乌塌菜叶绿体基因组特征及系统发育

doi:10.16420/j.issn.0513-353x.2024-0880

摘要/Abstract

摘要：

通过高通量测序技术和生物信息学方法，对乌塌菜（Brassica campestris L. ssp. chinensis var. rosularis Tsen）叶绿体基因组进行了组装和注释。结果显示，乌塌菜的叶绿体基因组为四分体环状结构，全长153 483 bp，包含大单拷贝区（LSC，83 282 bp）、小单拷贝区（SSC，17 775 bp）和反向重复区（IRs，26 213 bp）。乌塌菜叶绿体基因组注释共得到132个基因，包括87个蛋白编码基因、8个rRNA基因和37个tRNA基因，且密码子偏好性分析显示明显的A/U偏好。此外，乌塌菜叶绿体基因组中鉴定出28个重复结构和90个SSR变异位点，滑动窗口分析鉴定出6个高突变区域。系统发育分析显示，乌塌菜与芸薹属植物（大白菜、白菜、芥菜、甘蓝和欧洲油菜）位于同一分支，并与大白菜关系最为密切。

关键词: 乌塌菜, 叶绿体基因组, 序列特征, 密码子偏好, 系统发育

Abstract:

The chloroplast genome of Wucai（Brassica campestris L. ssp. chinensis var. rosularis Tsen）was assembled and annotated by high-throughput sequencing technology and bioinformatics methods. The results showed that the chloroplast genome of Wucai（Brassica campestris L. ssp. chinensis var. rosularis Tsen）was a tetrameric ring structure with a total length of 153 483 bp，containing a large single-copy region（LSC，83 282 bp），a small single-copy region（SSC，17 775 bp），and an inverted repeat region（IRs，26 213 bp）. A total of 132 genes，including 87 protein-coding genes，8 rRNA genes and 37 tRNA genes，were obtained from the annotation of the Wucai chloroplast genome，and the codon preference analysis showed a clear A／U preference. In addition，28 repetitive structures and 90 SSR variant sites were identified in the Wucai chloroplast genome，and six highly mutated regions were identified by sliding window analysis. Phylogenetic analyses showed that Wucai was located in the same branch with Brassica（B. rapa subsp. pekinensis，B. rapa，B. juncea，B. oleracea and B. napus）and was most closely related to B. pekinensis.

Key words: Wucai, chloroplast genome, sequence identity, codon preference, phylogeny

汪雨龙, 朱真希, 张豪英, 李雨, 陈可嘉, 汪承刚, 侯金锋, 陈国户, 唐小燕, 王文杰, 吴建强, 袁凌云. 乌塌菜叶绿体基因组特征及系统发育[J]. 园艺学报, 2025, 52(5): 1326-1340.

WANG Yulong, ZHU Zhenxi, ZHANG Haoying, LI Yu, CHEN Kejia, WANG Chenggang, HOU Jinfeng, CHEN Guohu, TANG Xiaoyan, WANG Wenjie, WU Jianqiang, YUAN Lingyun. Characterisation and Phylogeny of the Chloroplast Genome of Wucai（Brassica campestir）[J]. Acta Horticulturae Sinica, 2025, 52(5): 1326-1340.

