四川山胡椒叶绿体基因组特征及山胡椒属系统发育

doi:10.11707/j.1001-7488.20211217

摘要/Abstract

摘要：

目的: 四川山胡椒具有重要的药用价值，开展叶绿体基因组研究对山胡椒属物种鉴定、遗传多样性分析和资源保护具有重要的理论和实践意义。方法: 基于Illumina HiSeq 2000高通量测序平台进行测序，从头组装了完整的四川山胡椒叶绿体基因组，并对其基因组结构、基因构成及序列重复和系统发育进行分析。结果: 四川山胡椒叶绿体基因组全长152 851 bp，呈典型的四分结构，共编码125个基因，其中蛋白编码基因81个，tRNA基因36个，rRNA基因8个; 编码基因的鸟嘌呤和胞嘧啶碱基的出现频率GC3s为27.96%，21个最优密码子中有20个以A/U(T)结尾; 27对长序列重复中，正向重复和回文重复分别占比44%和41%，长度为30 bp和33 bp的序列分别占44%和30%; 181个SSR位点中，A/T单碱基重复占68%，位于基因间区的占55%; 鉴定了6个高变区(petA-psbJ、trnH-psbA、petK-psbI、ccsA-ndhD、rpl32-trnL和ycf1); 系统发育分析显示，山胡椒属分为5个聚类组，四川山胡椒与黑壳楠亲缘关系最近。结论: 四川山胡椒叶绿体基因组结构保守，偏好以A或U(T)结尾的密码子; 鉴定的高变区和SSR位点可作为山胡椒属物种鉴定的DNA条形码。研究结果可为山胡椒属分子标记开发、系统进化研究及优良品种选育提供参考。

关键词: 四川山胡椒, 密码子使用偏性, SSR, 系统发育, 突变热点

Abstract:

Objective: Lindera setchuenensis has important medicinal value. Researches of chloroplast genome possess essential theoretical and practical significance for species identification, analysis of genetic diversity and resource protection of the genus Lindera. Method: The complete chloroplast genome of L. setchuenensis was sequenced based on Illumina HiSeq 2000 platform, and was assembled through de novo. The genome structure, gene composition, repeats and phylogeny were analyzed. Result: The chloroplast genome of L. setchuenensis exhibited a typical quadripartite structure. A total of 125 functional genes were detected, including 81 protein coding genes, 36 tRNA genes, and eight rRNA genes. Frequency of guanine and cytosine bases(GC3s) of the genome encoding genes was 27.96%, 20 codons were ended with A/U(T) among 21 optimal codons. Among the 27 pairs of long repeats, forward repeats and palindromic repeats accounted for 44% and 41% respectively, and the length of 30 bp and 33 bp accounted for 44% and 30% respectively. Among the 181 SSRs, 68% were A/T repeats and 55% were located in the intergenic regions. Comparing the chloroplast genomes of the genus Lindera, it was indicated that six hyper-variable loci, petA-psbJ, trnH-psbA, petK-psbI, ccsA-ndhD, rpl32-trnL, and ycf1, could potentially be used as DNA barcodes candidates for species identification. Phylogenetic analysis revealed that the genus Lindera was divided into five clades. L. setchuenensis presented the closest relationship with L. megaphylla. Conclusion: The structure of chloroplast genome of L. setchuenensis is conservative and prefers codons ending with A or U(T). The hyper-variable regions and SSR loci can be used as DNA barcoding for species identification. The results provide a basis for the development of molecular markers, phylogeny and breeding of elite varieties of Lindera plants.

Key words: Lindera setchuenensis, codon usage bias, SSR, phylogeny, mutational hotspots

中图分类号:

S718.46

刘潮,唐利洲,韩利红. 四川山胡椒叶绿体基因组特征及山胡椒属系统发育[J]. 林业科学, 2021, 57(12): 167-174.

Chao Liu,Lizhou Tang,Lihong Han. Characterization of the Chloroplast Genome of Lindera setchuenensis and Phylogenetics of the Genus Lindera[J]. Scientia Silvae Sinicae, 2021, 57(12): 167-174.

