Abstract：
Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health-related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple-leaved assamica cultivar \"Zijuan\", the temperature-sensitive sinensis cultivar \"Anjibaicha\" and the wild accession \"L618\" whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene-centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene-centric variants, especially for Anthocyanidin synthases. We constructed a gene-centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.
摘要：
茶，全球消费最广泛的饮料之一，在其潜在的风味和与健康相关的化合物中表现出显著的基因组多样性。在这项研究中,我们介绍了一个由11个基因组组成的茶基因组的构建和分析，重点研究了三个新测序的基因组，包括紫叶assamica品种“子娟”，对温度敏感的中华品种“Anjibaicha”和野生登录号“L618”，其组合物表现出优异的质量分数，因为它们从最新的测序技术中获利。我们的分析包括对整个茶基因组的转座子补体的详细调查，揭示所研究基因组中转座子分布的共享模式，并通过长读技术提高转座子分辨率，如长终端重复(LTR)装配指数分析所示。此外，我们的研究包括以基因为中心的pangenome探索，通过我们的研究探索儿茶素途径的基因组景观，提供有关拷贝数改变和以基因为中心的变异的见解，尤其是花青素合成酶。我们通过使用相同的管道在结构和功能上注释所有可用的基因组，构建了以基因为中心的pangenome，这既增加了基因完整性，又允许高功能注释率。这种改进和一致注释的基因集将允许茶基因组之间的更好比较。我们使用这种改进的pangenome来捕获核心和可有可无的基因库，阐明茶树中存在的功能多样性。这种pangenome资源可能作为一个有价值的资源，用于理解特征的基本遗传基础，如风味，应力耐受性，和抗病性，对茶叶育种计划有影响。
