紫菜薹线粒体基因组SSR分布特征的比较分析

肖婉钰; 周贤玉; 任海龙; 黄红弟; 郑岩松; 张晶; 许东林

doi:10.19303/j.issn.1008-0384.2024.01.007

紫菜薹线粒体基因组SSR分布特征的比较分析

doi: 10.19303/j.issn.1008-0384.2024.01.007

肖婉钰^1,,
周贤玉¹,
任海龙^{1, 2, ,},
黄红弟³,
郑岩松¹,
张晶¹,
许东林¹

1.
广州市农业科学研究院，广东　广州　510308
2.
广东省农业科学院作物研究所/广东省农作物遗传改良重点实验室，广东　广州　510640
3.
广东省良种引进服务公司，广东　广州　510091

基金项目: 2022年省级乡村振兴战略专项资金种业振兴项目（2022-NPY-03-001）；广东省农业科技创新及推广项目（2023KJ133）

详细信息

作者简介:
肖婉钰（1991 —），女，硕士，农艺师，主要从事蔬菜遗传育种研究，E-mail：yuwanxiao22@126.com

通讯作者:
任海龙（1985 —），男，博士，副研究员，主要从事作物遗传育种研究，E-mail：renhailong_2006@163.com

中图分类号: S634.6
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出版历程
- 收稿日期: 2023-05-10
- 录用日期: 2024-01-08
- 修回日期: 2024-01-04
- 网络出版日期: 2024-01-25
- 刊出日期: 2024-01-28

Characteristics of SSRs in Zicaitai Mitochondrial Genome

1.
Guangzhou Institute of Agriculture Science, Guangzhou, Guangdong　510308, China
2.
Crop Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, Guangdong　510640, China
3.
Guangdong Provincial Improved Variety Introduce Service Corp., Guangzhou, Guangdong　510091, China

摘要

摘要: 目的分析紫菜薹（Brassica rapa var. purpuraria）线粒体基因组SSR序列的分布特征，并与芸薹属主要物种进行比较，为紫菜薹SSR分子标记的开发及遗传进化研究提供参考。方法利用MISA软件对紫菜薹及芸薹属6个基本种（包括白菜3个变种）的线粒体基因组进行搜索，并对搜索到的SSR序列分布特征进行比较分析。结果在紫菜薹及芸薹属6个基本种（包括白菜3个变种）的线粒体基因组中，分别筛选到168、170、167、168、180、280、185、165、179个完整的SSR序列，相对密度分别为764 、774 、760 、764 、775 、777、721 、744 、771 个·Mb⁻¹，SSR序列的总长度分别为1562、1577、1547、1562、1664、2564、1722、1524、1646 bp，占各自线粒体基因组序列总长度的比例分别为0.71%、0.72%、0.70%、0.71%、0.72%、0.71%、0.67%、0.69%和0.71%。在1～6个不同核苷酸重复单元中，紫菜薹及芸薹属6个基本种的SSR序列均是单核苷酸重复单元最多，然后依次是二核苷酸、四核苷酸、三核苷酸、五核苷酸，均未发现六核苷酸重复单元。其中，A/T、AG/CT、AT/AT和C/G是芸薹属线粒体基因组共有的常见重复单元类型。结论紫菜薹线粒体基因组大小为219 779 bp，共筛选出168个SSR分子标记，相对密度为764 个·Mb⁻¹，平均长度为9 bp，以单核苷酸重复单元的数量最多，其次为二、四核苷酸重复单元类型，具有较大的多态性标记开发潜力。
- 紫菜薹 /
- 芸薹属 /
- 线粒体 /
- SSR
Abstract: Objective The simple sequence repeats (SSRs) in the mitochondrial genome of zicaitai (Brassica rapa var. Purpuraria) were compared with those of other species in the genus. Method MISA software was used to search the mitochondrial genomes of zicaitai as well as 5 other major species and 3 mutants of Brassica rapa. The SSR sequence distributions of the specimens were compared and analyzed. Result In the mitochondrial genomes, 168, 170, 167, 168, 180, 280, 185, 165, and 179 complete SSRs were screened. The sequences showed relative densities of 764, 774, 760, 764, 775, 777, 721, 744, and 771 per Mb with total lengths of 1562, 1577, 1547, 1562, 1664, 2564, 1722, 1524, and 1646 bp that accounted for 0.71%, 0.72%, 0.70%, 0.71%, 0.72%, 0.71%, 0.67%, 0.69%, and 0.71% of the total sequence length of each specimen, respectively. Among the 1-6 different nucleotide repeat units in zicaitai and the other major Brassica species, most SSRs were mononucleotide, which was followed by dinucleotide, tetranucleotide, trinucleotide, and pentanucleotide, but no hexonucleotide. A/T, AG/CT, AT/AT, and C/G were the common repeat unit types in them. Conclusion The mitochondrial genome of zicaitai was 219779 bp with 168 SSRs at the relative density of 764 markers/Mb and 9 bp in length. Mono-, di-, and tetra-nucleotides were the most abundant repeat units, which could potentially be developed as highly polymorphic markers for species differentiation.
- Zicaitai /
- Brassica /
- mitochondrion /
- SSR

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图 1 紫菜薹及芸薹属线粒体基因组不同片段长度SSR数量

Figure 1. Number in SSR fragment lengths of mitochondrial genomes of zicaitai and other Brassica species

