Sorbus koehneana（Rosaceae）：Its Complete Chloroplast Genome and Phylogenetic Relationship with S. unguiculata

doi:10.16420/j.issn.0513-353x.2020-1021

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (3): 641-654.doi: 10.16420/j.issn.0513-353x.2020-1021

• Research Notes • Previous Articles Next Articles

Sorbus koehneana（Rosaceae）：Its Complete Chloroplast Genome and Phylogenetic Relationship with S. unguiculata

TANG Chenqian, QIU Zhixin, TAN Chao, QIAN Yuming, CHEN Xin^*()

Co-Innovation Center for Sustainable Forestry in Southern China,College of Biology and the Environment,Nanjing Forestry University,Nanjing 210037,China

Received:2021-04-02 Revised:2021-12-14 Online:2022-03-25 Published:2022-03-25
Contact: CHEN Xin E-mail:chenxinzhou@hotmail.com

Abstract

Abstract:

The complete chloroplast（cp）genome of Sorbus koehneana and its phylogenetic relationship with S. unguiculata were analyzed. The complete cp genome of S. koehneana is 159 873 bp in size with 36.60% GC content. It has a typical quadripartite structure including a small single copy（SSC）region of 19 218 bp,a large single copy（LSC）region of 87 899 bp and a pair of inverted repeat regions （IRs）of 26 378 bp. The cp genome encodes 108 genes,comprising 76 protein-coding genes,four rRNA genes and 28 tRNA genes. Additionally,47 simple sequence repeats（SSRs）and 48 interspersed nuclear elements（INEs）were identified. In Sorbus,cp genome is highly conserved in length,gene type,codon number,intron number and GC content. However,the different sequence repeats and 12 highly variable regions located in intergenic spacers may be used for population genetic and phylogenetic studies in future. Phylogenetic analyses revealed that S. koehneana,S. unguiculata and S. helenae are in the same lineage nested within Sorbus subg. Sorbus. However,S. unguiculata is sister to S. helenae instead of S. koehneana. So the treatment of S. unguiculata as a synonym of S. koehneana is not supported and the name S. unguiculata is proposed to be reinstated here.

Key words: Sorbus, chloroplast genome, genomic comparison, phylogenetic analysis

CLC Number:

S685.99

TANG Chenqian, QIU Zhixin, TAN Chao, QIAN Yuming, CHEN Xin. Sorbus koehneana（Rosaceae）：Its Complete Chloroplast Genome and Phylogenetic Relationship with S. unguiculata[J]. Acta Horticulturae Sinica, 2022, 49(3): 641-654.

