期刊
Horticulture Research （7.291/Q1）
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants
主要园艺和代表性植物全部完整基因编码序列的SSRs综合分析和数据库构建
Abstract
Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.
简单序列重复 (SSR) 是最重要的遗传标记之一，广泛存在于大多数物种中。在这里，我们从 112 株植物的 3,951,919 个基因中鉴定出 249,822 个 SSR。然后，我们对这些 SSR 进行了综合分析，并构建了植物 SSR 数据库（PSSRD）。有趣的是，在低等植物中发现的 SSR 比在高等植物中发现的多，这表明低等植物需要适应早期的极端环境。当与其他七种高等植物进行比较时，在低等植物莱茵衣藻中检测到四个特定的富集功能术语。此外，Guanylate_cyc存在于低等植物的基因中多于高等植物。在我们的 PSSRD 中，我们在图表界面中构建了交互式绘图功能，用户可以轻松查看 SSR 的详细信息。所有 SSR 信息，包括序列、引物和注释，都可以从我们的数据库中下载。此外，我们还开发了 Web SSR Finder 和 Batch SSR Finder 工具，可轻松用于识别 SSR。我们的数据库是使用 PHP、HTML、JavaScript 和 MySQL 开发的，可从 http://www.pssrd.info/ 免费获得。我们对 Myb 基因家族和开花基因作为 PSSRD 的两个应用进行了分析。进一步分析表明，全基因组复制和全基因组三复制在 Myb 基因家族的扩展中起主要作用。我们数据库中的这些 SSR 标记将极大地促进未来的比较基因组学和功能基因组学研究。
Introduction
Since molecular marker technology was developed in the 1980s, an increasing number of molecular marker types have been identified, which has rapidly accelerated genetic improvements in species. The development and comparative analysis of molecular markers could help us reveal genetic variation underlying various biological functional genes. To date, researchers have found several molecular markers, such as restriction fragment length polymorphisms, random amplified polymorphism DNA, sequence tag sites, amplified fragment length polymorphism, diversity array technology markers, single-nucleotide polymorphisms, specific locus amplified fragments, and simple sequence repeats (SSRs).
自 1980 年代开发分子标记技术以来，已鉴定出越来越多的分子标记类型，这迅速加速了物种的遗传改良。 分子标记的开发和比较分析可以帮助我们揭示各种生物功能基因的遗传变异。 迄今为止，研究人员已经发现了几种分子标记，如限制性片段长度多态性、随机扩增多态性DNA、序列标签位点、扩增片段长度多态性、多样性阵列技术标记、单核苷酸多态性、特定位点扩增片段和简单序列重复 （SSR）。
These molecular markers play important roles in genetic map construction, quantitative trait locus detection, marker-assisted selection (MAS), and fine localization of important functional genes to fulfill various demands of breeders. There have been many studies of molecular markers in model plants. For example, several kinds of molecular markers were used to identify genes related to leaf senescence, leaf shape, chlorophyll, and embryogenesis in Arabidopsis. Similarly, most genes determining disease resistance and major agronomic traits, such as grain quality, grain weight, and grain size, were also detected using molecular markers in rice. In horticultural plants, molecular markers are also widely used for plant breeding in most species, including Brassica rapa, Brassica oleracea, Solanum lycopersicum, Cucumis melo, Vitis vinifera, Fragaria ananassa, and pear. Furthermore, progress in molecular genetics, genomic selection, and genome editing has provided deep insights into the understanding of molecular markers and greatly complemented breeding strategies.
这些分子标记在遗传图谱构建、数量性状位点检测、标记辅助选择（MAS）以及重要功能基因的精细定位等方面发挥着重要作用，以满足育种者的各种需求。关于模式植物中分子标记的研究已经很多。例如，几种分子标记被用来鉴定与拟南芥叶片衰老、叶片形状、叶绿素和胚胎发生有关的基因。同样，大多数决定抗病性和主要农艺性状的基因，如谷粒质量、谷粒重量和谷粒大小，也使用水稻分子标记进行了检测。在园艺植物中，分子标记也广泛用于大多数物种的植物育种，包括白菜、甘蓝、番茄、甜瓜、葡萄、草莓和梨。此外，分子遗传学、基因组选择和基因组编辑的进展为理解分子标记提供了深刻的见解，并极大地补充了育种策略。
SSR markers are present in almost all species, particularly in eukaryotes. These markers have many applications, such as constructing linkage maps, fine mapping of genes, and selective breeding through genomic selection. SSRs have become extremely popular for phylogenetic analysis and have expanded our knowledge related to plant breeding. The development of bioinformatics technology has enabled the development of SSR markers for many species. Recently, there have been many reports on SSR development and application. These studies have confirmed that SSRs are the classic, popular molecular markers used in plant science.
SSR 标记几乎存在于所有物种中，尤其是真核生物中。 这些标记有许多应用，例如构建连锁图谱、基因的精细作图以及通过基因组选择进行选择性育种。 SSR 在系统发育分析中变得非常流行，并扩展了我们与植物育种相关的知识。 生物信息学技术的发展为许多物种开发了 SSR 标记。 最近，关于SSR的开发和应用的报道很多。 这些研究证实，SSR 是植物科学中使用的经典、流行的分子标记。
With an increasing number of plant genomes being released, it has become possible to construct a plant SSR database (PSSRD) using the SSRs identified from all genes in these plants. Compared with those in existing databases, all the species in the database in this study have undergone complete genome sequencing. In addition, the PSSRD provides primer information and Pfam function annotation, which allows researchers to use these SSRs in a more convenient manner than those in other databases. More importantly, we not only provide more comprehensive and representative SSR information with the construction of this database but also conduct large-scale systematic and comparative analyses of SSRs in 112 plants.
随着越来越多的植物基因组被释放，使用从这些植物的所有基因中鉴定的 SSR 构建植物 SSR 数据库（PSSRD）已成为可能。 与现有数据库相比，本研究数据库中的所有物种都经过了完整的基因组测序。 此外，PSSRD 提供引物信息和 Pfam 功能注释，使研究人员能够以比其他数据库更方便的方式使用这些 SSR。 更重要的是，我们不仅通过该数据库的构建提供了更全面、更具代表性的 SSR 信息，而且还对 112 种植物的 SSR 进行了大规模的系统比较分析。
。。。
好了，感兴趣的读者自行下载大佬的文章阅读一下吧。
网友评论