图/表 11

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基因功能 Gene function	基因分类 Group of genes	基因名 Name of gene
光合作用 Photosynthesis	光合系统Ⅰ PhotosystemⅠ	psaA，psaB，psaC，psaI，psaJ
	光合系统Ⅱ Photosystem Ⅱ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	细胞色素b/f复合体 Cytochrome b/f complex	petA，petB，petD*，petG，petL，petN*
	ATP合成酶 ATP synthase	atpA，atpB，atpE，atpF，atpH，atpI*
	NADH 脱氢酶 NADH dehydrogenase	ndhA，ndhB*（2），ndhC，ndhD，ndhE，ndhF，ndhG，ndhH， ndhI，ndhJ，ndhK*
自我复制 Self-replication	核糖体大亚基 Large subunit of ribosome	rpl14 rpl16，rpl2*（2），rpl20，rpl22，rpl23（2），rpl32，rpl33，rpl36*
	核糖体小亚基 Small subunit of ribosome	rps11，rps12（2），rps14，rps15，rps16，rps18，rps19，rps2，rps3，rps4，rps7（2），rps8*
	核糖双磷酸羧化酶大亚基 Large subunit of ribose bisphosphate carboxylase	rbcL
	RNA聚合酶 RNA polymerase	rpoA，rpoB，rpoC1，rpoC2*
	核糖体RNA Ribosomal RNA	rrn16S（2），rrn23S（2），rrn4.5S（2），rrn5S（2）
	转运RNA Transfer RNA	trnA-UGC（2），trnC-GCA，trnD-GUC，trnE-UUC，trnF-GAA，trnfM-CAU，trnG，trnG-GCC，trnH-GUG，trnI-CAU（2），trnI-GAU*（2），trnK-UUU*，trnL-CAA（2），trnL-UAA*，trnL-UAG，trnM-CAU，trnN-GUU（2），trnP-UGG，trnQ-UUG，trnR-ACG（2），trnR-UCU，trnS-GCU，trnS-GGA，trnS-UGA，trnT-GGU，trnT-UGU，trnV-GAC（2），trnV-UAC*，trnW-CCA，trnY-GUA*
其他基因 Other gene	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP**
	表膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD
	c-型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA
未知功能基因 Unknown function gene	保守假设叶绿体阅读框 Conserved hypothetical chloroplast reading frames	ycf1（2），ycf3*，ycf15（2），ycf2（2），ycf4*

基因功能 Gene function	基因分类 Group of genes	基因名 Name of gene
光合作用 Photosynthesis	光合系统Ⅰ PhotosystemⅠ	psaA，psaB，psaC，psaI，psaJ
	光合系统Ⅱ Photosystem Ⅱ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	细胞色素b/f复合体 Cytochrome b/f complex	petA，petB，petD*，petG，petL，petN*
	ATP合成酶 ATP synthase	atpA，atpB，atpE，atpF，atpH，atpI*
	NADH 脱氢酶 NADH dehydrogenase	ndhA，ndhB*（2），ndhC，ndhD，ndhE，ndhF，ndhG，ndhH， ndhI，ndhJ，ndhK*
自我复制 Self-replication	核糖体大亚基 Large subunit of ribosome	rpl14 rpl16，rpl2*（2），rpl20，rpl22，rpl23（2），rpl32，rpl33，rpl36*
	核糖体小亚基 Small subunit of ribosome	rps11，rps12（2），rps14，rps15，rps16，rps18，rps19，rps2，rps3，rps4，rps7（2），rps8*
	核糖双磷酸羧化酶大亚基 Large subunit of ribose bisphosphate carboxylase	rbcL
	RNA聚合酶 RNA polymerase	rpoA，rpoB，rpoC1，rpoC2*
	核糖体RNA Ribosomal RNA	rrn16S（2），rrn23S（2），rrn4.5S（2），rrn5S（2）
	转运RNA Transfer RNA	trnA-UGC（2），trnC-GCA，trnD-GUC，trnE-UUC，trnF-GAA，trnfM-CAU，trnG，trnG-GCC，trnH-GUG，trnI-CAU（2），trnI-GAU*（2），trnK-UUU*，trnL-CAA（2），trnL-UAA*，trnL-UAG，trnM-CAU，trnN-GUU（2），trnP-UGG，trnQ-UUG，trnR-ACG（2），trnR-UCU，trnS-GCU，trnS-GGA，trnS-UGA，trnT-GGU，trnT-UGU，trnV-GAC（2），trnV-UAC*，trnW-CCA，trnY-GUA*
其他基因 Other gene	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP**
	表膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD
	c-型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA
未知功能基因 Unknown function gene	保守假设叶绿体阅读框 Conserved hypothetical chloroplast reading frames	ycf1（2），ycf3*，ycf15（2），ycf2（2），ycf4*

