Chloroplast Genome Analysis of An Erect Semi-Wild Soybean

doi:10.11733/j.issn.1007-0435.2023.11.012

Acta Agrestia Sinica ›› 2023, Vol. 31 ›› Issue (11): 3334-3342.DOI: 10.11733/j.issn.1007-0435.2023.11.012

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Chloroplast Genome Analysis of An Erect Semi-Wild Soybean

GUO Ran-hao^1,2, ZHAO SHU-wen^1,2, MI FU-gui¹, HOU WEI-feng³, ZHAO LI-xing³

1. College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010000, China;
2. National Experimental Teaching Demonstration Center of Botany, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010000, China;
3. Hinggan League Institute of Agricultural and Animal Husbandry Sciences, Hinggan League, Inner Mongolia 137400, China

Received:2023-04-18 Revised:2023-05-31 Online:2023-11-15 Published:2023-12-01

直立型半野生大豆叶绿体基因组分析

郭冉昊^1,2, 赵淑文^1,2, 米福贵¹, 候伟峰³, 赵力兴³

1. 内蒙古农业大学草原与资源环境学院, 内蒙古呼和浩特 010000;
2. 内蒙古农业大学植物学国家级实验教学示范中心, 内蒙古呼和浩特 010000;
3. 兴安盟农牧科学研究所, 内蒙古兴安盟 137400

通讯作者: 赵淑文,E-mail:zhaoshuwen1226@163.com;米福贵,E-mail:mfgui@163.com
作者简介:郭冉昊(1997-),女,蒙古族,内蒙古巴彦淖尔人,主要从事牧草种质资源与利用方面研究,硕士研究生,E-mail:214597507@qq.com
基金资助:
兴安盟野生植物资源调查研究资助

Abstract

Abstract: Illumina high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of an erect semi-wild soybean (Glycine gracilis) to obtain a complete chloroplast genome,so as to explore its structural characteristics,and provide a basis for subsequent related analysis on chloroplast genome and diversity protection and phylogeny of soybean resources. The results demonstrated that the full-length chloroplast genome of that erect semi-wild soybean was 148 320 bp,which was a typical tetrad structure.108 genes were annotated,including 66 protein-coding genes,29 tRNA genes and 4 rRNA genes. A total of 87 SSR loci were detected in the genome sequence,of which 55,19,4,7 and 2 loci were corresponding to mononucleotide,dinucleotide,trinucleotide,tetranucleotide and pentanucleotide,respectively. Based upon the phylogeny analysis,that erect semi-wild soybean was closely related to the published common annual semi-wild soybean (Glycine gracilis),cultivated soybean (Glycine max),and wild soybean (Glycine soja).

Key words: Wild soybean, Chloroplast genome, Simple repeat sequence, Codon preference, Phylogeny analysis

摘要： 采用Illumina高通量测序技术对直立型半野生大豆(Glycine gracilis)叶绿体基因组(Chloroplast DNA，cpDNA)进行测序和组装，获得完整基因组，以探究其结构特征，为后续基于cpDNA的相关分析以及大豆资源多样性保护和系统发育等研究提供基础或依据。结果表明，直立型半野生大豆cpDNA全长148 320 bp，为典型四分体结构，注释基因108个，包含66个蛋白编码基因、29个tRNA基因和4个rRNA基因。基因组序列上共检测到87个SSR位点，其中与单核苷酸、双核苷酸、三核苷酸、四核苷酸、五核苷酸对应的位点分别为55，19，4，7，2个。在系统发育上，直立型半野生大豆与已公布的普通型一年生半野生大豆(Glycine gracilis)、栽培大豆(Glycine max)及野大豆(Glycine soja)亲缘关系较近。

关键词: 半野生大豆, cpDNA, 简单重复序列, 密码子偏好性, 系统发育

CLC Number:

S565.1

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.

郭冉昊, 赵淑文, 米福贵, 候伟峰, 赵力兴. 直立型半野生大豆叶绿体基因组分析[J]. 草地学报, 2023, 31(11): 3334-3342.

