Zhang Wenting, Chen Ke, Mei Yu, Wang Jihua
Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Guangdong, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China.
Plants (Basel). 2024 Nov 21;13(23):3262. doi: 10.3390/plants13233262.
is a rare and precious medicinal and ornamental plant of Orchidaceae. Abundant morphological characteristics have been observed among cultivated accessions. Our understanding of the genetic basis of morphological diversity is limited due to a lack of sequence data and candidate genes. In this study, a high-quality de novo transcriptome assembly of was generated. A total of 138,385 unigenes were obtained, and a BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis showed an assembly completeness of 98.8%. Multiple databases were used to obtain a comprehensive annotation, and the unigenes were functionally categorized using the GO (Gene Ontology), KOG (Eukaryotic Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes), and Nr databases. After comparing the phenotypic characteristics of five representative cultivars, a set of cultivar-specific, highly expressed unigenes was identified based on a comparative transcriptome analysis. Then, a WGCNA (Weighted Gene Co-expression Network Analysis) was performed to generate gene regulatory modules related to chlorophyll content (red) and sucrose synthase activity (black). In addition, the expression of six and four GO enrichment genes in the red and black modules, respectively, was analyzed using qRT-PCR to determine their putative functional roles in the leaves of the five cultivars. Finally, in silico SSR (Simple Sequence Repeat) mining of the assembled transcriptome identified 44,045 SSRs. Mononucleotide was the most dominant class of SSRs, followed by complex SSRs. In summary, this study reports on the phenomic and genomic resources of , combining SSR marker development and validation. This report aids in morphological diversity assessments of .
是兰科一种珍稀珍贵的药用和观赏植物。在栽培种质中观察到丰富的形态特征。由于缺乏序列数据和候选基因，我们对形态多样性遗传基础的了解有限。在本研究中，生成了高质量的从头转录组组装。共获得138,385个单基因，BUSCO（基准通用单拷贝直系同源物）分析显示组装完整性为98.8%。使用多个数据库进行全面注释，并使用GO（基因本体论）、KOG（真核直系同源组）、KEGG（京都基因与基因组百科全书）和Nr数据库对单基因进行功能分类。在比较五个代表性品种的表型特征后，基于比较转录组分析鉴定出一组品种特异性、高表达的单基因。然后，进行WGCNA（加权基因共表达网络分析）以生成与叶绿素含量（红色）和蔗糖合酶活性（黑色）相关的基因调控模块。此外，使用qRT-PCR分析红色和黑色模块中分别六个和四个GO富集基因的表达，以确定它们在五个品种叶片中的假定功能作用。最后，对组装的转录组进行电子SSR（简单序列重复）挖掘，鉴定出44,045个SSR。单核苷酸是SSR最主要的类别，其次是复杂SSR。总之，本研究报告了[植物名称]的表型组学和基因组资源，结合了SSR标记的开发和验证。本报告有助于[植物名称]的形态多样性评估。