编号 No.	重复长度/bp Repeat size	类型 Type	重复1开始 Repeat 1 start	重复1位置 Repeat 1 location	重复2开始 Repeat 2 start	重复2位置 Repeat 2 location	区域 Region
1	30	C	7938	IGS（trnS-GCU，trnG）	35449	IGS（psbZ，trnG-GCC）	LSC；LSC
2	37	C	7945	IGS（trnS-GCU，trnG）	35445	IGS（psbZ，trnG-GCC）	LSC；LSC
3	30	F	47039	trnF-GAA（partical：86.67%）	47093	IGS（trnF-GAA，ndhJ）	LSC；LSC
4	30	F	42958	ycf3-intron1	97933	IGS（rps12，trnV-GAC）	LSC；IRb
5	30	F	3759	trnK-UUU-intron1	6275	IGS（rps16，trnQ-UUG）	LSC；LSC
6	31	F	7636	trnS-GCU（partical：93.55%）	34499	trnS-UGA（partical：93.55%）	LSC；LSC
7	32	F	7950	IGS（trnS-GCU，trnG）	35449	IGS（psbZ，trnG-GCC）	LSC；LSC
8	32	F	88216	ycf2	88237	ycf2	IRb；IRb
9	32	F	148498	ycf2	148519	ycf2	IRa；IRa
10	34	F	106830	IGS（rrn4.5S，rrn5S）	106862	IGS（rrn4.5S，rrn5S）	IRb；IRb
11	34	F	129871	IGS（rrn5，rrn4.5）	129903	IGS（rrn5，rrn4.5）	IRa；IRa
12	37	F	97924	IGS（rps12，trnV-GAC）	119490	ndhA-intron1	IRb；SSC
13	42	F	27346	IGS（trnC-GCA，petN）	27366	IGS（trnC-GCA，petN）	LSC；LSC
14	43	F	37845	psaB	40069	psaA	LSC；LSC
15	46	F	37866	psaB	40090	psaA	LSC；LSC
16	54	F	47015	trnF-GAA（partical：92.59%）	47069	IGS（trnF-GAA，ndhJ）	LSC；LSC
17	32	P	88216	ycf2	148498	ycf2	IRb；IRa
18	32	P	88237	ycf2	148519	ycf2	IRb；IRa
19	34	P	106830	IGS（rrn4.5S，rrn5S）	129871	IGS（rrn5，rrn4.5）	IRb；IRa
20	34	P	106862	IGS（rrn4.5S，rrn5S）	129903	IGS（rrn5，rrn4.5）	IRb；IRa
21	36	P	9239	IGS（trnG，trnR-UCU）	9239	IGS（trnG，trnR-UCU）	LSC；LSC
22	37	P	119490	ndhA-intron1	138806	IGS（trnV-GAC，rps12）	SSC；IRa
23	40	P	28248	IGS（petN，psbM）	28248	IGS（petN，psbM）	LSC；LSC
24	44	P	73312	IGS（psbT，psbN）	73312	IGS（psbT，psbN）	LSC；LSC
25	45	P	75815	petD-intron1	75815	petD-intron1	LSC；LSC
26	31	R	173	IGS（trnH-GUG，psbA）	34594	IGS（trnS-UGA，psbZ）	LSC；LSC
27	31	R	12210	atpF-intron1	75815	petD-intron1	LSC；LSC
28	35	R	4589	IGS（trnK-UUU，rps16）	4589	IGS（trnK-UUU，rps16）	LSC；LSC

