广东省野生莼菜叶绿体基因组及其系统发育关系

doi:10.13560/j.cnki.biotech.bull.1985.2025-1418

摘要/Abstract

摘要：

目的探究广东省野生莼菜叶绿体基因组特征及系统发育关系，揭示其遗传变异与种群分化，为该物种的进化分类及水生植物保护与基因组学研究提供分子依据。方法对采自广东的莼菜进行基因组测序并组装和注释叶绿体基因组。随后，将其与不同物种及不同地理来源的同种个体的叶绿体基因组开展比较分析，涵盖基因组的结构与组成、重复序列的类型和数量、密码子使用偏好性、基因组边界差异、基因组比较、核苷酸多态性、基因统计及系统发育关系等多个方面。结果基因组呈环状四分体结构，由一个大的单拷贝区、两个反向重复区和一个小的单拷贝区构成。其基因组长度为158 974 bp，共鉴定出133个编码基因，GC含量为39%，其中蛋白编码基因87个，转运RNA基因38个，核糖体RNA基因8个。此外，该基因组含有25个SSR位点，其中单核苷酸重复最为丰富，主要以A/T碱基为主。鉴定出具有高核苷酸多样性的9个高度可变位点（ndhF、ndhD、psaC-ndhE、ndhE、ndhA、ndhH、ycf1、trnR-ACG-rrn5s和rrn23s）为潜在的分子标记。该植物的高频密码子为29个，偏好以A/U结尾。基于20个近缘物种及1个不同地理来源的同种个体的叶绿体基因组数据构建的系统发育树表明，莼菜属与水盾草属聚为一个高支持率的单系分支（即莼菜科）。该分支作为一个整体，与睡莲科的萍蓬草属亲缘关系最近，共同形成了一个更大的进化支。结论广东野生莼菜叶绿体基因组结构及组成保守性强，不同地区个体存在极小差异，且对A/T密码子偏好性强，与水盾草的亲缘关系密切。

关键词: 莼菜, 叶绿体基因组, 基因组比较分析, 系统发育, 结构特征, 密码子偏好性, 遗传变异

Abstract:

Objective This study aims to investigate the genomic characteristics and phylogenetic relationships of chloroplasts in the wild water shield found in Guangdong province. It seeks to elucidate genetic variations and population differentiation while providing molecular evidence for the evolutionary classification of this species. Additionally, the research contributes to the conservation and genomic studies of aquatic plants. Method The genome of Brasenia schreberi collected from Guangdong was sequenced, assembled and annotated for its chloroplast genome. Subsequently, comparative analyses were performed between it and the chloroplast genomes of different species, as well as those of conspecific individuals from various geographical sources. These analyses encompassed multiple aspects, including genome structure and composition, types and quantities of repeat sequences, codon usage preferences, differences in genomic boundaries, genomic comparisons, nucleotide polymorphisms, gene statistics, and phylogenetic relationships. Result The chloroplast genome exhibited the canonical quadripartite circular structure, consisting of a large single-copy region, a small single-copy region, and two inverted repeat regions, with a total length of 158 974 bp. The overall GC content was 39.0%. We annotated 133 genes, including 87 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. Analysis identified 25 simple sequence repeat (SSR) loci, predominantly mononucleotide repeats rich in A/T bases. Nucleotide diversity analysis revealed nine highly variable regions (ndhF, ndhD, psaC-ndhE, ndhE, ndhA, ndhH, ycf1, trnR-ACG-rrn5s, and rrn23s), which are proposed as potential molecular markers. Codon usage bias analysis showed a preference for A/U-ending codons, with 29 high-frequency codons identified. The phylogenetic tree constructed based on chloroplast genome data from 20 closely related species and one conspecific individual of different geographical origins indicates that the genera Brasenia and Cabomba cluster into a highly supported monophyletic clade (corresponding to the family Cabombaceae). As a whole, this clade is most closely related to the genus Nuphar within the family Nymphaeaceae, together forming a larger evolutionary clade. Conclusion The chloroplast genome of wild Brasenia schreberi from Guangdong exhibits a highly conserved structure and composition. Nevertheless, minimal sequence divergence was detected among populations from different regions, along with a strong preference for A/T-rich codons. Phylogenetic analysis further confirmed its close genetic relationship with the genus Cabomba.

