Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves

doi:10.3969/j.issn.1004-1524.20250193

Acta Agriculturae Zhejiangensis ›› 2026, Vol. 38 ›› Issue (2): 284-300.DOI: 10.3969/j.issn.1004-1524.20250193

• Horticultural Science • Previous Articles Next Articles

Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves

YIN Minghua¹^,²(), KANG Haiyan¹, ZHONG Keqing¹, WU Lijuan³^,⁴, HU Liexin³^,⁴, WU Chunfa³^,⁴, GONG Shuifei³^,⁴

1. College of Life Sciences, Shangrao Normal University, Shangrao 334001, Jiangxi, China
2. Shangrao Key Laboratory of Protection and Utilization of Medicinal and Edible Plant Resources, Shangrao 334001, Jiangxi, China
3. Jiangxi Qigexuan Ecological Agriculture Development Co., Ltd., Shangrao 334699, Jiangxi, China
4. Shangrao Qixuan Planting Professional Cooperative, Shangrao 334699, Jiangxi, China

Received:2025-03-12 Online:2026-02-25 Published:2026-03-24

Abstract

Abstract:

To investigate the structural characteristics and phylogenetic relationships of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja, this study used leaves of C. paliurus from Guangxin District, Shangrao City, Jiangxi Province as material. The complete chloroplast genome sequence was obtained through high-throughput sequencing, and its sequence characteristics, codon usage bias, and phylogenetic relationships were analyzed using bioinformatics methods. The results showed that the complete chloroplast genome of C. paliurus from Guangxin District, Shangrao City, was 160 992 bp in length, with an average GC content of 37.48%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. 84 simple sequence repeats (SSR) were identified, predominantly consisting of A/T repeats, along with 52 long repeats, mainly forward repeats and palindromic repeats. Comparison with 15 related species revealed that the gene types and arrangement order in the four boundary regions [LSC-IRB(JLB), SSC-IRB(JSB), SSC-IRA(JSA) and LSC-IRA(JLA)] of the C. paliurus chloroplast genome were largely consistent, with no significant differences in the extent of boundary expansion or contraction. Ten highly variable regions were identified in the LSC and SSC: matK_rps16, rps16_trnQ-UUG, psbK_psbI, trnS-GCU_trnG-GCC, trnT-GGU_psbD, ndhC_trnV-UAC, trnV-UAC, rpl22, ycf1, and rps15_ycf1. The overall codon usage bias in the C. paliurus chloroplast genome was weak and primarily influenced by natural selection. 15 optimal codons were identified: AAU, GAA, CAU, AAA, AUU, AUG, GGA, GGU, CCU, ACA, GUA, GUU, CGU, UUG and AGU, most of which end with U or A. Phylogenetic analysis indicated that C. paliurus from Guangxin District, Shangrao City, clusters closely with the diploid C. paliurus from Nanjing (MW531677, Cyclocarya paliurus isolate 2nPA), showing a close genetic relationship. The findings of this study provided a theoretical basis for research on genetic diversity, molecular breeding, and species identification of C. paliurus.

Key words: Cyclocarya paliurus(Batal.) Iljinskaja, chloroplast genome, sequence characteristic, codon bias, phylogenetic analysis

CLC Number:

S792.99

YIN Minghua, KANG Haiyan, ZHONG Keqing, WU Lijuan, HU Liexin, WU Chunfa, GONG Shuifei. Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves[J]. Acta Agriculturae Zhejiangensis, 2026, 38(2): 284-300.