编号 No.	重复长度/bp Repeat size	类型 Type	重复1开始 Repeat 1 start	重复1位置 Repeat 1 location	重复2开始 Repeat 2 start	重复2位置 Repeat 2 location	区域 Region
1	30	C	7938	IGS（trnS-GCU，trnG）	35449	IGS（psbZ，trnG-GCC）	LSC；LSC
2	37	C	7945	IGS（trnS-GCU，trnG）	35445	IGS（psbZ，trnG-GCC）	LSC；LSC
3	30	F	47039	trnF-GAA（partical：86.67%）	47093	IGS（trnF-GAA，ndhJ）	LSC；LSC
4	30	F	42958	ycf3-intron1	97933	IGS（rps12，trnV-GAC）	LSC；IRb
5	30	F	3759	trnK-UUU-intron1	6275	IGS（rps16，trnQ-UUG）	LSC；LSC
6	31	F	7636	trnS-GCU（partical：93.55%）	34499	trnS-UGA（partical：93.55%）	LSC；LSC
7	32	F	7950	IGS（trnS-GCU，trnG）	35449	IGS（psbZ，trnG-GCC）	LSC；LSC
8	32	F	88216	ycf2	88237	ycf2	IRb；IRb
9	32	F	148498	ycf2	148519	ycf2	IRa；IRa
10	34	F	106830	IGS（rrn4.5S，rrn5S）	106862	IGS（rrn4.5S，rrn5S）	IRb；IRb
11	34	F	129871	IGS（rrn5，rrn4.5）	129903	IGS（rrn5，rrn4.5）	IRa；IRa
12	37	F	97924	IGS（rps12，trnV-GAC）	119490	ndhA-intron1	IRb；SSC
13	42	F	27346	IGS（trnC-GCA，petN）	27366	IGS（trnC-GCA，petN）	LSC；LSC
14	43	F	37845	psaB	40069	psaA	LSC；LSC
15	46	F	37866	psaB	40090	psaA	LSC；LSC
16	54	F	47015	trnF-GAA（partical：92.59%）	47069	IGS（trnF-GAA，ndhJ）	LSC；LSC
17	32	P	88216	ycf2	148498	ycf2	IRb；IRa
18	32	P	88237	ycf2	148519	ycf2	IRb；IRa
19	34	P	106830	IGS（rrn4.5S，rrn5S）	129871	IGS（rrn5，rrn4.5）	IRb；IRa
20	34	P	106862	IGS（rrn4.5S，rrn5S）	129903	IGS（rrn5，rrn4.5）	IRb；IRa
21	36	P	9239	IGS（trnG，trnR-UCU）	9239	IGS（trnG，trnR-UCU）	LSC；LSC
22	37	P	119490	ndhA-intron1	138806	IGS（trnV-GAC，rps12）	SSC；IRa
23	40	P	28248	IGS（petN，psbM）	28248	IGS（petN，psbM）	LSC；LSC
24	44	P	73312	IGS（psbT，psbN）	73312	IGS（psbT，psbN）	LSC；LSC
25	45	P	75815	petD-intron1	75815	petD-intron1	LSC；LSC
26	31	R	173	IGS（trnH-GUG，psbA）	34594	IGS（trnS-UGA，psbZ）	LSC；LSC
27	31	R	12210	atpF-intron1	75815	petD-intron1	LSC；LSC
28	35	R	4589	IGS（trnK-UUU，rps16）	4589	IGS（trnK-UUU，rps16）	LSC；LSC

编号No.	类型Type	区域Region	具体位置Position	碱基Nucleobase
1	SNP	LSC	265	T
2	SNP	LSC	266	T
3	SNP	LSC	267	T
4	SNP	LSC	268	T
5	Insertion	LSC	8314	T
6	SNP	LSC	45072	G
7	SNP	LSC	45073	T
8	SNP	LSC	45074	T
9	SNP	LSC	66084	T
10	SNP	LSC	66085	T
11	SNP	LSC	66086	C
12	SNP	LSC	66087	T