猫尾草叶绿体基因组结构及其解析

吴民富; 李莎; 高柔敏; 吴民华; 黄琼林

doi:10.19303/j.issn.1008-0384.2023.09.011

猫尾草叶绿体基因组结构及其解析

doi: 10.19303/j.issn.1008-0384.2023.09.011

1.
佛山职业技术学院食品科学系，广东　佛山　528137
2.
广东医科大学基础医学院，广东　湛江　524023

基金项目: 广东省基础与应用基础研究基金项目（2020A1515110332）；湛江市科技计划项目（2019A01008）

详细信息

作者简介:
吴民富（1986 —），男，博士，副教授，主要从事食品质量与安全研究，E-mail：wmf@fspt.edu.cn

通讯作者:
黄琼林（1986 —），男，博士，副教授，主要从事医学生物化学研究，E-mail：perfecthql@163.com

中图分类号: S541
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- 被引次数: 0
出版历程
- 收稿日期: 2023-05-26
- 修回日期: 2023-07-04
- 网络出版日期: 2023-10-25
- 刊出日期: 2023-09-28

Structure of Uraria crinita Chloroplast Genome

1.
Department of Food Science, Foshan Polytechnic College, Foshan, Guangdong　528137, China
2.
School of Basic Medicine, Guangdong Medical University, Zhanjiang, Guangdong 52023, China

摘要

摘要: 目的阐明岭南药食两用植物猫尾草的叶绿体基因组结构特征，为猫尾草资源的保护、利用和开发提供理论依据。方法采用高通量测序技术开展猫尾草叶绿体基因组测序，并通过生物信息方法进行拼接、注释、解析以及系统进化分析。结果猫尾草叶绿体基因组是149 774 bp的环状双链四段式分子，包含128个基因，GC含量为38.2%。猫尾草叶绿体基因组含有26 015个密码子，偏好以A或T结尾；存在110个简单重复序列，以A或T单核苷酸重复居多。序列比对和进化分析显示猫尾草与同属狸尾豆的亲缘关系最近。结论首次报道猫尾草叶绿体基因组的全序列，并明确其结构特点，为猫尾草的栽培育种、遗传多样性和资源利用等奠定基础。
- 猫尾草 /
- 叶绿体基因组 /
- 结构分析 /
- 序列比对 /
- 系统进化关系
Abstract: Objective Structure of the chloroplast genome from Uraria crinita, a plant used as food as well as herbal medicine in Lingnan area of China, was studied. Methods The whole chloroplast genome was obtained by high-throughput sequencing and then assembled, annotated, and analyzed by bioinformatic means. Results The genome was an annular quadripartite molecule of 149 774 bp that harbored 128 genes. It had a low GC content of 38.2% containing 26 015 codons that mostly ended with A or T. There were 110 loci of simple sequence repeat detected with the mononucleotide largely formed by A or T. An alignment and phylogenetic analysis on the sequence indicated a close relationship between U. crinita and U. lagopodioides. Conclusion The chloroplast genome and structure of U. crinita were unveiled for the first time to aid future studies on the cultivation, breeding, genetics, and utilization of the valuable plant.
- Uraria crinita /
- chloroplast genome /
- structure analysis /
- sequence alignment /
- phylogenetic relationship

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图 1 猫尾草叶绿体基因组

Figure 1. Chloroplast genome of U. crinita

下载: 全尺寸图片幻灯片

图 2 猫尾草叶绿体基因组的相对同义密码子使用情况

Ala-丙氨酸; Arg-精氨酸; Asn-天冬酰胺; Asp-天冬氨酸; Cys-半胱氨酸; Glu-谷氨酸; Gln-谷氨酰胺; Gly-甘氨酸;His-组氨酸; Ile-异亮氨酸; Leu-亮氨酸; Lys-赖氨酸; Met-甲硫氨酸; Phe-苯丙氨酸; Pro-脯氨酸; Ser-丝氨酸; Thr-苏氨酸; Trp-色氨酸; Tyr-络氨酸; Val-缬氨酸; end-终止密码子。

Figure 2. Relative synonymous codon usage of U. crinita chloroplast genome

Ala: alanine; Arg: arginine; Asn: asparagine; Asp: aspartate; Cys: cysteine; Glu: glutamate; Gln: glutamine; Gly: glycine; His: histidine; Ile: isoleucine; Leu: leucine; Lys: lysine; Met: methionine; Phe: phenylalanine; Pro: proline; Ser: serine; Thr: threonine; Trp: tryptophan; Tyr: tyrosine; Val: valine; end: ending codon.

