矮牡丹与芍药属其他5个种叶绿体基因组特征的比较

doi:10.11707/j.1001-7488.20200409

摘要/Abstract

摘要：

目的: 中国特有的野生牡丹一直被国内外视为珍贵的种质资源。野生矮牡丹被认为是现代栽培牡丹品种重要的祖先种之一，开展矮牡丹在内的芍药属植物叶绿体基因组（cp DNA）特征分析对阐明牡丹系统进化、培育和改良栽培品种具有重要的理论与实践价值。方法: 在矮牡丹叶绿体高通量测序的基础上，从NCBI数据库下载凤丹牡丹、大花黄牡丹、滇牡丹、川赤芍和草芍药的cp DNA数据，利用Geneious 8.0、EMBOSS 6.4.0等软件，对芍药属6个种的cp DNA进行对比分析。结果: 矮牡丹cp DNA序列共152 628 bp，共有112个基因，使用25 988个密码子，编码蛋白78个；有19个基因（包括4个rRNA、7个tRNA、8个蛋白编码基因）在IR（反向重复）区重复。共搜索到143个SSR位点，单核苷酸重复基序位点最多，为116个（占81.12%），没有六核苷酸重复基序。尽管芍药属叶绿体基因组比较保守，但不同种间IR和LSC（大单拷贝区）的边界位置仍有一定变化，凤丹牡丹LSC/IR的rpl2基因有718 bp延伸至LSC区域，而其他种的rpl2基因均完整地位于IR区。结论: 从基因组大小和基因内容来看，芍药属cp DNA高度保守；草芍药与滇牡丹cp DNA最大，为152 698 bp；凤丹牡丹cp DNA最小，为152 153 bp。矮牡丹cp DNA蛋白编码基因密码子偏好使用A/T碱基，SSRs位点的碱基组成也偏好使用A/T碱基，143个SSRs位点中，A/T组成的位点有134个；矮牡丹cp DNA SSRs分布具有不均匀性，14个SSR位点位于IR区段，103个位于LSC区段，26个位于SSC区段。IR边界分析显示，芍药属LSC/IRb的边界变化是IR区扩张与收缩的主要原因。研究结果为芍药属植物的系统进化与栽培起源等研究提供支持，对芍药属植物分子标记开发及优良品种选育具有参考价值。

关键词: 芍药属, 矮牡丹, 高通量测序, 叶绿体基因组, SSR位点, IR边界分析

Abstract:

Objective: China's wild peony has been regarded as precious germplasm resources at home and abroad. Wild Paeonia jishanensis is considered as one of the most important ancestral species of cultivated tree peonies. The analysis of chloroplast genome (cp DNA) characteristics of Paeonia, including P. jishanensis, has important theoretical and practical values for elucidating the phylogeny of Paeonia and developing improved varieties. Method: Chloroplast data of P. jishanensis were obtained by high-throughput sequencing. The cp DNA data of P. ostii, P. ludlowii, P. delavayi, P. veitchii and P. obovata were downloaded from NCBI database. Comparative analysis of the six peony cp DNA was performed using Geneious 8.0 and EMBOSS 6.4.0. Result: The cp DNA sequence of P. jishanensis was 152 628 bp with 112 genes, 25 988 codons encoding 78 proteins. There are 19 genes (including 4 rRNA, 7 tRNA, 8 protein coding genes) repeat in the IR (Inverse Repeat) region. A total of 143 SSR loci were searched, the mononucleotide repeat are the most common (116, accounting for 81.12%), and there was no hexanucleotide repeat motif. Although the chloroplast genome of Paeonia is conservative, there are still some changes in the boundary of IR and LSC(large single-copy) between different species. The rpl2 gene of P. ostii extends 718 bp to the LSC region, while that of other species are completely located in the IR region. Conclusion: Paeonia cp DNA genome size and gene content are highly conserved. The cp DNA of P. obovata and P. delavayi was the largest (152 698 bp), and that of P. ostii was the smallest (152 153 bp). The codons of cp DNA protein coding genes and the base composition of SSR loci in P. jishanensis prefer to use A/T. Among 143 SSR loci, 134 loci were A/T loci. The distribution of cp DNA SSRs in P. jishanensis has heterogeneity, 14 SSR loci were located in IR region, 103 in LSC region and 26 in SSC region. Analysis showed that boundary change of LSC/IRb was the main reason for the expansion or contraction of IR region in Paeonia. The results provide a basis for the studies of phylogeny and origin of cultivation, and for the development of molecular markers and the breeding of elite cultivars of Paeonia plants.