Figures/Tables 8

References 57

[1]	Aldasoro J J, Aedo C, Garmendia F M, delaHoz F P, Navarro C. 2004. Revision of Sorbu subgenera Aria and Torminaria(Rosaceae-Maloideae). Systematic Botany Monographs, 69:1-148. doi: 10.2307/25027918 URL
[2]	Amiryousefi A, Hyvönen J, Poczai P. 2018. IRscope:an online program to visualize the junction sites of chloroplast genomes. Bioinformatics, 34(17):3030-3031. doi: 10.1093/bioinformatics/bty220 pmid: 29659705
[3]	Barrett C F, Baker W J, Comer J R, Conran J G, Lahmeyer S C, Leebens-Mack J H, Li J, Lim G S, MayfieldJones D R, Perez L, Medinz J, Pires J C, Santos C, Stevenson D W, Zomlefer W B, Davis J I. 2016. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytologist, 209:855-870. doi: 10.1111/nph.13617 pmid: 26350789
[4]	Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web:a web server for microsatellite prediction. Bioinformatics, 33(16):2583-2585. doi: 10.1093/bioinformatics/btx198 URL
[5]	Chris M, Michael B, Schwartz J R, Alexander P, Rubin E M, Frazer K A, Pachter L S, Inna D. 2000. VISTA:visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16(11):1046-1047. doi: 10.1093/bioinformatics/16.11.1046 URL
[6]	Chumley T W, Palmer J D, Mower J P, Fourcade H M, Calie P J, Boore J L, Jansen R K. 2006. The complete chloroplast genome sequence of Pelargonium × hortorum:organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution, 23:2175-2190. doi: 10.1093/molbev/msl089 URL
[7]	Dong Qing-hua, Wang Xi-cheng, Zhao Mi-zhen, Song Chang-nian, Ge An-jing, Wang Jing. 2011. Development of EST-derived SSR markers and their application in strawberry genetic diversity analysis. Scientia Agricultura Sinica, 44(17):3603-3612. (in Chinese)
	董清华, 王西成, 赵密珍, 宋长年, 葛安静, 王静. 2011. 草莓EST-SSR 标记开发及在品种遗传多样性分析中的应用. 中国农业科学, 44(17):3603-3612.
[8]	Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry, 19:11-15. doi: 10.1016/0031-9422(80)85004-7 URL
[9]	Dugas D V, Hernandez D, Koenen E J M, Schwarz E, Straub S, Hughes C E, Jansen R K, Nageswara R M, Staats M, Trujillo J T. 2015. Mimosoid legume plastome evolution:IR expansion,tandem repeat expansions,and accelerated rate of evolution in clpP. Scientific Reports, 5:16958. doi: 10.1038/srep16958 URL
[10]	Firetti F, Zuntini A R, Gaiarsa J W, Oliveira R S, Lohmann L G, Van Sluys M A. 2017. Complete chloroplast genome sequences contribute toplant species delimitation:a case study of the Anemopaegma species complex. American Journal of botany, 104:1493-1509. doi: 10.3732/ajb.1700302 URL
[11]	Fonseca L H M, Lohmann L G. 2017. Plastome rearrangements in the“Adenocalymma-Neojobertia”clade(Bignonieae,Bignoniaceae)and its phylogenetic implications. Frontiers in Plant Science, 8:1-13.
[12]	Gabrielian E. 1978. The genus Sorbus L. in western Asia and the Himalayas. USA:Academy of Sciences of the Armenian SSR:1-264.
[13]	Gao Yuan, Wang Da-jiang, Wang Kun, Li Lian-wen, Piao Ji-cheng. 2020. Genetic diversity of Malus Mill. based on the sequences of chloroplast fragments. Acta Agriculturae Boreali-sinica: 35(6):33-42. (in Chinese)
	高源, 王大江, 王昆, 李连文, 朴继成. 2020. 基于叶绿体片段序列的苹果属植物遗传多样性研究. 华北农学报: 35(6):33-42.
[14]	Greiner S, Lehwark P, Bock R. 2019. Organellar Genome DRAW(OGDRAW)version 1.3.1:expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 47:59-64.
[15]	Guisinger M M, Chumley T W, Kuehl J V, Boore J L, Jansen R K. 2010. Implications of the plastid genome sequence of Typha(Typhaceae,Poales) for understanding genome evolution in Poaceae. Journal of Molecular Evolution, 70(2):149-166. doi: 10.1007/s00239-009-9317-3 pmid: 20091301
[16]	Jin J J, Yu W B, Yang J B, Song Y, dePamphilis C W, Yi T S, Li D Z. 2020. GetOrganelle:a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21(1):1-31. doi: 10.1186/s13059-019-1906-x URL
[17]	Jung S, Abbott A, Jesudurai C, Tomkins J, Main D. 2005. Frequency,type,distribution and annotation of simple sequence repeats in Rosaceae ESTs. Functional Integrative Genomics,(3):136-143.
[18]	Katoh K, Standley D M. 2013. MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Molecular Biology and Evolution, 30(4):772-780. doi: 10.1093/molbev/mst010 URL
[19]	Khakhlova O, Bock R. 2006. Elimination of deleterious mutations in plastid genome by gene conversion. Plant Journal, 46(1):85-94. pmid: 16553897