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图 3 5种植物的叶绿体基因组SC/IR边界的比较

Figure 3. Comparison on boundaries of SC/IR in chloroplast genomes of 5 plants

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图 4 豆科蝶形亚科山蚂蝗族5种植物叶绿体基因组序列差异分析

Figure 4. Sequence differentiations among 5 chloroplast genomes from trib. Lespedezinae

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图 5 基于叶绿体基因组构建的猫尾草系统进化树

Figure 5. Phylogenetic tree of U. crinita based on chloroplast genome

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表 1 猫尾草叶绿体基因及其注释和功能归类

Table 1. Composition and classification of genes in U. crinita chloroplast genome

分类 Category	功能 Function	基因 Gene
蛋白质编码基因 Protein-coding gene	ATP 合成酶 ATP synthase	atpA, atpB, atpE, atpF¹, atpH, atpI
	细胞色素b/f复合物 Cytochrome b/f complex	petA, petB¹, petD¹, petG, petL, petN
	NADH脱氢酶 NADH dehydrogenase	ndhA¹, ndhB¹*, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
	光系统I Photosystem I	psaA, psaB, psaC, psaI, psaJ
	光系统II Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	核糖体蛋白质大亚基 Ribosomal proteins large submit	rps2, rps3, rps4, rps7*, rps8, rps11,rps12^#*, rps14, rps15,rps16¹, rps18, rps19*
	核糖体蛋白质小亚基 Ribosomal proteins small submit	rpl2¹*, rpl14, rpl16¹, rpl20,rpl22, rpl23**, rpl32,rpl33, rpl36
	RNA集合酶 RNA polymerase	rpoA, rpoB, rpoC1¹, rpoC2
	其他基因 Other genes	accD, ccsA, cemA, clpP², matK, rbcL, infA
	假定叶绿体阅读框 Hypothetical chloroplast reading frame	ycf1, ycf2, ycf3², ycf*4
核糖体RNA Ribosomal RNAs		rrn4.5, rrn5*, rrn16*, rrn23**
转运RNA Transfer RNAs		trnH-GUG, trnK-UUU¹, trnM-CAU, trnM-CAU, trnV-UAC¹, trnF-GAA, trnL-UAA¹, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnD-GUC, trnY-GUA, trnE-UUC, trnC-GCA, trnR-UCU, trnG-UCC¹, trnS-GCU, trnQ-UUG, trnW-CCA, trnP-UGG, trnI-CAU, trnL-CAA, trnV-GAC*, trnI-GAU¹, trnA-UGC¹, trnR-ACG*, trnN-GUU*, trnL-UAG*
基因右上角的数字表示该基因所含的内含子数；#表示该基因存在反式剪接情况；表示该基因为双拷贝基因。 Data on upper right corner stand for intron number in genes; # denotes trans-splicing in genes; represents genes with two copies.

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表 2 猫尾草叶绿体基因组SSR统计

Table 2. SSR information on U. crinita chloroplast genome

类型 Type	重复基序 Motif	数量 Number	比例 Ratio/%
单核苷酸 Mononucleotide	A/T	54	98.2
单核苷酸 Mononucleotide	C/G	1	1.8
二核苷酸 Dinucleotide	AG/CT	1	2.4
二核苷酸 Dinucleotide	AT/AT	41	97.6
三核苷酸 Trinucleotide	AAT/ATT	6	100.0
四核苷酸 Tetranucleotide	AAAT/ATTT	4	57.1
	AAGG/CCTT	1	14.3
	AAGT/ACTT	1	14.3
	AGAT/ATCT	1	14.3
总计 Total		110

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