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| 五种石斑鱼全基因组微卫星分布特征分析 |
| Distribution characteristics of microsatellites in the whole genome of five groupers |
| 投稿时间：2023-01-09 修订日期：2023-03-12 |
| DOI： |
| 中文关键词: 石斑鱼 全基因组 微卫星 分布特征 |
| 英文关键词: Grouper (Epinephelus) Whole genome Microsatellite Distribution characteristics |
| 基金项目:海南省重大科技计划(ZDKJ2021017); 海南省科技计划三亚崖州湾科技城联合项目(320LH030); 海南省省本级部门预算项目(KYL-2022-08) |
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| 中文摘要: |
| 为了解赤点石斑(Epinephelus akaara)、斜带石斑(Epinephelus coioides)、棕点石斑(Epinpehelus fuscoguttatus)、鞍带石斑(Epinephelus lanceolatus)、云纹石斑(Epinephelus moara)等五种石斑鱼全基因组中微卫星的分布特征,本研究使用Micro-Satellite(MISA)软件对公共数据库中获取的五种石斑鱼全基因组序列进行了微卫星筛选,分析了微卫星重复类别、拷贝类别及核心拷贝数的分布特征。结果显示,在五种石斑鱼全基因组中,均筛选出超过35万个微卫星位点,相对丰度介于345-375个/Mb之间,平均长度在19bp左右,微卫星数量在全基因组中的占比为0.66%~0.75%,其重复类别数量、相对丰度和占比的分布趋势一致,二碱基重复最多,其次为单碱基,且随着重复单元碱基数目的增加而减少。重复拷贝类别A、AC、AAT、AAG、AGC、AATC、AAAT、AGAT、AATG、AGAGG、AAAAT、AAGAT、ACAGAG、AAANNN、AANNNN(N为除A外其它三种碱基)为优势类别。不同重复类别微卫星核心拷贝数变化范围较大,但五种石斑鱼中每种重复类别的拷贝数变化趋势一致,即随着拷贝数增加,微卫星数目随之递减。总重复拷贝数为6和12时出现峰值,微卫星数量随着核心拷贝数的增加而递减。其中,各个重复类型均有数量尤为突出的种类：鞍带石斑中T、TA和AGACAG分别重复了502、803和48次,云纹石斑中GAG、CACT和CCACA分别重复了203、652和111次。五种石斑鱼全基因组微卫星分布特征基本一致,然而在重复拷贝数分布上鞍带石斑和云纹石斑与其他三种石斑均有显著差异。本研究可为五种石斑鱼高质量微卫星分子标记开发提供数据参考,并为其基因组进化、遗传变异、亲缘关系和新品种选育等方面的工作奠定了基础。 |
| 英文摘要: |
| In order to understand the distribution characteristics of microsatellites in the whole genome of Hong Kong grouper(Epinephelus akaara), orange-spotted grouper(Epinephelus coioides), brown-marbled grouper(Epinephelus fuscoguttatus), giant grouper(Epinephelus lanceolatus) and kelp grouper(Epinephelus moara), this study used Micro-Satellite (MISA) software to screen microsatellites of five groupers obtained from the public database, The script was compiled to analyze the screening results, and statistics were made on the overall distribution characteristics of microsatellites of each duplication type, the characteristics of each duplication copy type, and the duplication distribution of core copy number in the whole genome of five groupers. The results showed that more than 350,000 microsatellite sites were screened from the whole genome of five groupers, with relative abundance between 345-375, total length between 6.90 and 7.83 Mb, average length of about 19 bp, and the proportion of the number in the whole genome between 0.66% and 0.75%. The number, proportion, and relative abundance of the repetitive types were in the same order, with the largest number of double base repeats, followed by single base repeats, And it decreases with the increase of base number of repeat units. From the perspective of each duplicate copy type, A, AC, AAT, AAG, AGC, AATC, AAAT, AGAT, AATG, AGAGG, AAAAT, AAGAT, ACAGAG, AAANNN, AANNNN (N is any of the three bases except A) are the dominant type of each duplicate copy type. Type A accounted for 90.00% of single base repeats, while type AC was the most dominant type in double base repeats, accounting for nearly 80.00%; The content of CG duplication category is the least, accounting for only 0.04%~0.07% in the five grouper dibasic groups. The number of this type in most animals is very small, because the composition content of four bases in different species" genomes is different, on the other hand, there may be structural problems with different bases. The high frequency distribution of AGG and AGC in the dominant types of triple base repeats may play an important role in the expression and regulation of immune, disease and other genes in grouper; Some studies have shown that AGG is a known binding site for many transcription factors involved in the early growth and development of other species. The change of base repeat polymorphism of AGC category is directly related to genetic diseases and has evolutionary and medical research significance. Among the four, five, and six base repeat types, the dominant repeat types AAAN, AAAAN, and AAAAAN are highly distributed in mammals. In terms of the distribution of core copy numbers, the core copy numbers of different types of microsatellites vary widely and are quite different, but the number of duplicate copies of each type of five groupers is consistent with the change trend, and the number of microsatellites decreases with the increase of the number of duplicate copies. The number of single base repeat copies concentrated in 12~25 times, accounting for more than 95.00%; The main number of copies of two base repeats is between 6~32 times, of which there is a small increase between 11~14 times. Then the distribution number decreases with the increase of the number of duplicate copies; 3、 The number of four and five base repeats mainly concentrated on 5~16, 5~17, and 5~14, respectively. Among them, AGAT, AAAG, AAGAG, AATAT, and AGAGG still have a large number of copies when the number of copies is large, and the increase of the number of copies may represent the change of polymorphism of this locus, which may lead to the occurrence of disease or the change of corresponding functions. However, according to the distribution of the number of duplicate copies of each type of duplication, the number of its distribution has two peaks at 6 and 12 repetitions. With the increase of the number of core copies, the number of microsatellites decreases, and each type of duplication has a particularly prominent number of species: T, TA, AGACAG in the saddle belt grouper repeated 502, 803 and 48 times respectively, and GAG, CACT, CCACA in the moire grouper repeated 203, 652 and 111 times respectively, The number of repetitions of each type is the highest and the most extreme among the five groupers. On the whole, the distribution characteristics of microsatellites in the whole genome of the five groupers are basically the same. However, there are significant differences in the distribution of duplicate copy numbers between the saddle belt grouper and the moire grouper and the other three groupers. Therefore, it is important to further explore the role of microsatellite loci in order to better understand the evolutionary mechanism and functional expression of the five groupers. To sum up, the microsatellites of the whole genome of five groupers were screened and analyzed for their distribution characteristics, providing a data basis for the development of a large number of high-quality microsatellite molecular markers for five groupers, and laying a foundation for exploring genetic distance and kinship, selecting excellent varieties, and developing new varieties. |
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