[1]郑梦迪,陈斯琪,尹念念,等.黄精属植物叶绿体基因组系统发育与密码子使用偏好分析[J].江苏农业学报,2025,(09):1704-1713.[doi:doi:10.3969/j.issn.1000-4440.2025.09.005]
　ZHENG Mengdi,CHEN Siqi,YIN Niannian,et al.Phylogenetic analysis and codon bias in the chloroplast genomes of Polygonatum species[J].,2025,(09):1704-1713.[doi:doi:10.3969/j.issn.1000-4440.2025.09.005]
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黄精属植物叶绿体基因组系统发育与密码子使用偏好分析()

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2025年09期
页码:
1704-1713
栏目:
遗传育种·生理生化
出版日期:
2025-09-30

文章信息/Info

Title:
Phylogenetic analysis and codon bias in the chloroplast genomes of Polygonatum species
作者:
郑梦迪; 陈斯琪; 尹念念; 冯言熙
(西安医学院,陕西西安710021)
Author(s):
ZHENG Mengdi; CHEN Siqi; YIN Niannian; FENG Yanxi
(Xi’an Medical University, Xi’an 710021, China)
关键词:
黄精属; 叶绿体基因组; 密码子使用偏好; 系统发育分析
Keywords:
Polygonatum; chloroplast genome; codon bias; phylogenetic analysis
分类号:
S567
DOI:
doi:10.3969/j.issn.1000-4440.2025.09.005
文献标志码:
A
摘要:
为探索黄精属植物叶绿体基因组的进化、密码子选择倾向和相关影响要素。本研究利用MISA、IRscope、mVISTA等在线工具分析8种黄精属植物叶绿体基因组特征；利用CodonW 1.4.2、CUSP、Excel、MEGA11等软件进行密码子偏好性和系统发育分析。结果表明,碱基A和碱基T组成的单核苷酸重复序列被频繁使用；叶绿体基因组界限稳定,区域组成差异小。密码子中GC含量从第1碱基位到第3碱基位递减,末位偏好碱基A或碱基U；叶绿体基因组中密码子的选择倾向受多因素共同作用,其中自然选择是主要原因。最终筛选出8种黄精属植物共有9个相同的最优密码子。系统发育研究结果揭示独花黄精和距药黄精与黄精属其他6种植物的关系较远。本研究结果为黄精属植物的系统发育分析提供了支持,并为黄精药材的鉴定、品种优化及遗传育种工作奠定了理论基础。
Abstract:
To investigate the chloroplast genome phylogeny, codon usage bias patterns and related influencing factors of plants in the genus Polygonatum, the MISA, IRscope, and mVISTA were used to analyze chloroplast genome characteristics of eight plants in the genus Polygonatum. CodonW 1.4.2, CUSP, Excel, and MEGA11 were utilized to perform codon bias and phylogenetic analysis. The results indicated that mononucleotide repeat sequences composed of bases A and T were frequently utilized. The boundaries of the chloroplast genomes were highly conserved, exhibiting minimal variation in genomic composition. The GC content in codons progressively declined from the first to the third codon position, with a pronounced bias toward base A or U at the third position. Codon usage bias in chloroplast genomes was shaped by multiple factors, with natural selection serving as the primary driving force. Ultimately, nine identical optimal codons were identified as common to all eight studied Polygonatum species. Phylogenetic analysis revealed that Polygonatum hookeri and Polygonatum franchetii exhibited a distant relationship to the other six studied Polygonatum species. This study provides crucial support for phylogenetic analyses within the Polygonatum genus, while also laying a theoretical foundation for the authentication of Polygonatum medicinal materials, cultivar improvement, and genetic breeding efforts.