[20]	Koehne E. 1913. Plantae Wilsonianae:an enumeration of the woody plants collected in western China for the Arnold Arboretum of Harvard University during the years 1907,1908,and 1910. Cambridge: Cambridge University Press:457-483.
[21]	Kurtz S, Choudhuri J V, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. 2001. REPuter:the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29(22):4633-4642. pmid: 11713313
[22]	Li M, Tetsuo O T, Gao Y D, Xu B, Zhu Z M, Ju W B, Gao X F. 2017. Molecular phylogenetics and historical biogeography of Sorbus sensu stricto(Rosaceae). Molecular Phylogenetics and Evolution, 111:76-86. doi: 10.1016/j.ympev.2017.03.018 URL
[23]	Li N, Sun M H, Jiang Z S, Shu H R, Zhang S Z. 2016. Genome-wide analysis of the synonymous codon usage patterns in apple. Journal of Integrative Agriculture, 15(5):983-991. doi: 10.1016/S2095-3119(16)61333-3 URL
[24]	Li Qian, Guo Qiqiang, Gao Chao, Li Huie. 2021. Characterization of complete chloroplast genome of Camellia weiningensis in Weining,Guizhou Province. Acta Horticulturae Sinica, 47(4):779-787. (in Chinese)
	李倩, 郭其强, 高超, 李慧娥. 2020. 贵州威宁红花油茶的叶绿体基因组特征分析. 园艺学报, 47(4):779-787.
[25]	Li Ruo-yu, Zhang Xiao-dan, Ma Xin-yi, Guo Rui, Yan Shao-bin, Jin Guang, Zhou Ping. 2020. Analyses of codon usage patterns and codon usage bias in peach(Prunus persica). Molecular Plant Breeding, 19(3):799-807. (in Chinese)
	李若愚, 张小丹, 马昕怡, 郭瑞, 颜少宾, 金光, 周平. 2020. 桃基因密码子使用模式及其偏好性分析. 分子植物育种, 19(3):799-807.
[26]	Li Yongtan, Zhang Jun, Huang Yali, Fan Jianmin, Zhang Yiwen, Zuo Lihui. 2020. Analysis of chloroplast genome of Pyrus betulaefolia. Acta Horticulturae Sinica, 47(6):1021-1032. (in Chinese)
	李泳潭, 张军, 黄亚丽, 范建敏, 张益文, 左力辉. 2020. 杜梨叶绿体基因组分析. 园艺学报, 47(6):1021-1032.
[27]	Lu L T, Spongberg S A. 2003. Sorbus Linnaeus//Wu Z Y,Raven P H,Hong D Y. Flora of China,Vol. 9. Beijing: Science Press;USA:Missouri Botanical Garden Press:144-170.
[28]	Matthew K, Richard M, Amy W, Steven S H, Matthew C, Shane S, Simon B, Alex C, Sidney M, Chris D, Tobias T, Bruce A, Peter M, Alexei D. 2012. Geneious basic:an integrated and extend-able desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28:1647-1649. doi: 10.1093/bioinformatics/bts199 pmid: 22543367
[29]	McAllister H. 2005. The genus Sorbus Mountain Ash and other Rowans. London:Royal Botanical Gardens:1-252.
[30]	Meade J C, Shah P H, Lushbaugh W B . 1997. Trichomonas vaginalis:analysis of codon usage. Experimental Parasitology, 87:73-74. pmid: 9287961
[31]	Phipps J B, Robertson K R, Smith P G, Rohrer J R. 1990. A checklist of the subfamily Maloideae(Rosaceae). Canadian Journal of Botany, 68(10):2209-2269. doi: 10.1139/b90-288 URL
[32]	Posada D, Crandall K A. 1998. MODELTEST:testing the model of DNA substitution. Bioinformatics, 14:817-818. doi: 10.1093/bioinformatics/14.9.817 pmid: 9918953
[33]	Potter D, Eriksson T, Evans R C, Oh S, Smedmark J E E, Morgan D R, Kerr M, Robertson K R, Arsenault M, Dickinson T A, Campbell C S. 2007. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266(1-2):5-43. doi: 10.1007/s00606-007-0539-9 URL
[34]	Qu X J, Moore M J, Li D Z, Yi T S. 2019. PGA:a software package for rapid,accurateand flexible batch annotation of plastomes. Plant Methods, 15(1):1-12. doi: 10.1186/s13007-018-0385-5 URL
[35]	Reim S, Lochschmidt F, Proft A, Höfer M. 2020. Genetic integrity is still maintained in natural populations of the indigenous wild apple species Malus sylvestris(Mill.)in Saxony as demonstrated with nuclear SSR and chloroplast DNA markers. Ecology and Evolution, 10:11798-11809. doi: 10.1002/ece3.v10.20 URL
[36]	Rono P C, Dong X, Yang J X, Mutie F M, A. Oulo M, Malombe I, M. Kirika P, Hu G W, Wang Q F. 2020. Initial complete chloroplast genomes of Alchemilla(Rosaceae): comparative analysis and phylogenetic relationships. Frontiers in Genetics, 11:560368.
[37]	Ronquist F, Teslenko M, Mark P, Ayres D L, Darling A, Höhna S, Larget B, Liu L, Suchard M A, Huelsenbeck J P. 2012. MrBayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61:539-542. doi: 10.1093/sysbio/sys029 pmid: 22357727
[38]	Smith D R, Keeling P J. 2015. Mitochondrial and plastid genome architecture:reoccurring themes,but significant differences at the extremes. Proceedings of the National Academy of Sciences of the United States of America, 112:10177-10184.
[39]	Stamatakis A. 2014. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30:1312-1313. doi: 10.1093/bioinformatics/btu033 URL