Figures/Tables 13

References 53

[1]	郭春兰, 柳水香, 肖仁才, 等. 我国特有单种属珍稀资源植物青钱柳繁育技术研究进展[J]. 中国野生植物资源, 2024, 43(8): 64-69.
	GUO C L, LIU S X, XIAO R C, et al. Research progress on breeding technology of Cyclocarya paliurus, a rare plant of single species in China[J]. Chinese Wild Plant Resources, 2024, 43(8): 64-69.
[2]	刘夏岚, 宋子琪, 胡凤荣, 等. 青钱柳二倍体和四倍体叶特征比较研究[J]. 南京林业大学学报(自然科学版), 2024, 48(4): 76-84.
	LIU X L, SONG Z Q, HU F R, et al. A comparative study on leaf characters between diploid and tetraploid of Cyclocarya paliurus[J]. Journal of Nanjing Forestry University(Natural Sciences Edition), 2024, 48(4): 76-84.
[3]	杨杰, 董佳萍, 张露, 等. 青钱柳降糖降尿酸活性部位色谱指纹图谱研究及主成分含量测定[J]. 分析测试学报, 2024, 43(7): 955-962.
	YANG J, DONG J P, ZHANG L, et al. Chromatographic fingerprinting studies and the main ingredient content determination of hypoglycemic and uric acid-lowering active part of Cyclocarya paliurus[J]. Journal of Instrumental Analysis, 2024, 43(7): 955-962.
[4]	谷月营, 张赞培, 毛乾兴, 等. 青钱柳无性系对寒驯化的生理响应及其抗寒性初步评价[J]. 生态环境学报, 2024, 33(4): 531-538.
	GU Y Y, ZHANG Z P, MAO Q X, et al. Physiological response of Cyclocarya paliurus clones to cold acclimation and preliminary evaluation of their cold resistance[J]. Ecology and Environmental Sciences, 2024, 33(4): 531-538.
[5]	李进, 幸伟年, 何定军, 等. 青钱柳无性系子代测定林早期生长表现[J]. 南方林业科学, 2024, 52(2): 5-9.
	LI J, XING W N, HE D J, et al. Early growth performance on the clonal progeny test forest of Cyclocarya paliurus[J]. South China Forestry Science, 2024, 52(2): 5-9.
[6]	LI D M, PAN Y G, WU X Y, et al. Comparative chloroplast genomics, phylogenetic relationships and molecular markers development of Aglaonema commutatum and seven green cultivars of Aglaonema[J]. Scientific Reports, 2024, 14: 11820.
[7]	CHEN L L, ZHU W, SONG Y, et al. Complete chloroplast genome sequences of endangered tropical Fosbergia species (Family: Rubiaceae)[J]. Forests, 2024, 15(7): 1150.
[8]	YIN D B, MU Y T, LI X, et al. Comparison of the complete chloroplast genomes in the Astragalus[J]. Legume Research-an International Journal, 2024: 420-427.
[9]	LI B Y, HUANG K, CHEN X L, et al. Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis[J]. BMC Genomic Data, 2024, 25(1): 57.
[10]	GAO Z Y, WU Y Z, LI M Z, et al. The auxin response factor (ARF) gene family in Cyclocarya paliurus: genome-wide identification and their expression profiling under heat and drought stresses[J]. Physiology and Molecular Biology of Plants, 2024, 30(6): 921-944.
[11]	黄岩萌, 易炎, 卞国良, 等. 青钱柳染色体的制片技术及核型分析[J]. 东北林业大学学报, 2024, 52(4): 46-51.
	HUANG Y M, YI Y, BIAN G L, et al. The production technique and karyotype analysis of Cyclocarya paliurus chromosome[J]. Journal of Northeast Forestry University, 2024, 52(4): 46-51.
[12]	王纪, 方升佐. 不同抗褐化剂对青钱柳愈伤组织酶活性和生长的影响[J]. 南京林业大学学报(自然科学版), 2023, 47(6): 167-174.
	WANG J, FANG S Z. Effects of different anti-browning agents on enzyme activity and growth in callus of Cyclocarya paliurus[J]. Journal of Nanjing Forestry University(Natural Sciences Edition), 2023, 47(6): 167-174.
[13]	刘恭孝, 谢磊, 甄学静, 等. 青钱柳发酵物对2型糖尿病合并肝损伤大鼠糖脂代谢及肠道菌群的调节作用[J]. 食品与发酵工业, 2024, 50(12): 220-226.
	LIU G X, XIE L, ZHEN X J, et al. Exploration of Cyclocarya paliurus fermentation on glucolipid metabolism and intestinal microflora in type 2 diabetes mellitus rats combined with liver injury[J]. Food and Fermentation Industries, 2024, 50(12): 220-226.
[14]	QU Y Q, WANG Q, YU Y H, et al. Comparative analysis of the complete chloroplast genome between tetraploidy and diploidy of Cyclocarya paliurus(Batal.) Iljinskaja[J]. Mitochondrial DNA Part B, Resources, 2021, 6(9): 2669-2671.
[15]	HU Y H, YAN J, FENG X J, et al. Characterization of the complete chloroplast genome of wheel wingnut (Cyclocarya paliurus), an endemic in China[J]. Conservation Genetics Resources, 2017, 9(2): 273-275.
[16]	PAHLICH E, GERLITZ C. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochemistry, 1980, 19: 11-13.
[17]	LANGDON W B. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks[J]. BioData Mining, 2015, 8: 1.
[18]	DIERCKXSENS N, MARDULYN P, SMITS G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Research, 2017, 45(4): e18.
[19]	HUANG X, MADAN A. CAP3: a DNA sequence assembly program[J]. Genome Research, 1999, 9(9): 868-877.
[20]	TILLICH M, LEHWARK P, PELLIZZER T, et al. GeSeq-versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Research, 2017, 45(W1): W6-W11.
[21]	LOWE T M, EDDY S R. tRNAscan-SE a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Research, 1997, 25(5): 955-964.
[22]	LIU S Y, NI Y, LI J L, et al. CPGView: a package for visualizing detailed chloroplast genome structures[J]. Molecular Ecology Resources, 2023, 23(3): 694-704.
[23]	THIEL T, MICHALEK W, VARSHNEY R, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theoretical and Applied Genetics, 2003, 106(3): 411-422.
[24]	KURTZ S, CHOUDHURI J V, OHLEBUSCH E, et al. REPuter: the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Research, 2001, 29(22): 4633-4642.
[25]	SHARP P M, LI W H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications[J]. Nucleic Acids Research, 1987, 15(3): 1281-1295.