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表 1 紫菜薹及芸薹属线粒体基因组信息

Table 1. Mitochondrial genome sequences of zicaitai and other Brassica species

物种 Species	染色体数 Number of chromosomes	GenBank 登录号 GenBank accession	线粒体基因组大小 Genome size/bp
紫菜薹 Brassica rapa var. purpuraria	AA, 2n = 2x = 20	OP729396.1	219779
芜菁 Brassica rapa ssp. rapa	AA, 2n = 2x = 20	NC_049892.1	219736
芸薹 Brassica rapa subsp. Campestris	AA, 2n = 2x = 20	NC_016125.1	219747
大白菜 Brassica rapa L. ssp. pekinensis	AA, 2n = 2x = 20	MN910310	219778
黑芥 Brassica nigra	BB, 2n = 2x = 16	NC_029182.1	232407
甘蓝 Brassica oleracea	CC, 2n = 2x = 18	NC_016118.1	360271
芥菜 Brassica juncea	AABB, 2n = 4x = 36	MG872829.1	256592
甘蓝型油菜 Brassica napus	AACC, 2n = 4x = 38	NC_008285.1	221853
埃塞俄比亚芥 Brassica carinata	BBCC, 2n = 4x = 34	NC_016120.1	232241

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表 2 紫菜薹及芸薹属线粒体基因组中SSR的分布概况

Table 2. Distribution of SSRs in mitochondrial genomes of zicaitai and other Brassica species

物种 Species	SSR总长度 Total length of SSR/bp	SSR数量 SSR number	SSR分布密度 SSR density/(个·Mb⁻¹）	SSR平均长度 Average length of SSR/bp	SSR长度占比 Length ratio of SSR/%
紫菜薹 Brassica rapa var. purpuraria	1562	168	764	9	0.71
芜菁 Brassica rapa ssp. rapa	1577	170	774	9	0.72
芸薹 Brassica rapa subsp. Campestris	1547	167	760	9	0.70
大白菜 Brassica rapa L. ssp. pekinensis	1562	168	764	9	0.71
黑芥 Brassica nigra	1664	180	775	9	0.72
甘蓝 Brassica oleracea	2564	280	777	9	0.71
芥菜 Brassica juncea	1722	185	721	9	0.67
甘蓝型油菜 Brassica napus	1524	165	744	9	0.69
埃塞俄比亚芥 Brassica carinata	1646	179	771	9	0.71

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表 3 紫菜薹及芸薹属线粒体基因组SSR重复单元的数目和占比

Table 3. Number and proportion of SSR repeat types in mitochondrial genomes of zicaitai and other Brassica species

物种 Species	单核苷酸 Mononucleotide	二核苷酸 Dinucleotide	三核苷酸 Trinucleotide	四核苷酸 Tetranucleotide	五核苷酸 Pentanucleotide
紫菜薹 Brassica rapa var. purpuraria	83 （49.40%）	61 （36.31%）	5 （2.98%）	18 （10.71%）	1 （0.60%）
芜菁 Brassica rapa ssp. rapa	84 （49.41%）	61 （35.88%）	5 （2.94%）	19 （11.18%）	1 （0.59%）
芸薹 Brassica rapa subsp. Campestris	82 （49.10%）	61 （36.53%）	5 （2.99%）	18 （10.78%）	1 （0.60%）
大白菜 Brassica rapa L. ssp. pekinensis	82 （48.81%）	62 （36.90%）	5 （2.98%）	18 （10.71%）	1 （0.60%）
黑芥 Brassica nigra	85 （47.22%）	69 （38.33%）	6 （3.33%）	19 （10.56%）	1 （0.56%）
甘蓝 Brassica oleracea	137 （48.93%）	106 （37.86%）	6 （2.14%）	29 （10.36%）	2 （0.71%）
芥菜 Brassica juncea	78 （42.16%）	71 （38.38%）	7 （3.78%）	28 （15.14%）	1 （0.54%）
甘蓝型油菜 Brassica napus	84 （50.91%）	58 （35.15%）	4 （2.42%）	18 （10.91%）	1 （0.61%）
埃塞俄比亚芥 Brassica carinata	85 （47.49%）	68 （37.99%）	6 （3.35%）	19 （10.61%）	1 （0.56%）

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表 4 紫菜薹及芸薹属线粒体基因组SSR的重复基元类型及数量

Table 4. Number of SSRs of mitochondrial genomes in zicaitai and other Brassica species

重复基元类型 Motif types	紫菜薹 Brassica rapa var. purpuraria	芜菁 Brassica rapa ssp. rapa	芸薹 Brassica rapa subsp. Campestris	大白菜 Brassica rapa L. ssp. pekinensis	黑芥 Brassica nigra	甘蓝 Brassica oleracea	芥菜 Brassica juncea	甘蓝型油菜 Brassica napus	埃塞俄比亚芥 Brassica carinata
A/T	67	68	66	67	71	112	65	68	70
AG/CT	36	36	36	37	41	62	45	34	41
AT/AT	19	19	19	19	19	34	19	18	18
C/G	16	16	16	15	14	25	13	16	15
AATG/ATTC	5	5	5	5	5	8	5	5	5
AC/GT	4	4	4	4	7	7	5	4	7
AAG/CTT	4	4	4	4	4	5	5	3	4
AAAG/CTTT	4	4	4	4	3	6	10	5	3
AAAC/GTTT	3	4	3	3	4	5	4	3	4
AAAT/ATTT	3	3	3	3	3	4	3	3	3
CG/CG	2	2	2	2	2	3	2	2	2
AAC/GTT	1	1	1	1	1	1	1	1	1
AACG/CGTT	1	1	1	1	2	2	2	1	2
ACTC/AGTG	1	1	1	1	1	2	2	—	1
CCGG/CCGG	1	1	1	1	1	2	1	1	1
ACTAG/AGTCT	1	1	1	1	1	2	1	1	1
AGC/CTG	—	—	—	—	1	—	1	—	1
ACTG/AGTC	—	—	—	—	—	—	1	—	—

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