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References

[1] GRAY J C. Genetic manipulation of the chloroplast genome[J]. Biotechnology,1989(12):317-335
[2] JULIAN T F,NEVILL P G,DIXON K,et al. What can we do with 1000 plastid genomes?[J]. The Plant Journal:for Cell and Molecular Biology,2017,90(4):808-818
[3] ZHOU J,CHEN X L,CUI Y X,et al. Molecular structure and phylogenetic analyses of complete chloroplast genomes of two Aristolochia medicinal species[J]. International Journal of Molecular Sciences,2017,18(9):1839
[4] YU X Q,DREW B T,YANG J B,et al.. Comparative chloroplast genomes of eleven Schima (Theaceae) species:insights into DNA barcoding and phylogeny[J]. PLoS One,2017,12(6):e0178026
[5] 刘昊. 大豆线粒体和cpDNA的组装及演化分析[D]. 西安:西北大学,2022
[6] 邱丽娟.大豆种质资源描述规范和数据标准[M].北京:中国农业出版社,2006:1
[7] SKVORTZOW B V. The soybean-wild and cultivated in Eastern Asia[J]. Proc Manchurian Res Soc,Nat History Sect Publ Ser A,1927(22):1-8
[8] 刘洋,李向华,肖鑫辉,等. 大豆Soja亚属内种子大小的遗传差异及半野生类型分类归属[J]. 分子植物育种,2010,8(2):231-239
[9] GU Z L,ZHU Z,LI Z,et al. Cytoplasmic and nuclear genome variations of rice hybrids and their parents inform trajectory and strategy of hybrid rice breeding[J]. Molecular Plant,2021,14(12):2056-2071
[10] HYMOWITZ T. On the domestication of the soybean[J]. Economic Botany,1970,24(4):408-421
[11] XU H,ABE J,GAI Y,et al. Diversity of chloroplast DNA SSRs in wild and cultivated soybeans:evidence for multiple origins of cultivated soybean[J]. Theoretical and Applied Genetics,2002,105(5):645-653
[12] QIU J,WANG Y,WU S L,et al. Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression[J]. PLoS One,2014,9(9):e108479
[13] SHI L C,CHEN H M,JIANG M,et al. CPGAVAS2,an integrated plastome sequence annotator and analyzer[J]. Nucleic Acids Research,2019,47(W1):65-73
[14] ZHENG S Y,POCZAI P,HYVÖNEN J,et al. Chloroplot:an online program for the versatile plotting of organelle genomes[J]. Frontiers in Genetics,2020(11):576124
[15] HE J,YAO M,LYU R D,et al.. Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus asteropyrum (Ranunculaceae)[J]. Scientific Reports,2019,9(1):15285
[16] YANG J W,ZENG X,GUO S X,et al. Characterization of the complete chloroplast genome of the perennial herb aconitum carmichaelii (Ranunculales:Ranunculaceae)[J]. Conservation Genetics Resources,2018,10(4)
[17] LIU K,WANG R,GUO X X,et al.. Comparative and phylogenetic analysis of complete chloroplast genomes in eragrostideae (Chloridoideae,poaceae)[J]. Plants,2021,10(1):109
[18] SHIELDS D C,SHARP P M. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases[J]. Nucleic Acids Research,1987,15(19):8023-8040
[19] ZHANG D,GAO F L,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
[20] JANSEN R K,CAI Z Q,RAUBESON L A,et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns[J]. Proceedings of the National Academy of Sciences of the United States of America,2007,104(49):19369-19374
[21] WAMBUGU P W,BROZYNSKA M,FURTADO A,et al. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences[J]. Scientific Reports,2015,5(1):13957
[22] DANIELL H,LIN C S,YU M,et al. Chloroplast genomes:diversity,evolution,and applications in genetic engineering[J]. Genome Biology,2016,17(1):134
[23] LIU Y C,DU H L,LI P C,et al. Pan-genome of wild and cultivated soybeans[J]. Cell,2020,182(1):162-176
[24] GAO Y,THIELE W,SALEH O,et al. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation[J]. The Plant Cell,2022,34(5):2056-2079
[25] ZHANG T W,FANG Y J,WANG X M,et al.. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica:Insights into the evolution of plant organellar genomes[J]. PLoS One,2012,7(1):e30531
[26] 叶友菊,倪州献,白天道,等. 马尾松cpDNA密码子偏好性分析[J]. 基因组学与应用生物学,2018,37(10):4464-4471.
[27] 田春育,武自念,李贤松,等. 扁蓿豆叶绿体基因组密码子偏好性分析[J]. 草地学报，2021,29(12)：2678-2684
[28] 孙志轩,敖平星,毕玉芬,等. '德钦’紫花苜蓿叶绿体基因组序列及特征分析[J]. 草地学报，2022,30(2):320-328
[29] SAJJAD A,MUHAMMAD W,ABDUL L K,et al.The complete chloroplast genome of wild rice (Oryza Minuta) and its comparison to related species[J]. Frontiers in Plant Science,2017(8):304
[30] KUANG D Y,WU H,WANG Y L,et al. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae):implication for DNA barcoding and population genetics[J]. Genome,2011,54(8):663-673
[31] KANE N C,CRONK Q. Botany without borders:barcoding in focus[J]. Molecular Ecology,2008,17(24):5175-5176
[32] NOCK C J,WATERS D L E,EDWARDS M A,et al. Chloroplast genome sequences from total DNA for plant identification[J]. Plant Biotechnology Journal,2011,9(3):328-333

Chloroplast Genome Analysis of An Erect Semi-Wild Soybean

直立型半野生大豆叶绿体基因组分析

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