[26]	KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Molecular Biology and Evolution, 2013, 30(4): 772-780.
[27]	AMIRYOUSEFI A, HYVÖNEN J, POCZAI P. IRscope: an online program to visualize the junction sites of chloroplast genomes[J]. Bioinformatics, 2018, 34(17): 3030-3031.
[28]	ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 2017, 34(12): 3299-3302.
[29]	张晶晶, 袁庆, 魏瑶, 等. 忍冬属囊管组植物叶绿体基因组进化分析[J]. 中草药, 2024, 55(9): 3085-3097.
	ZHANG J J, YUAN Q, WEI Y, et al. Evolutionary analysis of chloroplast genomes of Sect. Isika(Lonicera) species[J]. Chinese Traditional and Herbal Drugs, 2024, 55(9): 3085-3097.
[30]	SUEOKA N. Directional mutation pressure and neutral molecular evolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 1988, 85(8): 2653-2657.
[31]	WRIGHT F. The ‘effective number of codons’ used in a gene[J]. Gene, 1990, 87(1): 23-29.
[32]	ROMERO H, ZAVALA A, MUSTO H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces[J]. Nucleic Acids Research, 2000, 28(10): 2084-2090.
[33]	SUEOKA N. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position[J]. Gene, 1999, 238(1): 53-58.
[34]	郭佳星, 黄祥, 杨梅花, 等. 桦木科叶绿体基因组密码子偏好性及系统发育分析[J]. 中国农业科技导报, 2023, 25(10): 74-83.
	GUOJIA X, HUANG X, YANG M H, et al. Analysis of codon usage bias and phylogenetic in chloroplast genome of Betulaceae[J]. Journal of Agricultural Science and Technology, 2023, 25(10): 74-83.
[35]	LLOYD A T, SHARP P M. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae[J]. Nucleic Acids Research, 1992, 20(20): 5289-5295.
[36]	PRICE M N, DEHAL P S, ARKIN A P. FastTree 2: approximately maximum-likelihood trees for large alignments[J]. PLoS One, 2010, 5(3): e9490.
[37]	MOHANTA T K, KHAN A L, HASHEM A, et al. Genomic and evolutionary aspects of chloroplast tRNA in monocot plants[J]. BMC Plant Biology, 2019, 19(1): 39.
[38]	YAN L J, WANG H L, HUANG X, et al. Chloroplast genomes of genus Tilia: comparative genomics and molecular evolution[J]. Frontiers in Genetics, 2022, 13: 925726.
[39]	HU S Q, SHI W B, HUANG Y H, et al. Comparative analysis of complete chloroplast genomes of five Anemone species and phylogenetic analysis within Tribe Anemoneae(Ranunculaceae)[J]. Journal of Plant Biochemistry and Biotechnology, 2024, 33(3): 271-287.
[40]	QU K, CHEN Y, LIU D, et al. Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure[J]. Plant Cell Reports, 2024, 43(6): 150.
[41]	PEI D, YU X, FU W H, et al. The evolution and formation of centromeric repeats analysis in Vitis vinifera[J]. Planta, 2024, 259(5): 99.
[42]	HAN F C, BI C W, ZHAO Y X, et al. Unraveling the complex evolutionary features of the Cinnamomum camphora mitochondrial genome[J]. Plant Cell Reports, 2024, 43(7): 183.
[43]	XU S J, TENG K, ZHANG H, et al. Chloroplast genomes of four Carex species: long repetitive sequences trigger dramatic changes in chloroplast genome structure[J]. Frontiers in Plant Science, 2023, 14: 1100876.
[44]	LI L, HU Y F, HE M, et al. Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia[J]. BMC Genomics, 2021, 22(1): 138.
[45]	CHEN S Y, LI K, CAO W Q, et al. Codon-resolution analysis reveals a direct and context-dependent impact of individual synonymous mutations on mRNA level[J]. Molecular Biology and Evolution, 2017, 34(11): 2944-2958.
[46]	罗秦欢, 段炼, 赵月梅. “红阳”猕猴桃叶绿体基因组密码子使用偏性分析[J]. 西南林业大学学报(自然科学), 2024, 44(6): 81-88.
	LUO Q H, DUAN L, ZHAO Y M. Codon usage bias of chloroplast genome in Actinidia chinensis ‘Hongyang’[J]. Journal of Southwest Forestry University(Natural Sciences), 2024, 44(6): 81-88.
[47]	WALIA G K, DHILLON G K. DNA barcoding and molecular phylogeny of genus Pseudagrion(Odonata: Coenagrionidae) based on mitochondrial COI ND1 and 16S rRNA genes[J]. International Journal of Tropical Insect Science, 2024, 44(4): 1567-1590.
[48]	WANG H J, WU Z G, LI T, et al. Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata[J]. BMC Plant Biology, 2024, 24(1): 644.
[49]	NOROOZI M, GHAHREMANINEJAD F, RIAHI M, et al. Phylogenomics and plastome evolution of lithospermeae (Boraginaceae)[J]. BMC Plant Biology, 2024, 24(1): 957.
[50]	DELSUC F, BRINKMANN H, PHILIPPE H. Phylogenomics and the reconstruction of the tree of life[J]. Nature Reviews Genetics, 2005, 6(5): 361-375.
[51]	QU Y Q, SHANG X L, ZENG Z Y, et al. Whole-genome duplication reshaped adaptive evolution in a relict plant species, Cyclocarya paliurus[J]. Genomics, Proteomics & Bioinformatics, 2023, 21(3): 455-469.
[52]	田慧, 陈宏夏, 黄勇, 等. 青钱柳种质资源SCoT分子标记遗传多样性分析[J]. 世界科学技术-中医药现代化, 2022, 24(7): 2732-2739.
	TIAN H, CHEN H X, HUANG Y, et al. Genetic diversity of germplasm resource SCoT of Cyclocarya paliurus(Batal.) Iljinsk by molecular markers[J]. World Science and Technology-Modernization of Traditional Chinese Medicine, 2022, 24(7): 2732-2739.
[53]	陈秀娟, 柏明娥, 王丽玲, 等. 青钱柳种质资源亲缘关系的ISSR分析评价[J]. 中国林副特产, 2016(4): 6-10.
	CHEN X J, BAI M E, WANG L L, et al. ISSR analysis and evaluation of genetic relationship of Cyclocarya paliurus germplasm resources[J]. Forest By-Product and Speciality in China, 2016(4): 6-10.

