濒危植物峨眉凤仙花叶绿体基因组分析

赵秋燕; 曹孟会; 李新艺; 周敏; 魏春梅; 张茜; 瞿素萍; 黄海泉; 黄美娟

doi:10.19303/j.issn.1008-0384.2023.02.007

濒危植物峨眉凤仙花叶绿体基因组分析

doi: 10.19303/j.issn.1008-0384.2023.02.007

1.
西南林业大学园林园艺学院/西南林业大学园林园艺花卉研发中心，云南　昆明　650224
2.
云南省农业科学院花卉研究所，云南　昆明　650205

基金项目: 国家自然科学基金项目（32060364、32060366、31860230）；云南省重大科技专项（202102AE090052）；云南省园林植物遗传改良与高效繁育博士生导师团队和云南省中青年学术和技术带头人培养项目（503210103、2015HB046、2018HB024）

详细信息

作者简介:
赵秋燕（1995−），女，硕士，研究方向：园林植物资源调查及分析（E-mail：1378219465@qq.com）

通讯作者:
黄美娟（1972−），女，博士，教授，博士生导师，研究方向：园林植物研究（E-mail：xmhhq2001@163.com）

中图分类号: S685.99；Q943.2
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出版历程
- 收稿日期: 2022-07-04
- 录用日期: 2022-07-04
- 修回日期: 2022-10-21
- 网络出版日期: 2023-03-28
- 刊出日期: 2023-02-28

Complete Chloroplast Genome of Endangered Impatiens omeiana

1.
College of Landscape and Horticulture, Southwest Forestry University/Landscape, Horticulture and Flower R & D Center, Southwest Forestry University, Kunming, Yunnan　650224, China
2.
Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650205, China

摘要

摘要: 目的对峨眉凤仙花（Impatiens omeiana Hook.f.）叶绿体基因组的结构特征及系统发育进行研究，为其资源保护及开发利用提供理论依据。方法基于峨眉凤仙花叶绿体基因组序列，利用生物信息学软件，对叶绿体基因组进行组装、注释、基因特征、序列重复和系统发育分析。结果峨眉凤仙花完整的叶绿体基因组长度为152527 bp，共有130个基因，包括86个蛋白质编码基因、8个rRNA基因和36个tRNA基因，GC含量为37%，且具有保守的四分体结构，包括大单拷贝区、小单拷贝区各1个和2个相同的反向重复区域，其长度分别为83150、17903、25 737 bp，其中13个基因有1个内含子，2个基因有2个内含子。特征分析表明：峨眉凤仙花叶绿体全基因组中共检测到76个SSR序列，且多以A/T单核苷酸序列为主，其长度为10~91 bp；检测到50842个密码子，其中以亮氨酸（Leu）最多，色氨酸（Tyr）最少；密码子偏好性分析显示33个RSCU≥1的密码子多数以A/U结尾。通过邻接法（NJ）构建系统发育树发现，峨眉凤仙花与贵州凤仙花亲缘关系最近，均属于棒凤仙花亚属植物。结论峨眉凤仙花叶绿体基因组呈典型的四分体结构，SSR序列以A/T单碱基为主；系统发育分析结果将其归为棒凤仙花亚属，上述结果为峨眉凤仙花系统发育学地位及物种鉴定工作提供了重要的分子信息。
- 峨眉凤仙花 /
- 叶绿体基因组 /
- 序列结构与特征分析 /
- 系统发育
Abstract: Objective Chloroplast genome structure and phylogeny of the endangered Impatiens omeiana Hook.f. endemic species in China were studied. Method Gene assembly, annotation, characteristics, sequence duplication, and phylogenetics of I. omeiana were analyzed based on the chloroplast genome sequence using bioinformatic software. Results The genome was 152527 bp consisting of 130 gene, including 86 protein-coding, 8 rRNA, and 36 tRNA genes. It had a GC content of 37% and a conservative tetrad structure with regions of a large single-copy of 83150 bp, a small single-copy of 17903 bp, and two identical reverse repeats of 25 737 bp. Thirteen of the genes had one intron, and two had two. There were 76 SSR sequences detected in the genome mainly of A/T single nucleotides with a length ranging from 10 bp to 91 bp. A total of 50842 codons were found in the entire genome. Among the amino acids, leucine (Leu) was the most numerous and tryptophan (Tyr) the least. A codon bias analysis showed those of 33 RSCU＞1 had A/U on their ends. Using the Neighbor Joining method (NJ), a phylogenetic tree was constructed based on the chloroplast genomes from different plants to show a close relationship of I. omeiana with I. guizhouensis belonging to the subgenus Clavicarpa. Conclusion The chloroplast genome of I. omeiana had a typical tetrad structure of many SSR repeated sequences with A/T single base. Phylogenetically, I. omeiana was a Clavicarpa subgenus. These results provide important molecular information for the phylogenetic status and species identification of I. omeiana.
- Impatiens omeiana /
- chloroplast genome /
- sequence structure and characteristic analysis /
- phylogeny

