Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth

doi:10.11924/j.issn.1000-6850.casb2025-0638

Abstract

Abstract:

In order to understand the sequence characteristics, codon usage preferences, and phylogenetic relationships of the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, the leaves of wild Ilex asprella (Hook.et Arn.) Champ.ex Benth from Guangxin District, Shangrao were used as materials. The DNBSEQ-T7 BGI gene sequencer was used to sequence, assemble, annotate, and analyze the chloroplast genome of Ilex asprella (Hook.et Arn.) Champ.ex Benth, and bioinformatics analysis software was used to analyze its codon usage preferences and species relationships. The results showed that the chloroplast genome size of Ilex asprella was 157871 bp, with an average GC content of 37.62%. It had a four zone circular structure consisting of one LSC, one SSC, and two IRs. The chloroplast genome of Ilex asprella was annotated with a total of 136 genes, including 91 CDS genes, 37 tRNA genes, and 8 rRNA genes. A total of 56 SSRs (including only 53 A/T single nucleotide repeats, 2 AT/AT dinucleotide repeats, and 1 AAT/ATT trinucleotide repeat) and 43 Longrepeats (including only 22 forward repeats and 21 palindromic repeats) were detected in the chloroplast genome of Ilex asprella. The chloroplast genome boundaries of Ilex asprella were highly conserved, with small differences in gene location and boundaries, and 10 highly variable regions (rps16_trnQ-UUG, trnS-UGA, trnS-UGA_lhbA, lhbA, ycf4_cemA, petD, rpl32_trnL-UAG, ndhD, ndhD_psaC, psaC); The codon usage bias of the chloroplast genome in Ilex asprella was relatively weak, mainly influenced by natural selection, followed by internal mutation pressure. The chloroplast genes of Ilex asprella had five optimal codons (UAA, GUA, CGU, CUU, and UCA), all ending in U or A. The genetic relationship between Ilex asprella and Ilex asprella OP104164 was relatively close. A high-quality chloroplast genome of Ilex asprella (Hook.et Arn.) Champ. ex BenthWe had been successfully assembled, obtaining the sequence structure, sequence characteristics, and codon usage preference information of its chloroplast genome, which laying the foundation for the identification, evolution, and phylogenetic research of medicinal plants in the genus Ilex.

Key words: Ilex asprella (Hook.et Arn.) Champ.ex Benth, chloroplast genome, sequence structure characteristics, codon bias, phylogenetic evolution

CLC Number:

S793.9

HONG Senrong, ZHANG Zhiyao, MIN Lingrui, DU Jingyi, ADILE Wumar, HE Lingting, HARIMILLAN Ahemaiti, WU Lijuan, HU Liexin. Sequence Characteristics, Codon Bias, and Phylogenetic Analysis of Chloroplast Genome of Ilex asprella (Hook.et Arn.) Champ. ex Benth[J]. Chinese Agricultural Science Bulletin, 2026, 42(8): 67-76.

Figures/Tables 5

References 36

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基因功能	基因类型	基因名	基因数量
光合作用	光系统Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
	光系统Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbG、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	16
	NADH脱氢酶	ndhA、ndhB、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体	petA、petB、petD、petG、petL、petN	6
	ATP合成酶	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制	核糖体大亚基蛋白质	rpl14、rpl16、rpl2、rpl20、rpl22、rpl23*、rpl32、rpl33、rpl36*	11
	核糖体小亚基蛋白质	rps11、rps12、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7*、rps8*	14
	核糖体大亚基	rbcL	1
	RNA聚合酶	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体	rrn16、rrn23*、rrn4.5*、rrn5**	8
	转运	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*	37
其他基因	成熟酶	matK	1
	蛋白酶	clpP1	1
	囊膜蛋白	cemA	1
	乙酰辅酶A羧化酶	accD	1
	c-型细胞色素合成基因	ccsA	1
	翻译起始因子	infA	1
未知功能基因	保守假设叶绿体阅读框架	ycf1、ycf15*、ycf2、ycf68、ycf3(pafI)、ycf4(pafII*)	10

基因功能	基因类型	基因名	基因数量
光合作用	光系统Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
	光系统Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbG、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	16
	NADH脱氢酶	ndhA、ndhB、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体	petA、petB、petD、petG、petL、petN	6
	ATP合成酶	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制	核糖体大亚基蛋白质	rpl14、rpl16、rpl2、rpl20、rpl22、rpl23*、rpl32、rpl33、rpl36*	11
	核糖体小亚基蛋白质	rps11、rps12、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7*、rps8*	14
	核糖体大亚基	rbcL	1
	RNA聚合酶	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体	rrn16、rrn23*、rrn4.5*、rrn5**	8
	转运	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*	37
其他基因	成熟酶	matK	1
	蛋白酶	clpP1	1
	囊膜蛋白	cemA	1
	乙酰辅酶A羧化酶	accD	1
	c-型细胞色素合成基因	ccsA	1
	翻译起始因子	infA	1
未知功能基因	保守假设叶绿体阅读框架	ycf1、ycf15*、ycf2、ycf68、ycf3(pafI)、ycf4(pafII*)	10

密码子	氨基酸	相对同义密码子使用度	RSCU低表达	RSCU高表达	RSCU差值
UAA	Ter	1.54945	1.000000	1.800000	0.800
GUA	Val	1.46402	1.234040	1.666670	0.433
CGU	Arg	1.28024	0.726115	0.857143	0.131
CUU	Leu	1.28587	1.209880	1.666670	0.457
UCA	Ser	1.22864	1.681320	2.000000	0.319

密码子	氨基酸	相对同义密码子使用度	RSCU低表达	RSCU高表达	RSCU差值
UAA	Ter	1.54945	1.000000	1.800000	0.800
GUA	Val	1.46402	1.234040	1.666670	0.433
CGU	Arg	1.28024	0.726115	0.857143	0.131
CUU	Leu	1.28587	1.209880	1.666670	0.457
UCA	Ser	1.22864	1.681320	2.000000	0.319