基因功能 Gene function	基因类型 Gene type	基因名 Gene name	基因数量 Number of genes
光合作用	光系统Ⅰ Photosystem Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis	光系统Ⅱ Photosystem Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	15
	NADH脱氢酶 NADH dehydrogenase	ndhA、ndhB^、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN	6
	ATP合成酶ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制 Self replication	核糖体大亚基蛋白质 Ribosomal large subunit protein	rpl14、rpl16、rpl2^、rpl20、rpl22、rpl23^、rpl32、rpl33、rpl36	11
	核糖体小亚基蛋白质 Ribosomal small subunit protein	rps11、rps12^、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7^、rps8	14
	核糖体大亚基Ribosomal large subunit	rbcL	1
	RNA聚合酶RNA polymerase	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体RNA Ribosomal RNA	rrn16^、rrn23^、rrn4.5^、rrn5^	8
	转运RNA transfer RNA	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Other genes	成熟酶Mature enzyme	matK	1
	蛋白酶Protease	clpP1	1
	囊膜蛋白Envelope 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
	翻译起始因子Translation initiation factor	infA	1
未知功能基因 Unknown genes	保守假设叶绿体阅读框架 Conservative assumption of chloroplast reading framework	ycf1^、ycf15^、ycf2^、ycf3(pafI)、ycf4(pafII*)	8

