.543 2
	GGG	281	0.638 4		CCU	414	1.527 6		GUU	519	1.468 0
	GGU	591	1.342 4	Gln	CAA	724	1.538 8	Trp	UGG	453	1.000 0
His	CAC	153	0.491 2		CAG	217	0.461 2	Tyr	UAC	192	0.396 6
	CAU	470	1.508 8						UAU	776	1.603 4

氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU
Ter	UAA	55	1.918 5	Ile	AUA	685	0.917 7	Arg	AGA	466	1.801 8
	UAG	16	0.558 0		AUC	472	0.632 4		AGG	170	0.657 0
	UGA	15	0.523 2		AUU	1 082	1.449 9		CGA	361	1.395 6
Ala	GCA	378	1.093 2	Lys	AAA	1 014	1.498 8		CGU	345	1.333 8
	GCC	225	0.650 8		AAG	339	0.501 2	Ser	AGC	124	0.363 0
	GCG	151	0.436 8	Leu	CUA	383	0.835 2		AGU	414	1.211 4
	GCU	629	1.819 2		CUC	187	0.408 0		UCA	419	1.225 8
Cys	UGC	81	0.540 0		CUG	179	0.390 6		UCC	320	0.936 0
	UGU	219	1.460 0		CUU	580	1.264 8		UCG	195	0.570 6
Asp	GAC	226	0.408 0		UUA	855	1.864 8		UCU	579	1.693 8
	GAU	882	1.592 0		UUG	567	1.236 6	Thr	ACA	388	1.176 8
Glu	GAA	1 045	1.498 2	Met	AUG	622	1.996 8		ACC	242	0.734 0
	GAG	350	0.501 8	Asn	AAC	298	0.465 2		ACG	155	0.470 0
Phe	UUC	528	0.720 4		AAU	983	1.534 8		ACU	534	1.619 6
	UUU	938	1.279 6	Pro	CCA	311	1.147 6	Val	GUA	515	1.456 8
Gly	GGA	718	1.630 8		CCC	199	0.734 4		GUC	188	0.532 0
	GGC	171	0.388 4		CCG	160	0.590 4		GUG	192	0.543 2
	GGG	281	0.638 4		CCU	414	1.527 6		GUU	519	1.468 0
	GGU	591	1.342 4	Gln	CAA	724	1.538 8	Trp	UGG	453	1.000 0
His	CAC	153	0.491 2		CAG	217	0.461 2	Tyr	UAC	192	0.396 6
	CAU	470	1.508 8						UAU	776	1.603 4

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