HTML全文

图 1 峨眉凤仙花叶绿体基因组图谱

Figure 1. Chloroplast genome map of I. omeiana

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图 2 基于15个物种叶绿体基因组序列构建的邻接法系统发育树

Figure 2. Neighbor Joining phylogenetic tree constructed from chloroplast genome sequences of 15 species

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表 1 峨眉凤仙花叶绿体基因组基因信息

Table 1. Information on chloroplast genome of I. omeiana

基因类别Category of genes	基因分类Group of genes	基因名称Name of gene
自我复制Self-replication	核糖体的小亚基Small subunit of ribosome	rps11、rps14、rps15、rps16、rps18、rps2、rps3、rps4、rps8、rps7（×2）、rps12（×2）、rps19（×2）
	核糖体的大亚基Large subunit of ribosome	rpl14、rpl16、rpl20、rpl22、rpl33、rpl36、rpl2（×2）、rpl23（×2）
	依赖于DNA的RNA聚合酶DNA dependent RNA polymerase	rpoA、rpoB、rpoC1、rpoC2
光合作用Photosynthesis	光系统I亚基Subunits of photosystem I	psaA、psaB、psaC、psaI、psaJ
	光系统II亚基Subunits of photosystem II	psbA、psbB、psbC、psbD、psbE、psbF、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ、ycf3
	NADH脱氢酶亚基Subunits of NADH-dehydrogenase	ndhA、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK、ndhB（×2）
	细胞色素b/f复合体Subunits of cytochrome b/f complex	petA、petB、petD、petG、petL、petN
	ATP合酶亚基Subunits of ATP synthase	atpA、atpB、atpE、atpF、atpH、atpI
	二磷酸核酮糖羧化酶Subunit of rubisco	rbcL
rRNA	rRNA 基因rRNA genes	rrn5S（×2）、rrn16S（×2）、rrn4.5S（×2）、rrn23S（×2）
tRNA	tRNA基因tRNA genes	36 trn 基因（5 个内含子）
其他Others	乙酰辅酶A羧化酶亚基Subunit of Acetyl-CoA-carboxylase	accD
	C型细胞色素合成酶c-type cytochrom synthesis gene	ccsA
	外膜蛋白Envelop membrane protein	cemA
	蛋白酶Protease	clpP
	翻译起始因子Translational initiation factor	infA
	成熟酶Maturase	matK
未知功能Unknown	保守的开放阅读框Conserved open reading frames	ycf1、ycf4、ycf2（×2）

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表 2 峨眉凤仙花叶绿体基因组中内含子和外显子位置及长度

Table 2. Positions and lengths of introns and exons in chloroplast genome of I. omeiana

基因名称Gene name	起始位置Start/bp	终点位置End/bp	序列长度Length of sequence/bp
基因名称Gene name	起始位置Start/bp	终点位置End/bp	第一外显子Exon I	第一内含子Intron I	第二外显子Exon II	第二内含子Intron II	第三外显子Exon III
trnK-UUU	1642	4242	37	2528	36
rps16	4905	5950	40	809	197
atpF	10711	11913	145	648	410
rpoC1	19925	22723	432	750	1617
ycf3	41988	43909	124	711	230	704	153
trnL-UAA	46816	47428	35	528	50
trnV-UAC	50658	51332	38	602	35
accD	56549	58045	648	33	816
clpP	69103	71130	71	795	294	645	223
rpl2	83406	84895	391	665	434
ndhB	93523	95728	775	673	758
trnE-UUC	101206	102209	32	932	40
trnA-UGC	102273	103146	37	801	36
ndhA	118162	120335	547	1088	539
ycf1	122240	127192	1642	30	3281
trnA-UGC	132532	133405	37	801	36
trnE-UUC	133469	134472	32	932	40
ndhB	139950	142155	775	673	758
rpl2	150783	152272	391	665	434

