Chloroplast Genome Characteristics and Phylogenetic analysis of Potentilla fragarioides

doi:10.11733/j.issn.1007-0435.2024.11.005

Acta Agrestia Sinica ›› 2024, Vol. 32 ›› Issue (11): 3383-3390.DOI: 10.11733/j.issn.1007-0435.2024.11.005

Chloroplast Genome Characteristics and Phylogenetic analysis of Potentilla fragarioides

GUO Song^1,2, LIANG Xiang-lan¹, PENG Zi³, LU Quan³, ZENG Zhen-gui³

1. Smart Agriculture College(Internet of Things Engineering College) of Guangxi Science &Technology Normal University, Laibin, Guangxi Province 546199, China;
2. Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science & Technology Normal University, Laibin, Guangxi Province 546199, China;
3. College of Biology and Food Engnineering of Guangxi Science & Technology University, Laibin, Guangxi Province 546199, China

Received:2024-03-19 Revised:2024-04-22 Published:2024-11-29

莓叶委陵菜叶绿体基因组特征及其系统发育分析

郭松^1,2, 梁湘兰¹, 彭姿³, 卢全³, 曾珍贵³

1. 广西科技师范学院智慧农业学院(物联网工程学院), 广西来宾 546199;
2. 广西科技师范学院壮瑶药品质生物学重点实验室, 广西来宾 546199;
3. 广西科技师范学院生物与食品工程学院, 广西来宾 546199

通讯作者: 郭松,E-mail:guosong0804@163.com
作者简介:郭松(1987-),男,汉族,河南信阳人,博士,副教授,主要从事瑶药资源开发与利用,E-mail:lxl12311124@163.com
基金资助:
广西高校中青年教师科研基础能力提升项目(2021KY0862)；广西科技师范学院壮瑶药品质生物学重点实验室经费(GXKSKYPT2021007)；广西科技基地与人才专项(2021AC19423)资助

Abstract

Abstract: In order to determine the chloroplast genome characteristics of Potentilla fragarioides and to investigate its phylogenetic relationship within Rosaceae species,this study performed sequencing,assembly,and annotation of the chloroplast DNA genome of P. fragarioides,and obtained comprehensive information about its chloroplast genome by integrating bioinformatics methods. Based on this,a phylogenetic tree was constructed. The results showed that P. fragarioides complete chloroplast genome is 156 844 bp,which has a typical quadripartite structure with GC content of GC₃21,and a codon usage bias with A/T ending. The analysis of the IR boundary indicated that the genome structure of P. fragarioides is relatively conservative. Through phylogenetic analysis of 13 species in the Rosaceae family,including Fragaria,Rosa,and Potentilla,P. fragarioides was found to be closely related to Potentilla indica,with a bootstrap value of 100%. This study will contribute to the systematic and genetic research of P. fragarioides.

Key words: Potentilla fragarioides, Chloroplast genome, Phylogeny, Yao traditional medicine

摘要： 为解析莓叶委陵菜叶绿体基因组特征，探究其在蔷薇科物种中的发育关系，本研究通过莓叶委陵菜叶绿体基因组的测序、组装、注释以及结合生物信息方法获得其叶绿体全基因组特征信息，并构建了系统发育进化树。结果表明，莓叶委陵菜叶绿体基因组全长156 844 bp，为一个典型的四分体结构，GC含量GC₃21，密码子偏好以A/T结尾，IR边界分析表明，其基因组结构较为保守。通过与蔷薇科下草莓属、蔷薇属、委陵菜属的13个物种进行系统发育分析，得到莓叶委陵菜与蛇莓的亲缘关系较近，以100%自举值聚到一起。本研究将有助于莓叶委陵菜的系统发育和遗传研究。

关键词: 莓叶委陵菜, 叶绿体基因组, 系统发育, 瑶药

CLC Number:

Q789

GUO Song, LIANG Xiang-lan, PENG Zi, LU Quan, ZENG Zhen-gui. Chloroplast Genome Characteristics and Phylogenetic analysis of Potentilla fragarioides[J]. Acta Agrestia Sinica, 2024, 32(11): 3383-3390.

郭松, 梁湘兰, 彭姿, 卢全, 曾珍贵. 莓叶委陵菜叶绿体基因组特征及其系统发育分析[J]. 草地学报, 2024, 32(11): 3383-3390.

