Oasis Systems Research Unit, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, Rabat 10090, Morocco.
Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, 4 Avenue Ibn Batouta, B.P. 1014, Rabat 10000, Morocco.
Database (Oxford). 2024 Nov 27;2024. doi: 10.1093/database/baae118.
Microsatellites [simple sequence repeats (SSRs)] are one of the most widely used sources of genetic markers, particularly prevalent in plants. Despite their importance in various applications, a comprehensive genome-wide identification of coding sequence (CDS)-associated SSR markers in the Argania spinosa L. genome has yet to be conducted. In this study, 66 280 CDSs containing 5351 SSRs within 4535 A. spinosa L. CDSs were identified. Among these, tri-nucleotide motifs (58.96%) were the most common, followed by hexa-nucleotide (15.71%) and di-nucleotide motifs (13.32%). The predominant SSR motif in the tri-nucleotide category was AAG (24.4%), while AG (94.1%) was the most abundant among di-nucleotide repeats. Furthermore, the extracted CDSs containing SSRs were subjected to functional annotation; 3396 CDSs (74.88%) exhibited homology with known proteins, 3341 CDSs (73.7%) were assigned Gene Ontology terms, 1004 CDSs were annotated with Enzyme Commission numbers, and 832 (18.3%) were annotated with KEGG pathways. A total of 3475 primer pairs were designed, out of which 3264 were successfully validated in silico against the A. spinosa L. genome, with 99.6% representing high-resolution markers yielding no more than three products. Additionally, the SSR markers demonstrated a low rate of transferability through in-silico verification in two species within the Sapotaceae family. Furthermore, we developed an online database, the "Argania spinosa L. SSR database: https://as-fmmdb.shinyapps.io/asssrdb/" (AsSSRdb) to provide access to the CDS-associated SSRs identified in this study. Overall, this research provides valuable marker resources for DNA fingerprinting, genetic studies, and molecular breeding in argan and related species. Database URL: https://as-fmmdb.shinyapps.io/asssrdb/.
微卫星[简单序列重复（SSR）]是最广泛使用的遗传标记之一，在植物中尤为普遍。尽管它们在各种应用中很重要，但在阿甘树（Argania spinosa L.）基因组中进行全面的编码序列（CDS）相关 SSR 标记的全基因组鉴定尚未进行。在这项研究中，在 4535 个阿甘树 L. CDS 中鉴定出 66280 个包含 5351 个 SSR 的 CDS。其中，三核苷酸基序（58.96%）最为常见，其次是六核苷酸（15.71%）和二核苷酸基序（13.32%）。三核苷酸类别中的主要 SSR 基序是 AAG（24.4%），而二核苷酸重复中最丰富的是 AG（94.1%）。此外，提取的包含 SSR 的 CDS 进行了功能注释；3396 个 CDS（74.88%）与已知蛋白质具有同源性，3341 个 CDS（73.7%）被分配了基因本体论术语，1004 个 CDS 被注释了酶委员会编号，832 个 CDS（18.3%）被注释了 KEGG 途径。设计了 3475 对引物，其中 3264 对在阿甘树 L. 基因组上进行了成功的计算机验证，99.6%的标记分辨率高，产生的产物不超过三个。此外，通过在两个沙椤科物种中的计算机验证，这些 SSR 标记的可转移性较低。此外，我们开发了一个在线数据库，名为“阿甘树 L. SSR 数据库：https://as-fmmdb.shinyapps.io/asssrdb/”（AsSSRdb），以提供本研究中鉴定的 CDS 相关 SSR 的访问权限。总的来说，这项研究为阿甘树和相关物种的 DNA 指纹分析、遗传研究和分子育种提供了有价值的标记资源。数据库网址：https://as-fmmdb.shinyapps.io/asssrdb/。