[40]	Sun J H, Shi S, Li J L, Jing Y, Wang L, Yang X Y, Guo L, Zhou S L, Sun F J. 2018. Phylogeny of Maleae(Rosaceae)based on multiple chloroplast regions:implications to genera Circumscription. BioMed Research International,doi: 10.1155/2018/7627191. doi: 10.1155/2018/7627191 URL
[41]	Sun J H, Wang Y H, Liu Y L, Xu C, Yuan Q J, Guo L P, Huang L Q. 2020. Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. Scientific Reports, 10(1):11466. doi: 10.1038/s41598-020-58234-w URL
[42]	Thode V A, Lohmann L G. 2019. Comparative chloroplast genomics at low taxonomic levels:a case study using Amphilophium(Bignonieae,Bignoniaceae). Frontiers in Plant Science, 10:1-17. doi: 10.3389/fpls.2019.00001 URL
[43]	Wang Guo-xun, Zhang Ming-li. 2011. A molecular phylogeny of Sorbus(Rosaceae) based on ITS sequence. Acta Horticulturae Sinica, 38(12):2387-2394. (in Chinese)
	王国勋, 张明理. 2011. 应用核DNA ITS序列探讨广义花楸属(Sorbus L.)属下系统关系. 园艺学报, 38(12):2387-2394.
[44]	Wang L, Guo Z H, Shang Q H, Sa W, Wang L. 2021. The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species:genome structure,sequence divergence,and phylogenetic analysis. Brazilian Journal of Botany, 44:85-95. doi: 10.1007/s40415-020-00685-6 URL
[45]	Wang Q, Niu Z Y, Li J B, Zhu K L, Chen X. 2020a. The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis(Rosaceae)and its phylogenetic analysis. Nordic Journal of Botany, 38(2):1-11.
[46]	Wang W, Yang T, Wang H L, Li Z J, Ni J W, Su S, Xu X Q. 2020b. Comparative and phylogenetic analyses of the complete chloroplast genomes of six almond species(Prunus spp. L.). Scientific Reports, 10(1):10137. doi: 10.1038/s41598-019-56728-w URL
[47]	Wick R R, Schultz M B, Justin Z, Holt K E. 2015. Bandage:interactive visualization of de novo genome assemblies. Bioinformatics, 31(20):3350-3352. doi: 10.1093/bioinformatics/btv383 URL
[48]	Wicke S, Schneeweiss G M, dePamphilis C W, Müller K F, Quandt D. 2011. The evolution of the plastid chromosome in land plants:gene content,gene order,gene function. Plant Molecular Biology, 76:273-297. doi: 10.1007/s11103-011-9762-4 URL
[49]	Wilgenbusch J C, Swofford D. 2003. Inferring evolutionary trees with PAUP*. Current Protocols in Bioinformatics, 6(4):1-28.
[50]	Wu Wei-feng, Chen Ming-jie, Chen Fa-xing. 2020. Codon bias analysis of Prunus salicina‘Huangguan’malate transporter ALMT4,ALMT9 and tDT genes. Journal of Agricultural Biotechnology, 28(1):42-57. (in Chinese)
	巫伟峰, 陈明杰, 陈发兴. 2020. ‘皇冠李’苹果酸转运体基因ALMT4、ALMT9和tDT密码子偏好性分析. 农业生物技术学报, 28(1):42-57.
[51]	Yan Xiu-qin, Lu Min, An Hua-ming. 2015. Analysis on SSR information in transcriptome and development of molecular markers in Rosa roxburghii. Acta Horticulturae Sinica, 42(2):341-349. (in Chinese)
	鄢秀芹, 鲁敏, 安华明. 2015. 刺梨转录组SSR信息分析及其分子标记开发. 园艺学报, 42(2):341-349.
[52]	Yang Yameng, Jiao Jian, Fan Xiucai, Zhang Ying, Jiang Jianfu, Li Min, Liu Chonghuai. 2019. Complete chloroplast genome sequence and characteristics analysis of Vitis ficifolia. Acta Horticulturae Sinica, 46(4):635-648. (in Chinese)
	杨亚蒙, 焦健, 樊秀彩, 张颖, 姜建福, 李民, 刘崇怀. 2019. 桑叶葡萄叶绿体基因组及其特征分析. 园艺学报, 46(4):635-648.
[53]	Yü De-jun, Guan Ke-jian. 1963. Taxa Nova Rosacearum Sinicarum(Ⅰ). Journal of Systematics and Evolution, 8(3):202-235. (in Chinese)
	俞德浚, 关克俭. 1963. 中国蔷薇科植物分类之研究(一). 植物分类学报, 8(3):202-235.
[54]	Yü De-jun, Lu Ling-di. 1974. Spiraea,Dichotomanthes,Cotoneaster,Sorbus,Chaenomeles. Flora of China//Yü Te-tisun. Flora Republicae Popularis,Sinicae,Vol. 36. Beijing: Science Press:283-344. (in Chinese)
	俞德浚, 陆玲娣. 1974. 绣线菊属,牛筋条属,栒子属,花楸属,木瓜海棠属//俞德浚. 中国植物志,第36卷. 北京: 科学出版社:283-344.
[55]	Zhang M Y, Fan L, Liu Q Z, Song Y, Wei S W, Zhang S L, Wu J. 2014. A novel set of EST-derived SSR markers for pear and cross-species transferability in Rosaceae. Plant Molecular Biology Reporter, 32:290-302. doi: 10.1007/s11105-013-0638-4 URL
[56]	Zhang S D, Jin J J, Chen S Y, Chase M W, Soltis D E, Li H T, Yang J B, Li D Z, Yi T S. 2017. Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics. New Phytologist, 214:13-55.
[57]	Zheng Yi, Zhang Hui, Wang Qinmei, Gao Yue, Zhang Zhihong, Sun Yuxin. 2020. Complete chloroplast genome sequence of Clivia miniata and its characteristics. Acta Horticulturae Sinica, 47(12):2439-2450. (in Chinese)
	郑祎, 张卉, 王钦美, 高悦, 张志宏, 孙玉新. 2020. 大花君子兰叶绿体基因组及其特征. 园艺学报, 47(12):2439-2450.