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表 3 峨眉凤仙花叶绿体基因组SSR类型及分布

Table 3. SSR types and distribution of chloroplast genome of I. omeiana

重复类型Repeat type	重复单元Repeat unit	重复频率Repetition frequency	数量Number	不同类型SSR的分布起始位点Distribution initiation loci of different SSR types/bp
单核苷酸Mononucleotides	A	10	15	5313,6149,7515,7680,7924,31792,44011,46201,50989, 55996,70336,80231,108748,133991,137883
	A	11	3	7807,44377,69853
	A	12	5	1803,11479,29832,108859,111109
	A	13	1	111913
	A	14	1	60218
	T	10	14	7133,25317,26410,30416,31579,47674,48233,49787,97786,101678,113939, 126921,69853,126569
	T	11	14	7300,10671,13405,17614,34889,45803,75910,81044,113373,116058,118964,124837,124972,125993
	T	12	8	11343,26853,29527,53623,59969,81205,124351,126808
	T	13	3	77265,79172,109650
	T	14	2	2906,77053
	T	17	1	64052
二核苷酸Dinucleotides	AT	6	2	46389,53926
二核苷酸Dinucleotides	TA	7	2	96020,139645
三核苷酸Trinucleotides	ATT	4	2	65188,119570
四核苷酸Tetranucleotides	AATA	3	1	114206
	AATT	3	1	62783
	TTCT	3	1	56243

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表 4 峨眉凤仙花叶绿体基因组密码子RSCU分布情况

Table 4. RSCU distribution of chloroplast genome codons of I. omeiana

氨基酸Amino acid	密码子Codon	数量Number	密码子偏好性值RSCU	氨基酸Amino acid	密码子Codon	数量Number	密码子偏好性值RSCU
苯丙氨酸Phe	UUU	2298	1.24	脯氨酸Pro	CCU	649	1.10
苯丙氨酸Phe	UUC	1397	0.76		CCC	571	0.97
亮氨酸Leu	UUA	1197	1.37		CCA	743	1.26
	UUG	1013	1.16		CCG	388	0.66
	CUU	1058	1.21	苏氨酸Thr	ACU	645	1.22
	CUC	659	0.76		ACC	512	0.97
	CUA	838	0.96		ACA	649	1.22
	CUG	469	0.54		ACG	316	0.60
异亮氨酸Ile	AUU	1770	1.23	丙氨酸Ala	GCU	522	1.32
	AUC	1033	0.72		GCC	349	0.88
	AUA	1507	1.05		GCA	474	1.20
蛋氨酸Met	AUG	812	1.00		GCG	241	0.61
缬氨酸Val	GUU	786	1.36	甘氨酸Gly	GGU	538	0.95
	GUC	409	0.71		GGC	344	0.61
	GUA	709	1.22		GGA	866	1.53
	GUG	413	0.71		GGG	513	0.91

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续上表
氨基酸Amino acid	密码子Codon	数量Number	密码子偏好性值RSCU	氨基酸Amino acid	密码子Codon	数量Number	密码子偏好性值RSCU
丝氨酸Ser	UCU	1130	1.47	组氨酸His	CAU	836	1.39
	UCC	854	1.11	组氨酸His	CAC	365	0.61
	UCA	1050	1.36	谷氨酰胺Gln	CAA	1011	1.36
	UCG	559	0.73	谷氨酰胺Gln	CAG	474	0.64
	AGU	612	0.79	天冬酰胺Asn	AAU	1657	1.40
	AGC	421	0.55	天冬酰胺Asn	AAC	705	0.60
络氨酸Tyr	UAU	1346	1.37	赖氨酸Lys	AAA	2241	1.38
络氨酸Tyr	UAC	618	0.63	赖氨酸Lys	AAG	1005	0.62
半胱氨酸Cys	UGU	649	1.21	天冬氨酸Asp	GAU	1070	1.46
半胱氨酸Cys	UGC	425	0.79	天冬氨酸Asp	GAC	397	0.54
末端TER	UAA	1135	1.13	精氨酸Arg	CGU	332	0.64
	UAG	806	0.80		CGC	244	0.47
	UGA	1072	1.07		CGA	603	1.17
谷氨酸Glu	GAA	1323	1.39		CGG	340	0.66
谷氨酸Glu	GAG	585	0.61		AGA	1046	2.03
色氨酸Trp	UGG	709	1.00		AGG	534	1.03.

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