图/表 7

图1

表1

四川山胡椒叶绿体基因组相对同义密码子使用度①"

氨基酸 Amino acid	密码子 Codon	相对同义密码子使用度 Relative synonymous codon usage			氨基酸 Amino acid	密码子 Codon	相对同义密码子使用度 Relative synonymous codon usage
氨基酸 Amino acid	密码子 Codon	基因组 Genome	高表达基因 High expression gene	低表达基因 Low expression gene	氨基酸 Amino acid	密码子 Codon	基因组 Genome	高表达基因 High expression gene	低表达基因 Low expression gene
蛋氨酸 Met	ATG	1.00	1.00	1.00	色氨酸 Trp	TGG	1.00	1.00	1.00
丙氨酸	GCA	1.15	1.04	1.16	脯氨酸	CCA^**	1.10	1.19	0.89
Ala	GCC	0.65	0.46	0.99	Pro	CCC	0.89	1.05	1.22
	GCG	0.43	0.12	0.41		CCG	0.52	0.07	0.50
	GCT^***	1.77	2.38	1.45		CCT^**	1.50	1.68	1.39
半胱氨酸	TGC	0.51	0.29	0.62	谷氨酰胺	CAA^*	1.47	1.37	1.29
Cys	TGT^**	1.50	1.71	1.39	Gln	CAG	0.53	0.63	0.71
天冬氨酸	GAC	0.43	0.50	0.62	精氨酸	AGA^*	1.80	2.08	1.78
Asp	GAT^*	1.58	1.50	1.38	Arg	AGG	0.70	0.46	0.86
谷氨酸	GAA^*	1.48	1.62	1.38		CGA^*	1.35	1.44	1.19
Glu	GAG	0.52	0.38	0.62		CGC	0.36	0.23	0.53
苯丙氨酸	TTC	0.82	1.12	0.87		CGG	0.43	0.17	0.33
Phe	TTT	1.18	0.88	1.13		CGT^*	1.36	1.62	1.32
甘氨酸	GGA^*	1.56	1.56	1.43	丝氨酸	AGC	0.34	0.44	0.48
Gly	GGC	0.46	0.49	0.39	Ser	AGT	1.17	1.39	1.26
	GGG	0.72	0.44	0.79		TCA	1.24	0.66	1.08
	GGT^*	1.26	1.51	1.39		TCC	1.05	1.02	1.08
组氨酸	CAC	0.48	0.64	0.67		TCG	0.63	0.44	0.54
His	CAT	1.52	1.36	1.33		TCT^**	1.57	2.05	1.56
异亮氨酸	ATA	0.91	0.80	0.97	苏氨酸	ACA	1.15	0.94	1.30
Ile	ATC	0.65	0.70	0.62	Thr	ACC	0.83	1.18	0.85
	ATT^*	1.44	1.50	1.41		ACG	0.48	0.18	0.34
赖氨酸	AAA	1.48	1.48	1.49		ACT^*	1.54	1.71	1.52
Lys	AAG	0.52	0.53	0.52	缬氨酸	GTA^*	1.42	1.68	1.52
亮氨酸	CTA	0.89	0.87	0.79	Val	GTC	0.52	0.70	0.64
Leu	CTC	0.44	0.40	0.23		GTG	0.63	0.32	0.69
	CTG	0.44	0.20	0.45		GTT^*	1.43	1.30	1.15
	CTT	1.22	1.33	1.59	络氨酸	TAC	0.44	0.55	0.49
	TTA^*	1.76	1.73	1.64	Tyr	TAT	1.56	1.46	1.51
	TTG^*	1.27	1.47	1.30	终止	TAA^***	1.37	2.10	1.20
天冬酰胺	AAC	0.48	0.77	0.29	密码子 TER	TAG	0.76	0.30	1.20
Asn	AAT	1.52	1.23	1.71	密码子 TER	TGA	0.87	0.60	0.60