基因功能 Function of gene	基因分类 Group of genes	基因代码 Code	基因 Gene
自我复制 Self replication	rRNA	rrn	rrn4.5^c,rrn5^c,rrn16^c,rrn23^c
	tRNA	trn	trnA-UGC^ac,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-UCC,trnH-GUG,trnI-CAU^c,trnI-GAU^ac,trnK-UUU^a,trnL-CAA^c,trnL-UAA^a,trnL-UAG,trnM-CAU,trnN-GUU^c,trnP-UGG,trnQ-UUG,trnR-ACG^c,trnR-UCU,trnS-GCU,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC^c,trnV-UAC^a,trnW-CCA,trnY-GUA
	核糖体小亚基 Ribosomal proteins（SSU）	rps	rps2,rps3,rps4,rps7^c,rps8,rps11,rps12^acd,rps14,rps15,rps16^a,rps18,rps19
	核糖体大亚基 Ribosomal proteins（LSU）	rpl	rpl2^ac,rpl14,rpl16^a,rpl20,rpl22,rpl23^ac,rpl32,rpl33,rpl336
	RNA 聚合酶亚基RNA polymerase	rpo	rpoA,rpoB,rpoC1^a,rpoC2
光合作用 Genes for photosynthesis	光合系统Ⅰ Photosystem Ⅰ	psa	psaA,psaB,psaJ,psaI
	光合系统Ⅱ Photosystem Ⅱ	psb	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbM,psbN,psbT,psbZ
	细胞色素复合物Cytochrome b/f complex	pet	petA,petB^a,petD^a,petG,petL,petN
	ATP合成酶ATP synthase	atp	atpA,atpB,atpE,atpF^a,atpH,atpI
	NADH脱氢酶 Subunits of NADH-dehydrogenase	ndh	ndhA^a,ndhB^ac,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	二磷酸核酮糖羧化酶大亚基 Subunit of rubisco	rbc	rbcL
其他基因 Other genes	乙酰CoA羧化酶 Subunit of Acetyl-CoA-carboxylase	acc	accD
	膜包被蛋白基因 Envelop membrane protein gene	cem	cemA
	c型细胞色素合成基因 c-type cytochrom synthesis gene	ccs	ccsA
	蛋白酶基因Protease gene	clp	clpP^b
	成熟酶基因Maturase gene	mat	matK
未知功能 Unknow function	假想叶绿体读码框 Hypothetical chloroplast reading frames	ycf	ycf1,ycf2^c,ycf3^b,ycf4