0
/ / Recommend

Add to citation manager EndNote|Ris|BibTeX

URL: https://manu40.magtech.com.cn/Jweb_cdxb/EN/10.11733/j.issn.1007-0435.2024.11.005

https://manu40.magtech.com.cn/Jweb_cdxb/EN/Y2024/V32/I11/3383

References

[1] 刘新波,李凤华,张利民,等.莓叶委陵菜的引种栽培[J].北方园艺,1998(Z1):142
[2] MAN-KYU H U H,HONG-WOOK H U H. Patterns of genetic diversity and population structure of the clonal herb,Potentilla fragarioides var. sprengeliana (Rosaceae) in Korea[J]. Journal of Integrative Plant Biology,2000,42(1):64-70
[3] 张艳. 7种委陵菜属植物光适应性研究[D].北京:北京林业大学,2021:1-6
[4] 马蓓蓓,辛华. 莓叶委陵菜营养成分和微量元素的测定和分析[J].中国野生植物资源,2011,30(2):54-56
[5] LI Y,LI K,YAO H. Chemical constituents from Potentilla fragarioides L[J]. Biochemical Systematics and Ecology,2020,93:104172
[6] TOMCZYK M,LESZCZYŃSKA K,JAKONIUK P. Antimicrobial activity of Potentilla species[J]. Fitoterapia,2008,79(7-8):592-594
[7] 张国娟,刘旻霞,李博文,等.玛曲高寒草甸植物黄帚橐吾与莓叶委陵菜种群点格局分析[J].生态学杂志,2021,40(6):1660-1668
[8] 卢政阳,于凤扬,肖月娥,等.北陵鸢尾叶绿体基因组及其特征分析[J].草地学报,2023,31(6):1656-1664
[9] DANIELL H,LIN C S,YU M,et al. Chloroplast genomes:diversity,evolution,and applications in genetic engineering[J]. Genome Biology,2016,17:1-29
[10] 张冬冬,韩宏伟,余镇藩,等. 12种蔷薇科植物叶绿体基因组密码子偏好性分析[J].中国农业科技导报,2023,25(8):65-75
[11] 龚意辉,周桂花,李丽梅,等.黄桃叶绿体基因组的组装与序列分析[J].热带作物学报,2022,43(8):1545-1553
[12] YU J,FU J,FANG Y,et al. Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus[J]. BMC Genomics,2022,23(1):32
[13] DIERCKXSENS N,MARDULYN P,SMITS G. Unraveling heteroplasmy patterns with NOVOPlasty[J]. NAR Genomics and Bioinformatics, 2020,2(1):lqz011
[14] SHI L,CHEN H,JIANG M,et al. CPGAVAS2,an integrated plastome sequence annotator and analyzer[J]. Nucleic Acids Research,2019,47(W1):W65-W73
[15] 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
[16] ZHANG D,GAO F,JAKOVLIC‘ I,et al. PhyloSuite:An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies[J]. Molecular Ecology Resources,2020,20(1):348-355
[17] BEIER S,THIEL T,MÜNCH T,et al. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics,2017,33(16):2583-2585
[18] 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
[19] BENSON G. Tandem repeats finder:a program to analyze DNA sequences[J]. Nucleic Acids Research,1999,27(2):573-580
[20] 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
[21] ROZEWICKI J,LI S,AMADA K M,et al. MAFFT-DASH:integrated protein sequence and structural alignment[J]. Nucleic Acids Research,2019,47(W1):W5-W10
[22] 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
[23] LI L,HU Y,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,2021,22:1-22
[24] 孙哲,李澳旋,杜晓蓉等.房山紫堇叶绿体基因组特征及其系统进化关系[J].草地学报,2022,30(8):1982-1989
[25] 李述成,郭生虎,贝盏临.小檗属植物叶绿体基因组序列结构及系统发育分析[J].中草药,2022,53(3):818-826
[26] 郝新艳,赵淑文,刘嘉伟,等.杂花苜蓿叶绿体基因组特征及系统发育分析[J].草地学报,2023,31(6):1665-1672
[27] WANG L,GUO Z,SHANG Q,et al. The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species:genome structure,sequence divergence,and phylogenetic analysis[J]. Brazilian Journal of Botany,2021,44:85-95
[28] TANG D,WEI F,CAI Z,et al. Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth[J]. Development Genes and Evolution,2021,231:1-9
[29] FAGES-LARTAUD M,HUNDVIN K,HOHMANN-MARRIOTT M F. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii[J]. The Plant Journal,2022,112(4):919-945
[30] 杨国锋,苏昆龙,赵怡然,等.蒺藜苜蓿叶绿体密码子偏好性分析[J].草业学报,2015,24(12):171-179
[31] XUE C,GENG F D,LI J J,et al. Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations:Evidence from plastid genome data[J]. Molecular Ecology,2021,30(22):5796-5813
[32] WANG Z,CAI Q,WANG Y,et al. Comparative analysis of codon bias in the chloroplast genomes of theaceae species[J]. Frontiers in Genetics,2022,13:824610

Chloroplast Genome Characteristics and Phylogenetic analysis of Potentilla fragarioides