表1

图2

图3

图4

图5

图6

参考文献 0

	崔鸿宾. 山胡椒属系统的研究. 植物分类学报, 1987, 25 (3): 161- 171.
	Cui H P . A study on the system of Lindera. Acta Phytotaxonomica Sinica, 1987, 25 (3): 161- 171.
	蒋明, 柯世省, 王军峰. 多脉铁木叶绿体基因组的序列特征和系统发育. 林业科学, 2020, 56 (5): 60- 68.
	Jiang M , Ke S S , Wang J F . Characterization and phylogenetic analysis of Ostrya multinervi. chloroplast genome. Scientia Silvae Sinicae, 2020, 56 (5): 60- 68.
	袁娟娟. 2018. 四川山胡椒和尖叶蓝花楹化学成分及生物活性的研究. 成都: 西南交通大学硕士学位论文.
	Yuan J J. 2018. Study on the chemical constituents and bioactivities of Lindera setchuenensis Gamble and Jacaranda cuspidifolia Mart. Chengdu: MS thesis of Southwest Jiaotong University. [in Chinese]
	张嘉穗. 2016. 四川山胡椒的化学成分及三种山胡椒属植物成分的活性筛选. 成都: 西南交通大学硕士学位论文.
	Zhang J S. 2016. Studies on the chemical constituents of Lindera setchuenensis Gamble and bioactivities of compounds from three plants of Lindera. Chengdu: MS thesis of Southwest Jiaotong University. [in Chinese]
	郑祎, 张卉, 王钦美, 等. 大花君子兰叶绿体基因组及其特征. 园艺学报, 2020, 47 (12): 2439- 2450.
	Zheng Y , Zhang H , Wang Q M , et al. Complete chloroplast genome sequence of Clivia miniata and its characteristics. Acta Horticulturae Sinica, 2020, 47 (12): 2439- 2450.
	周晓君, 张凯, 彭正锋, 等. 矮牡丹与芍药属其他5个种叶绿体基因组特征的比较. 林业科学, 2020, 56 (4): 82- 88.
	Zhou X J , Zhang K , Peng Z F , et al. Comparative analysis of chloroplast genome characteristics between Paeonia jishanensi. and other five species of Paeonia. Scientia Silvae Sinicae, 2020, 56 (4): 82- 88.
	Beier S , Thiel T , Münch T , et al. MISA-web: a web server for microsatellite prediction. Bioinformatics, 2017, 33 (16): 2583- 2585. doi: 10.1093/bioinformatics/btx198
	Boel G , Letso R , Neely H , et al. Codon influence on protein expression in E. coli correlates with mRNA levels. Nature, 2016, 529 (7586): 358- 363. doi: 10.1038/nature16509
	Daniell H , Lin C S , Yu M , et al. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology, 2016, 17 (1): 134. doi: 10.1186/s13059-016-1004-2
	Doyle J J , Dickson E E . Preservation of plant samples for DNA restriction endonuclease analysis. Taxon, 1987, 36 (4): 715- 722. doi: 10.2307/1221122
	Duan H , Zhang Q , Wang C , et al. Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints. PeerJ, 2021, 9, e10787.
	Greiner S , Lehwark P , Bock R . OrganellarGenomeDRAW(OGDRAW) version 1. 3. 1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 2019, 47 (W1): W59- W64.
	Jin J J , Yu W B , Yang J B , et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 2020, 21 (1): 241. doi: 10.1186/s13059-020-02154-5
	Katoh K , Rozewicki J , Yamada K D . MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 2019, 20 (4): 1160- 1166. doi: 10.1093/bib/bbx108
	Kurtz S , Choudhuri J V , Ohlebusch E , et al. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 2001, 29 (22): 4633- 4642. doi: 10.1093/nar/29.22.4633
	Minh B Q , Schmidt H A , Chernomor O , et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 2020, 37 (5): 1530- 1534. doi: 10.1093/molbev/msaa015
	Niu Y , Gao C , Liu J . Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes. PeerJ, 2021, 9, e10774. doi: 10.7717/peerj.10774
	Rozas J , Ferrer-Mata A , Sánchez-Delbarrio J C , et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 2017, 34 (12): 3299- 3302. doi: 10.1093/molbev/msx248
	Sharp P M , Li W . The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 1987, 15 (3): 1281- 1295. doi: 10.1093/nar/15.3.1281
	Song Y , Yu W B , Tan Y , et al. Evolutionary comparisons of the chloroplast genome in Lauraceae and insights into loss events in the Magnoliids. Genome Biology and Evolution, 2017, 9 (9): 2354- 2364. doi: 10.1093/gbe/evx180
	Song Y , Yu W B , Tan Y H , et al. Plastid phylogenomics improve phylogenetic resolution in the Lauraceae. Journal of Systematics and Evolution, 2020, 58 (4): 423- 439. doi: 10.1111/jse.12536
	Tian X , Ye J , Song Y . Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae. PeerJ, 2019, 7, e7662. doi: 10.7717/peerj.7662
	Wei G Q , Chen H , Kong L , et al. Composition and bioactivity of the essential oil from the leaves of Lindera setchuenensis. Chemistry of Natural Compounds, 2016, 52 (3): 520- 522. doi: 10.1007/s10600-016-1696-2
	Xie D F , Tan J B , Yu Y , et al. Insights into phylogeny, age and evolution of Allium(Amaryllidaceae) based on the whole plastome sequences. Annals of Botany, 2020, 125 (7): 1039- 1055. doi: 10.1093/aob/mcaa024
	Zhao D N , Ren Y , Zhang J Q . Conservation and innovation: Plastome evolution during rapid radiation of Rhodiola on the Qinghai-Tibetan Plateau. Molecular Phylogenetics and Evolution, 2020, 144, 106713. doi: 10.1016/j.ympev.2019.106713
	Zhao M L , Song Y , Ni J , et al. Comparative chloroplast genomics and phylogenetics of nine Lindera species(Lauraceae). Scientific Reports, 2018, 8 (1): 8844. doi: 10.1038/s41598-018-27090-0
	Zheng G , Wei L , Ma L , et al. Comparative analyses of chloroplast genomes from 13 Lagerstroemia(Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. Plant Molecular Biology, 2020, 102 (6): 659- 676. doi: 10.1007/s11103-020-00972-6
	Zhu B , Qian F , Hou Y F , et al. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa(Brassicaceae). PLoS ONE, 2021, 16 (3): e0248556. doi: 10.1371/journal.pone.0248556