基因功能 Function of gene	基因分类 Group of genes	基因代码 Code	基因 Gene
自我复制 Self replication	rRNA	rrn	rrn4.5^c,rrn5^c,rrn16^c,rrn23^c
	tRNA	trn	trnA-UGC^ac,trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,trnfM-CAU,trnG-UCC,trnH-GUG,trnI-CAU^c,trnI-GAU^ac,trnK-UUU^a,trnL-CAA^c,trnL-UAA^a,trnL-UAG,trnM-CAU,trnN-GUU^c,trnP-UGG,trnQ-UUG,trnR-ACG^c,trnR-UCU,trnS-GCU,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC^c,trnV-UAC^a,trnW-CCA,trnY-GUA
	核糖体小亚基 Ribosomal proteins（SSU）	rps	rps2,rps3,rps4,rps7^c,rps8,rps11,rps12^acd,rps14,rps15,rps16^a,rps18,rps19
	核糖体大亚基 Ribosomal proteins（LSU）	rpl	rpl2^ac,rpl14,rpl16^a,rpl20,rpl22,rpl23^ac,rpl32,rpl33,rpl336
	RNA 聚合酶亚基RNA polymerase	rpo	rpoA,rpoB,rpoC1^a,rpoC2
光合作用 Genes for photosynthesis	光合系统Ⅰ Photosystem Ⅰ	psa	psaA,psaB,psaJ,psaI
	光合系统Ⅱ Photosystem Ⅱ	psb	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbM,psbN,psbT,psbZ
	细胞色素复合物Cytochrome b/f complex	pet	petA,petB^a,petD^a,petG,petL,petN
	ATP合成酶ATP synthase	atp	atpA,atpB,atpE,atpF^a,atpH,atpI
	NADH脱氢酶 Subunits of NADH-dehydrogenase	ndh	ndhA^a,ndhB^ac,ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	二磷酸核酮糖羧化酶大亚基 Subunit of rubisco	rbc	rbcL
其他基因 Other genes	乙酰CoA羧化酶 Subunit of Acetyl-CoA-carboxylase	acc	accD
	膜包被蛋白基因 Envelop membrane protein gene	cem	cemA
	c型细胞色素合成基因 c-type cytochrom synthesis gene	ccs	ccsA
	蛋白酶基因Protease gene	clp	clpP^b
	成熟酶基因Maturase gene	mat	matK
未知功能 Unknow function	假想叶绿体读码框 Hypothetical chloroplast reading frames	ycf	ycf1,ycf2^c,ycf3^b,ycf4