基因功能 Gene function	基因类型 Gene type	基因名 Gene name	基因数量 Number of genes
光合作用	光系统Ⅰ Photosystem Ⅰ	psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis	光系统Ⅱ Photosystem Ⅱ	psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psaJ、psbK、psbL、psbM、psbT、psbZ、psbN(pbf1)	15
	NADH脱氢酶 NADH dehydrogenase	ndhA、ndhB^、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK*	12
	细胞色素b/f复合体 Cytochrome b/f complex	petA、petB、petD、petG、petL、petN	6
	ATP合成酶ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI	6
自我复制 Self replication	核糖体大亚基蛋白质 Ribosomal large subunit protein	rpl14、rpl16、rpl2^、rpl20、rpl22、rpl23^、rpl32、rpl33、rpl36	11
	核糖体小亚基蛋白质 Ribosomal small subunit protein	rps11、rps12^、rps14、rps15、rps16、rps18、rps19、rps2、rps3、rps4、rps7^、rps8	14
	核糖体大亚基Ribosomal large subunit	rbcL	1
	RNA聚合酶RNA polymerase	rpoA、rpoB、rpoC1、rpoC2	4
	核糖体RNA Ribosomal RNA	rrn16^、rrn23^、rrn4.5^、rrn5^	8
	转运RNA transfer RNA	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Other genes	成熟酶Mature enzyme	matK	1
	蛋白酶Protease	clpP1	1
	囊膜蛋白Envelope 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
	翻译起始因子Translation initiation factor	infA	1
未知功能基因 Unknown genes	保守假设叶绿体阅读框架 Conservative assumption of chloroplast reading framework	ycf1^、ycf15^、ycf2^、ycf3(pafI)、ycf4(pafII*)	8