Key words: Brasenia schreberi, chloroplast genome, comparative genome analysis, phylogeny, structural features, codon preference, genetic variation

王杰, 李清, 罗永坚, 江洁明, 刘军. 广东省野生莼菜叶绿体基因组及其系统发育关系[J]. 生物技术通报, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1418.

WANG Jie, LI Qing, LUO Yong-jian, JIANG Jie-ming, LIU Jun. Chloroplast Genome of Wild Brasenia schreberi in Guangdong Province and Its Phylogenetic Relationships[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1418.

图/表 10

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基因组特征 Genome feature	莼菜 B. schreberi	水生金鱼藻 C. aquatica	卡罗莱纳金鱼藻 C. caroliniana	叉枝金鱼藻 C. furcata
基因组大小 Genome size （bp）	158 974	159 487	164 057	160 271
LSC长度 LSC length （bp）	88 779	89 434	82 090	90 038
SSC长度 SSC length （bp）	19 513	19 115	18 827	19 385
IR长度 IR length （bp）	25 341	25 469	31 570	25 424
基因总数 Number of genes	133	135	146	135
蛋白质编码基因数 Number of protein-coding genes	87	89	111	89
rRNA基因数 Number of rRNA genes	8	8	8	8
tRNA基因数 Number of tRNA genes	38	38	37	38
GC含量 GC content （%）	39.0	38.0	38.3	38.1
LSC中GC含量 GC content in LSC （%）	37.5	36.4	36.8	36.4
SSC中GC含量 GC content in SSC （%）	34.3	32.7	33.1	32.9
IR中GC含量 GC content in IR （%）	43.5	43.1	41.8	43.2

基因组特征 Genome feature	莼菜 B. schreberi	水生金鱼藻 C. aquatica	卡罗莱纳金鱼藻 C. caroliniana	叉枝金鱼藻 C. furcata
基因组大小 Genome size （bp）	158 974	159 487	164 057	160 271
LSC长度 LSC length （bp）	88 779	89 434	82 090	90 038
SSC长度 SSC length （bp）	19 513	19 115	18 827	19 385
IR长度 IR length （bp）	25 341	25 469	31 570	25 424
基因总数 Number of genes	133	135	146	135
蛋白质编码基因数 Number of protein-coding genes	87	89	111	89
rRNA基因数 Number of rRNA genes	8	8	8	8
tRNA基因数 Number of tRNA genes	38	38	37	38
GC含量 GC content （%）	39.0	38.0	38.3	38.1
LSC中GC含量 GC content in LSC （%）	37.5	36.4	36.8	36.4
SSC中GC含量 GC content in SSC （%）	34.3	32.7	33.1	32.9
IR中GC含量 GC content in IR （%）	43.5	43.1	41.8	43.2