莓叶委陵菜叶绿体基因组特征及其系统发育分析

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 14

Recommended Articles

Metrics

Comments

[1]	YU Zhi-wei, CHEN Yuan, GUO Feng-xia, DONG Peng-bin, WANG Hong-yan. Codon Usage Bias Analysis of the Chloroplast Genome of Isatis Indigotica [J]. Acta Agrestia Sinica, 2024, 32(8): 2374-2385.
[2]	DENG Niao-xu, LUO Zhong-yuan, SUN Zhi-xuan, MENG Jing, ZHAO Yan. Chloroplast Genome Evolution and Phylogenetic Analysis of Medicago sect. Spirocarpos [J]. Acta Agrestia Sinica, 2024, 32(8): 2394-2407.
[3]	WANG Tao, XU Cheng-ti, TANG Chu-yu, CAO Zheng-fei, XIAO Meng-jun, HE Min, LI Xiu-zhang, LI Yu-ling. Morphological Analysis of Pedicularis Based on Ancestral Character Evolution and Chloroplast Genome [J]. Acta Agrestia Sinica, 2024, 32(7): 2039-2053.
[4]	DU Ming-chuan, WANG Wei, BAO Hai-juan, GE Cuo, ZHANG Rui, WANG Jiu-li, LIU Jing. Analysis of Codon Bias in Chloroplast Genome of Trigonella Foenum-graecum [J]. Acta Agrestia Sinica, 2024, 32(2): 409-418.
[5]	LU Zheng-yang, YU Feng-yang, XIAO Yue-e, SHI Yu, BI Xiao-ying. Complete Chloroplast Genomes and Characteristics Analysis of Iris typhifolia [J]. Acta Agrestia Sinica, 2023, 31(6): 1656-1664.
[6]	HAO Xin-yan, ZHAO Shu-wen, LIU Jia-wei, SHI Rui, WANG Xiao-long, LI Ying, WANG Xiao-yu, MI Fu-gui. Characteristics and Phylogenetic Analysis of Chloroplast Genome of Medicago varia [J]. Acta Agrestia Sinica, 2023, 31(6): 1665-1672.
[7]	HONG Sen-rong, LIN Shun-lai, LI Ying-ping, LI Yun-yun, LI He-yue, ZHANG Qing-bao. Analysis of the Complete Chloroplast Genome Sequence Characteristics and Its Code Usage Bias of Sorghum bicolor [J]. Acta Agrestia Sinica, 2023, 31(12): 3636-3650.
[8]	GUO Ran-hao, ZHAO SHU-wen, MI FU-gui, HOU WEI-feng, ZHAO LI-xing. Chloroplast Genome Analysis of An Erect Semi-Wild Soybean [J]. Acta Agrestia Sinica, 2023, 31(11): 3334-3342.
[9]	QI He-xing, WANG Hai-chun, LU Guang-xin, LI Zong-ren, TIAN Feng, HE Chen-bang, XU Cheng-ti, ZOU Hai-tao, LEI Sheng-yan, LI Hong-fang, TANG Hai-peng. Isolation,Identification and Pathogenicity Analysis of Helminthosporioid Fungi from Silage Maize [J]. Acta Agrestia Sinica, 2023, 31(1): 40-49.
[10]	SUN Zhe, LI Ao-xuan, DU Xiao-rong, SONG Yun, QIAO Yong-gang. Phylogenetic Relationship and Characterization of the Complete Chloroplast Genome of Corydalis fangshanensis W. T. Wang ex S. Y. He [J]. Acta Agrestia Sinica, 2022, 30(8): 1982-1989.
[11]	SUN Zhi-xuan, AO Ping-xing, BI Yu-fen, ZHAO Yan. Complete Chloroplast Genome Sequence and Characteristics Analysis of Medicago sativa ‘Deqin’ [J]. Acta Agrestia Sinica, 2022, 30(2): 320-328.
[12]	AN Ming-zhu, HAN Bo, JIANG Hua, DUAN Xin-hui, WEN Yi-fu, ZHOU Kai. Research Progress of Dactylis Species Origin and Phylogeny Analysis [J]. Acta Agrestia Sinica, 2021, 29(12): 2637-2644.
[13]	TIAN Chun-yu, WU Zi-nian, LI Xian-song, LI Zhi-yong. Codon Usage Bias of Chloroplast Genome in Medicago ruthenica [J]. Acta Agrestia Sinica, 2021, 29(12): 2678-2684.
[14]	ZHENG Hong-mei, HU Tian-ming. Study on Seed Germination Characteristics and Molecular Phylogeny of Kobresia Willd.in Tibetan Plateau [J]. , 2008, 16(5): 542-544.