Key words: Paeonia, Paeonia jishanensis, high-throughput sequencing, chloroplast genome, SSR loci, IR boundary analysis

中图分类号:

S718.46

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.

Xiaojun Zhou,Kai Zhang,Zhengfeng Peng,Shanshan Sun,Huiyuan Ya,Yanzhao Zhang,Yanwei Cheng. Comparative Analysis of Chloroplast Genome Characteristics between Paeonia jishanensis and Other Five Species of Paeonia[J]. Scientia Silvae Sinicae, 2020, 56(4): 82-88.

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基因组特征 Genome feature	草芍药 P. obovata	凤丹牡丹 P. ostii	大花黄牡丹 P. ludlowii	滇牡丹 P. delavayi	川赤芍 P. veitchii	矮牡丹 P. jishanensis
GenBank登录号GenBank number	KJ206533	MG585274	KY817592	KY817591	KT894821	MG991935
基因组大小Size/bp/G+C (%)	152 698/38.4	152 153/38.4	152 687/38.4	152 698/38.4	152 682/38.4	152 628/38.4
大单拷贝区长度LSC/bp/G+C (%)	84 387/36.7	85 373/36.7	84 426/36.7	86 057/36.7	84 398/36.7	84 292/36.7
小单拷贝区长度SSC/bp/G+C (%)	17 028/32.7	17 054/32.7	16 983/32.7	17 050/32.7	16 978/32.7	17 044/32.7
反向重复序列长度IR/bp/G+C (%)	25 642/43.1	24 863/43.1	25 639/43.1	25 649/43.1	25 653/43.1	25 646/43.1

基因分类 Category	基因分组 Group of genes	基因名称 Name of genes
表达相关基因 Translation related genes	核糖体大亚基基因 Large subunit of ribosomal proteins	rpl2^a, 14, 16^, 20, 22, 23^a, 33, 36
	核糖体小亚基基因 Small subunit of ribosomal proteins	rps2, 3, 4, 7^a, 8, 11, 12^a, 14, 15, 16^, 18, 19
	RNA聚合酶亚基基因 DNA-dependent RNA polymerase	rpoA	rpoB	rpoC1^*	rpoC2
	核糖体RNA基因rRNA genes	rrn16S ^a	rrn23S ^a	rrn4.5S ^a	rrn5S ^a
	转运RNA基因 tRNA genes	trnA-UGC^*a	trnG-GCC	trnL-CAA^a	trnQ-UUG	trnT-GGU
		trnC-GCA	trnG-UCC	trnL-UAA ^*	trnR-ACG^a	trnT-UGU
		trnD-GUC	trnH-GUG	trnL-UAG	trnR-UCU	trnV-GAC^a
		trnE-UUC	trnI-CAU^a	trnM-CAU	trnS-GCU	trnV-UAC ^*
		trnF-GAA	trnI-GAU	trnN-GUU^a	trnS-GGA	trnW-CCA
		trnfM-CAU	trnK-UUU	trnP-UGG	trnS-UGA	trnY-GUA
光合作用 Photosynthesis	光合系统Ⅰ基因Photosystem Ⅰ	psaA, B, C, I, J
	光合系统Ⅱ基因Photosystem Ⅱ	psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z
	NADH氧化还原酶NADH oxidoreductase	ndhA^, B^a, C, D, E, F, G, H, I, J, K
	细胞色素复合物基因 PCytochrome b/f complex	petA, B^, D^, G, L, N
	ATP合酶基因ATP synthase	atpA, B, E, F^*, H, I
	二磷酸核酮糖羧化酶Rubisco	rbcL
其他基因 Other genes	成熟酶基因Maturase	matK
	蛋白酶Protease	clpP^*
	包裹膜蛋白基因Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基基因 Subunit acetyl-CoA-carboxylase	accD
	c型细胞色素合成基因 c-type cytochrome synthesis	ccsA
	保守的开放阅读框 Conserved open reading frames	ycf1 ^a, 2 ^a, 3^*, 4, 15^a

重复基序类型 Motif type	数量 Number	重复基序类型 Motif type	数量 Number	重复基序类型 Motif type	数量 Number
A/T	111	AAT/ATT	3	ATCT/AGAT	1
AT/AT	12	AAAT/ATTT	2	CTTT/AAAG	1
C/G	5	TC/GA	1	TATAA/TTATA	1
ATA/TAT	3	AAAC/GTTT	1	(A)₁₄(AAT)₄	1
				(T)₉(A)₁₉	1

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