密码子 Codon	氨基酸 Amino acid	相对同义密码子使用度 Relative synonymous codon usage	RSCU低表达 RSCU low expression	RSCU高表达 RSCU high expression	RSCU差值 RSCU difference
AAU	天冬酰胺Asn	1.535	1.375	1.500	0.125
GAA	谷氨酸Glu	1.508	1.556	1.714	0.159
CAU	组氨酸His	1.574	1.000	1.200	0.200
AAA	赖氨酸Lys	1.494	1.000	1.333	0.333
AUU	异亮氨酸Ile	1.461	1.200	1.800	0.600
AUG	蛋氨酸Met	2.981	1.000	1.556	0.556
GGA	甘氨酸Gly	1.634	1.647	1.846	0.199
GGU	甘氨酸Gly	1.333	0.706	0.923	0.217
CCU	脯氨酸Pro	1.502	1.143	1.500	0.357
ACA	苏氨酸Thr	1.213	1.091	1.500	0.409
GUA	缬氨酸Val	1.566	0.923	2.000	1.077
GUU	缬氨酸Val	1.445	1.154	1.333	0.179
CGU	精氨酸Arg	1.304	0.278	0.545	0.268
UUG	亮氨酸Leu	1.187	0.938	1.059	0.121
AGU	丝氨酸Ser	1.216	1.053	1.455	0.402

密码子 Codon	氨基酸 Amino acid	相对同义密码子使用度 Relative synonymous codon usage	RSCU低表达 RSCU low expression	RSCU高表达 RSCU high expression	RSCU差值 RSCU difference
AAU	天冬酰胺Asn	1.535	1.375	1.500	0.125
GAA	谷氨酸Glu	1.508	1.556	1.714	0.159
CAU	组氨酸His	1.574	1.000	1.200	0.200
AAA	赖氨酸Lys	1.494	1.000	1.333	0.333
AUU	异亮氨酸Ile	1.461	1.200	1.800	0.600
AUG	蛋氨酸Met	2.981	1.000	1.556	0.556
GGA	甘氨酸Gly	1.634	1.647	1.846	0.199
GGU	甘氨酸Gly	1.333	0.706	0.923	0.217
CCU	脯氨酸Pro	1.502	1.143	1.500	0.357
ACA	苏氨酸Thr	1.213	1.091	1.500	0.409
GUA	缬氨酸Val	1.566	0.923	2.000	1.077
GUU	缬氨酸Val	1.445	1.154	1.333	0.179
CGU	精氨酸Arg	1.304	0.278	0.545	0.268
UUG	亮氨酸Leu	1.187	0.938	1.059	0.121
AGU	丝氨酸Ser	1.216	1.053	1.455	0.402

Structural characterization and phylogenetic analysis of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja leaves

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References 53

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重复单元碱基类型 Repetitive unit base type	重复单元重复次数Repetitive unit repetition times													总数 Total number
重复单元碱基类型 Repetitive unit base type	5	6	7	8	9	10	11	12	13	14	15	16	17	总数 Total number
A/T	0	0	0	0	0	27	20	13	5	6	0	1	1	73
C/G	0	0	0	0	0	2	0	0	0	0	0	0	0	2
AT/AT	0	2	4	2	0	0	0	0	0	0	0	0	0	8
AAT/ATT	1	0	0	0	0	0	0	0	0	0	0	0	0	1

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[6]	PU Lusha, SU Shibo, CHEN Xiaohan, ZHAO Lili, CHEN Hongyan. Prokaryotic expression and phylogenetic analysis of ORF2 gene of goose astrovirus [J]. , 2020, 32(5): 789-797.
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