基因功能分类 Category of gene function	基因类别 Gene group	基因名称 Gene name
光合作用相关 Photosynthesis-related	光系统Ⅰ Photosystem I	psaA， psaB， psaC， psaI， psaJ
	光系统Ⅱ Photosystem Ⅱ	psbA， psbB， psbC， psbD， psbE， psbF， psbI， psbJ， psbK， psbL， psbM， psbN， psbT， psbZ， ycf3**
	NADH氧化还原酶基因 NADH dehydrogenase	ndhA， ndhB（2）， ndhC， ndhD， ndhE， ndhF， ndhG， ndhH， ndhI， ndhJ， ndhK
	细胞色素b/f复合体 Cytochrome b/f complex	petA， petB， petD， petG， petL， petN
	ATP酶 ATP synthase	atpA， atpB， atpE， atpF， atpH， atpI*
	二磷酸核酮糖羧化酶大亚基 Rubisco large subunit	RbcL
自我复制基因 Self-replication	核糖体蛋白大亚基 Large subunit of ribosome	rpl14， rpl16， rpl2（2）， rpl20， rpl22， rpl23（2），rpl32， rpl33， rpl36
	核糖体蛋白小亚基 Small subunit of ribosome	rps11， rps12（3）， rps14， rps15， rps16， rps18， rps19， rps2， rps3， rps4， rps7（2）， rps8*
	RNA聚合酶 RNA polymerase	rpoA， rpoB， rpoC1， rpoC2*
	核糖体RNAs Ribosomal RNAs	rrn16（2），rrn23（2），rrn4.5（2），rrn5（2）
	转运RNA Transfer RNA	trnH-GUG， trnK-UUU， trnQ-UUG， trnS-GCU， trnS-CGA， trnR-UCU， trnC-GCA， trnD-GUC， trnY-GUA， trnE-UUC， trnT-GGU， trnS-UGA， trnG-GCC， trnM-CAU（4）， trnS-GCU， trnT-UGU， trnL-UAA， trnF-GAA， trnV-UAC， trnW-CCA， trnP-UGG， trnL-CAA（2）， trnV-GAC（2）， trnI-GAU（2）， trnA-UGC（2）， trnR-ACG（2）， trnL-UAG， trnN-GUU（2）
其他基因 Other genes	成熟酶 Maturase	MatK
	蛋白酶 Protease	ClpP**
	包膜蛋白基因 Envelope membrane protein gene	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	转录起始因子 Transcription initiation factor	infA
	乙酰辅酶A羧化酶的亚基 Subunit of Acetyl-CoA-carboxylase	accD
未知基因 Unknown genes	保守开放阅读框 Conserved open reading frame	ycf1， ycf15（2）， ycf2（2）， ycf4

基因功能分类 Category of gene function	基因类别 Gene group	基因名称 Gene name
光合作用相关 Photosynthesis-related	光系统Ⅰ Photosystem I	psaA， psaB， psaC， psaI， psaJ
	光系统Ⅱ Photosystem Ⅱ	psbA， psbB， psbC， psbD， psbE， psbF， psbI， psbJ， psbK， psbL， psbM， psbN， psbT， psbZ， ycf3**
	NADH氧化还原酶基因 NADH dehydrogenase	ndhA， ndhB（2）， ndhC， ndhD， ndhE， ndhF， ndhG， ndhH， ndhI， ndhJ， ndhK
	细胞色素b/f复合体 Cytochrome b/f complex	petA， petB， petD， petG， petL， petN
	ATP酶 ATP synthase	atpA， atpB， atpE， atpF， atpH， atpI*
	二磷酸核酮糖羧化酶大亚基 Rubisco large subunit	RbcL
自我复制基因 Self-replication	核糖体蛋白大亚基 Large subunit of ribosome	rpl14， rpl16， rpl2（2）， rpl20， rpl22， rpl23（2），rpl32， rpl33， rpl36
	核糖体蛋白小亚基 Small subunit of ribosome	rps11， rps12（3）， rps14， rps15， rps16， rps18， rps19， rps2， rps3， rps4， rps7（2）， rps8*
	RNA聚合酶 RNA polymerase	rpoA， rpoB， rpoC1， rpoC2*
	核糖体RNAs Ribosomal RNAs	rrn16（2），rrn23（2），rrn4.5（2），rrn5（2）
	转运RNA Transfer RNA	trnH-GUG， trnK-UUU， trnQ-UUG， trnS-GCU， trnS-CGA， trnR-UCU， trnC-GCA， trnD-GUC， trnY-GUA， trnE-UUC， trnT-GGU， trnS-UGA， trnG-GCC， trnM-CAU（4）， trnS-GCU， trnT-UGU， trnL-UAA， trnF-GAA， trnV-UAC， trnW-CCA， trnP-UGG， trnL-CAA（2）， trnV-GAC（2）， trnI-GAU（2）， trnA-UGC（2）， trnR-ACG（2）， trnL-UAG， trnN-GUU（2）
其他基因 Other genes	成熟酶 Maturase	MatK
	蛋白酶 Protease	ClpP**
	包膜蛋白基因 Envelope membrane protein gene	cemA
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	转录起始因子 Transcription initiation factor	infA
	乙酰辅酶A羧化酶的亚基 Subunit of Acetyl-CoA-carboxylase	accD
未知基因 Unknown genes	保守开放阅读框 Conserved open reading frame	ycf1， ycf15（2）， ycf2（2）， ycf4