参考文献/References:

[1]陶弘景. 名医别录[M]. 尚志钧，辑校. 北京:中国中医药出版社,2013.
[2]葛洪. 抱朴子内篇[M]. 梅全喜，郝近大，冉懋雄，等，编译. 北京:中国中医药出版社,1997.
[3]中国药典委员会. 中华人民共和国药典[S]. 北京:中国医学出版社,2015.
[4]MA C D, CHANG H, YANG Y C, et al. Herbal textual research on polygonati rhizoma in famous classical formulas[J]. Chinese Journal of Experimental Traditional Medical Formulae,2022,28(10):193-206.
[5]GRANTHAM R, GAUTIER C, GOUY M, et al. Codon catalog usage is a genome strategy modulated for gene expressivity[J]. Nucleic Acids Research,1981,9(1):43-74.
[6]刘蒙蒙,邢咏梅,郭顺星. 基于转录组数据分析药用真菌猪苓密码子使用偏好性[J]. 药学学报,2020,55(5):1050-1055.
[7]王杰敏,马东来,韩晓伟,等. 24份忍冬属材料叶绿体基因组密码子使用偏好性分析[J]. 植物资源与环境学报,2023,32(3):12-23.
[8]GUSTAFSSON C, GOVINDARAJAN S, MINSHULL J. Codon bias and heterologous protein expression[J]. Trends in Biotechnology,2004,22(7):346-353.
[9]THODE V A, LOHMANN L G, SANMARTN I. Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels:a case study using Amphilophium (Bignonieae,Bignoniaceae)[J]. Journal of Systematics and Evolution,2020,58(6):1071-1089.
[10]覃雨倩. 天门冬科黄精属系统发育基因组学研究[D]. 吉首:吉首大学,2023.
[11]石乃星,谢平选,李立,等. 滇黄精叶绿体全基因组序列及其密码子使用偏性分析[J]. 热带亚热带植物学报,2022,30(3):336-348.
[12]BEIER S, THIEL T, MNCH T, et al. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics,2017,33(16):2583-2585.
[13]AMIRYOUSEFI A, HYVNEN J, POCZAI P. IRscope:an online program to visualize the junction sites of chloroplast genomes[J]. Bioinformatics,2018,34(17):3030-3031.
[14]FRAZER K A, PACHTER L, POLIAKOV A, et al. VISTA:computational tools for comparative genomics[J]. Nucleic Acids Research,2004,32:273-279.
[15]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.
[16]SUEOKA N. Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses[J]. Journal of Molecular Evolution,2001,53(4/5):469-476.
[17]NOVEMBRE J A. Accounting for background nucleotide composition when measuring codon usage bias[J]. Molecular Biology and Evolution,2002,19(8):1390-1394.
[18]ROMERO H, ZAVALA A, MUSTO H, et al. The influence of translational selection on codon usage in fishes from the family Cyprinidae[J]. Gene,2003,317:141-147.
[19]XIANG H, ZHANG R Z, BUTLER R B, et al. Comparative analysis of codon usage bias patterns in microsporidian genomes[J]. PLoS One,2015,10(6):0129223.
[20]KUMAR S, STECHER G, TAMURA K. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution,2016,33(7):1870-1874.
[21]WANG W W, LANFEAR R. Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants[J]. Genome Biology and Evolution,2019,11(12):3372-3381.
[22]韩凤,黄靖,章文伟,等. 多花黄精白绢病病原菌鉴定及室内药剂筛选[J]. 江苏农业学报,2024,40(12):2244-2253.
[23]何艳艳,龙晓明,杨虎权,等. 思茅松林下黄精田节肢动物群落组成结构及多样性分析[J]. 南方农业学报,2024,55(1):117-127.
[24]马菁华,刘芳,任启飞,等. 多花黄精致病真菌筛选及致病力鉴定[J]. 江苏农业学报,2023,39(7):1472-1482.
[25]钱丽华,严建立,吴晓疆,等. 基于滇黄精转录组序列的SSR标记开发及其在黄精属资源分析中的应用[J]. 江苏农业学报,2023,39(5):1120-1131.
[26]黄博,邓利娟,杨双琳,等. 云南3种黄精根系丛枝菌根真菌群落结构特征差异研究[J]. 南方农业学报,2023,54(6):1656-1666.
[27]SUEOKA N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons [J]. Journal of Molecular Evolution,1996,42:323.

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备注/Memo

备注/Memo:
收稿日期：2024-11-06基金项目：陕西省自然科学基础研究计划项目(2021JQ-782)；西安医学院科研能力提升计划项目(2022NLTS084、2024NLTS122)作者简介：郑梦迪(1988-),女,陕西咸阳人,博士,副教授,主要从事药用植物研究。(E-mail)670677492@qq.com
更新日期/Last Update: 2025-10-27