基因 Gene	位置 Location	内含子 I/bp Intron I	内含子II/bp Intron II	外显子 I/bp Exon I	外显子II/bp Exon II	外显子 III/bp Exon III
atpF	LSC	729		144	411
petB	LSC	797		5	643
petD	LSC	724		7	476
rpl16	LSC	977		10	398
rpoC1	LSC	741		435	1 611
rps16	LSC	867		40	230
trnL-UAA	LSC	514		37	50
trnV-UAC	LSC	592		39	37
ndhA	SSC	1 120		552	540
ndhB	IR	669		777	756
rpl2	IR	686		389	436
rps12	IR	541		231	30
clpP	LSC	823	638	71	289	228
ycf3	LSC	698	745	126	228

基因 Gene	位置 Location	内含子 I/bp Intron I	内含子II/bp Intron II	外显子 I/bp Exon I	外显子II/bp Exon II	外显子 III/bp Exon III
atpF	LSC	729		144	411
petB	LSC	797		5	643
petD	LSC	724		7	476
rpl16	LSC	977		10	398
rpoC1	LSC	741		435	1 611
rps16	LSC	867		40	230
trnL-UAA	LSC	514		37	50
trnV-UAC	LSC	592		39	37
ndhA	SSC	1 120		552	540
ndhB	IR	669		777	756
rpl2	IR	686		389	436
rps12	IR	541		231	30
clpP	LSC	823	638	71	289	228
ycf3	LSC	698	745	126	228

氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number	氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number	氨基酸 Amino acid	密码子 Codon	RSCU	数量 Number
苯丙氨酸Phe	UUU	1.29	932	脯氨酸Pro	CCU	1.50	375	谷氨酸Glu	GAA	1.46	957
	UUC	0.71	516		CCC	0.75	186		GAG	0.54	350
亮氨酸Leu	UUA	1.92	857		CCA	1.18	294	半胱氨酸Cys	UGU	1.44	245
	UUG	1.20	537		CCG	0.57	143		UGC	0.56	95
	CUU	1.28	571	苏氨酸Thr	ACU	1.57	509	色氨酸Trp	UGG	1.00	457
	CUC	0.41	182		ACC	0.71	232	精氨酸Arg	CGU	1.20	317
	CUA	0.79	351		ACA	1.24	402		CGC	0.41	107
	CUG	0.40	179		ACG	0.48	156		CGA	1.37	361
异亮氨酸Ile	AUU	1.47	1 082	丙氨酸Ala	GCU	1.82	591		CGG	0.49	128
	AUC	0.59	435		GCC	0.65	212		AGA	1.83	482
	AUA	0.94	696		GCA	1.10	358		AGG	0.70	184
甲硫氨酸Met	AUG	1.00	591		GCG	0.43	140	络氨酸Tyr	UAU	1.57	780
缬氨酸Val	GUU	1.47	493	组氨酸His	CAU	1.52	466		UAC	0.43	214
	GUC	0.44	149		CAC	0.48	146	甘氨酸Gly	GGU	1.29	551
	GUA	1.52	511	谷氨酰胺Gln	CAG	1.52	698		GGC	0.41	177
	GUG	0.56	189		CAA	0.48	218		GGA	1.61	687
丝氨酸Ser	UCU	1.64	561	天冬酰胺Asn	AAU	1.51	961		GGG	0.69	293
	UCC	0.99	338		AAC	0.49	313	终止子	UAA	1.17	65
	UCA	1.19	407	赖氨酸Lys	AAA	1.47	1 027	Terminator	UAG	0.86	48
	UCG	0.61	209		AAG	0.53	373		UGA	0.97	54
	AGU	1.14	389	天冬氨酸Asp	GAU	1.61	846
	AGC	0.44	151		GAC	0.39	202
总计Total			25 726

Sorbus koehneana（Rosaceae）：Its Complete Chloroplast Genome and Phylogenetic Relationship with S. unguiculata

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类型 Type	重复序列 SSR repeat sequence	重复次数 Number of copies																					总计 Total
类型 Type	重复序列 SSR repeat sequence	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	总计 Total
单核苷酸（34） Mononucleotide	A										6	4	3	2		1		1				1	18
单核苷酸（34） Mononucleotide	T										3	1	4	3	3		1			1			16
二核苷酸（4） Dinucleotide	AT				2																		2
二核苷酸（4） Dinucleotide	TA				2																		2
三核苷酸（0） Trinucleotide																							0
四核苷酸（7） Tetranucleotide	AATA	1																					1
	TTAT	1																					1
	TTTA	5																					5
五核苷酸（2） Pentanucleotide	AATGT	1																					1
五核苷酸（2） Pentanucleotide	TCCAA	1																					1

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