[1]	彭欣,王瀚棠,郭春晖,杨振德,周静,王雪,丁芷柔. 入侵性致瘿害虫桉树枝瘿姬小蜂(膜翅目: 姬小蜂科)EST-SSR开发及隐种鉴定[J]. 林业科学, 2021, 57(9): 140-151.
[2]	蔡金峰,杨晓明,郁万文,汪贵斌,曹福亮. 基于苦楝转录组测序的SSR分子标记开发[J]. 林业科学, 2021, 57(6): 85-92.
[3]	杜超群,孙晓梅,谢允慧,侯义梅. 北亚热带日本落叶松不同改良水平群体的遗传多样性[J]. 林业科学, 2021, 57(5): 68-76.
[4]	王正,马晓乾,周勤政,郑桂恒,夏吾加,张艳明,王成立,晋鹏非,吕全,张星耀. 中国齿小蠹属昆虫的鉴定[J]. 林业科学, 2021, 57(12): 79-91.
[5]	孟艺宏,徐刚标,卢孟柱,姜小龙,郭飞龙. 长柄双花木种群遗传结构及种群历史[J]. 林业科学, 2020, 56(7): 55-62.
[6]	蒋明,柯世省,王军峰. 多脉铁木叶绿体基因组的序列特征和系统发育[J]. 林业科学, 2020, 56(5): 60-68.
[7]	周晓君,张凯,彭正锋,孙姗姗,押辉远,张延召,程彦伟. 矮牡丹与芍药属其他5个种叶绿体基因组特征的比较[J]. 林业科学, 2020, 56(4): 82-88.
[8]	耿显胜,舒金平,盛建立,张威,彭瀚. 非刚竹属5种竹子丛枝病病原菌的分离和鉴定[J]. 林业科学, 2020, 56(3): 82-89.
[9]	张守科, 方林鑫, 刘亚宁, 王毅, 张威, 舒金平, 张亚波, 汪阳东, 王浩杰. 茶籽象ATP合成酶基因在不同海拔选择压力下的遗传分化及结构变异[J]. 林业科学, 2019, 55(6): 65-73.
[10]	韩小红, 卢赐鼎, 华银, 林浩宇, 是雨霏, 吴松青, 张飞萍, 梁光红. 星天牛转录组及三大解毒酶家族相关基因系统发育分析[J]. 林业科学, 2019, 55(5): 104-113.
[11]	于涛, 张宇阳, 高健, 柯蕾, 马文宝, 李俊清. 极小种群濒危植物盐桦叶绿体基因组特征分析[J]. 林业科学, 2019, 55(2): 41-49.
[12]	杜会聪,王瑶,方加兴,张珍荫,张苏芳,刘福,张真,孔祥波. 马尾松毛虫线粒体全基因组的测定与分析[J]. 林业科学, 2019, 55(12): 162-172.
[13]	金玲, 刘明国, 董胜君, 吴月亮, 张欣. 97个山杏无性系的遗传多样性及SSR指纹图谱[J]. 林业科学, 2018, 54(7): 51-61.
[14]	李雯雯, 赵文霞, 林若竹, 姚艳霞, 李娟, 淮稳霞. 基于ITS和β-tubulin基因分析的居间疫霉菌系统发育[J]. 林业科学, 2018, 54(3): 73-82.
[15]	包文泉, 乌云塔娜, 杜红岩, 李铁柱, 刘慧敏, 王淋, 白玉娥. 基于SSR标记的西藏光核桃群体遗传多样性和遗传结构分析[J]. 林业科学, 2018, 54(2): 30-41.