Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms. In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei’s (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What’s more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods. The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.

中文翻译：

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基于 RNA 测序的 SSR 标记的开发及其在 Carex L. 物种之间和内部的验证

Carex L. 是莎草科最大的属之一，也是生态系统中重要的维管植物。然而，Carex的遗传背景复杂，分类不明确。为了研究Carex的基因功能注释，进行了RNA测序分析。基于 Illumina 数据生成简单序列重复 (SSR)，然后用于研究 79 个 Carex 种质的遗传特征。在本研究中，基于GO、KOG、KEGG、NR数据库获得并注释了36,403个unigenes，总长度为41,724,615 bp。研究结果为基因功能探索提供了理论依据。在 8776 个 SSR 中，随机选择了 96 对引物。以42对多态性较高的引物为基础，扩增出180条多态性条带，多态性率为100%。每个引物平均条带数为4.3，平均距离值为0.548，多态信息含量为0.133～0.494。观察到的等位基因数 (Na)、有效等位基因 (Ne)、Nei's (1973) 基因多样性 (H) 和香农信息指数 (I) 分别为 2.000、1.376、0.243 和 0.391。NJ聚类分为三组，来自新西兰的种质表现出相似的遗传属性并聚类为一组。UPGMA 和 PCoA 分析也显示了相同的结果。分子方差分析 (AMOVA) 揭示了种质内的遗传多样性比基于地理起源聚类和 NJ 聚类的种质之间的遗传多样性更高。此外，本研究建立了79种苔藓属植物的指纹图谱。不同的引物对组合可同时识别多个Carex，克服了传统识别方法的困难。转录组学分析揭示了注释基因的功能类别，并将促进未来的基因功能研究。遗传特征分析表明，79种苔藓属植物之间存在广泛的基因流动。这些标记可用于研究 Carex 和相关物种的进化历史，以及作为未来育种项目的指南。克服了传统识别方法的难点。转录组学分析揭示了注释基因的功能类别，并将促进未来的基因功能研究。遗传特征分析表明，79种苔藓属植物之间存在广泛的基因流动。这些标记可用于研究 Carex 和相关物种的进化历史，以及作为未来育种项目的指南。克服了传统识别方法的难点。转录组学分析揭示了注释基因的功能类别，并将促进未来的基因功能研究。遗传特征分析表明，79种苔藓属植物之间存在广泛的基因流动。这些标记可用于研究 Carex 和相关物种的进化历史，以及作为未来育种项目的指南。