Department of Biochemistry, College of Medicine, University of Hail, 2440, Hail, Saudi Arabia.
CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India.
Antonie Van Leeuwenhoek. 2024 Jan 3;117(1):11. doi: 10.1007/s10482-023-01915-z.
To better understand the structure and evolution of the genomes of four plant pathogenic species of Zymoseptoria, we analyzed the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in their whole genome and transcriptome sequences. In this study, SSRs are defined as repeats of more than 12 bases in length. The genome and transcriptome sequences of Zymoseptoria ardabiliae show the highest RA (201.1 and 129.9) and RD (3229.4 and 1928.2) of SSRs, while those of Zymoseptoria pseudotritici show the lowest RA (167.2 and 118.5) and RD (2482.2 and 1687.0). The majority of SSRs in the genomic and transcriptome sequences of species were trinucleotide SSRs, while dinucleotide SSRs were the least common. The most common trinucleotide motifs in the transcriptomic sequences across all species were those that encoded the amino acid arginine. As per our motif conservation study, Zymoseptoria tritici (12.4%) possessed the most unique motifs, while Z. pseudotritici (3.9%) had the fewest. Overall, only 38.1% of the motifs were found to be conserved among the species. Gene enrichment studies reveal that three of the species, Z. ardabiliae, Zymoseptoria brevis, and Z. pseudotritici, have SSRs in their genes related to cellular metabolism, while the remaining Z. tritici harbors SSRs in genes related to DNA synthesis and gene expression. In an effort to improve the genetic resources for the orphan species of pathogenic Zymoseptoria, a total of 73,134 primers were created. The genomic resources developed in this study could help with analyses of genetic relatedness within the population and the development of species-specific markers.
为了更好地理解 4 种植物病原性链格孢菌的基因组结构和进化，我们分析了它们的全基因组和转录组序列中简单重复序列（SSR）的发生、相对丰度（RA）和密度（RD）。在本研究中，SSR 被定义为长度超过 12 个碱基的重复序列。Zymoseptoria ardabiliae 的基因组和转录组序列显示出最高的 SSR RA（201.1 和 129.9）和 RD（3229.4 和 1928.2），而 Zymoseptoria pseudotritici 的 RA（167.2 和 118.5）和 RD（2482.2 和 1687.0）最低。各物种基因组和转录组序列中的大多数 SSR 为三核苷酸 SSR，二核苷酸 SSR 最少。所有物种转录组序列中最常见的三核苷酸基序是编码氨基酸精氨酸的基序。根据我们的基序保守性研究，Zymoseptoria tritici（12.4%）拥有最多的独特基序，而 Z. pseudotritici（3.9%）拥有最少的独特基序。总体而言，只有 38.1%的基序在物种间是保守的。基因富集研究表明，Z. ardabiliae、Zymoseptoria brevis 和 Z. pseudotritici 这 3 个物种的基因中存在与细胞代谢相关的 SSR，而其余的 Z. tritici 则在与 DNA 合成和基因表达相关的基因中存在 SSR。为了改善病原性链格孢菌的孤儿种的遗传资源，共设计了 73134 个引物。本研究开发的基因组资源有助于分析种群内的遗传关系和开发物种特异性标记。
