State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
School of Computer and Artificial Intelligence, Hefei Normal University, Hefei 230061, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D1661-D1667. doi: 10.1093/nar/gkad701.
The genus Camellia consists of about 200 species, which include many economically important species widely used for making tea, ornamental flowers and edible oil. Here, we present an updated tea plant information archive for Camellia genomics (TPIA2; http://tpia.teaplants.cn) by integrating more novel large-scale genomic, transcriptomic, metabolic and genetic variation datasets as well as a variety of useful tools. Specifically, TPIA2 hosts all currently available and well assembled 10 Camellia genomes and their comprehensive annotations from three major sections of Camellia. A collection of 15 million SNPs and 950 950 small indels from large-scale genome resequencing of 350 diverse tea accessions were newly incorporated, followed by the implementation of a novel 'Variation' module to facilitate data retrieval and analysis of the functionally annotated variome. Moreover, 116 Camellia transcriptomes were newly assembled and added, leading to a significant extension of expression profiles of Camellia genes to 13 developmental stages and eight abiotic/biotic treatments. An updated 'Expression' function has also been implemented to provide a comprehensive gene expression atlas for Camellia. Two novel analytic tools (e.g. Gene ID Convert and Population Genetic Analysis) were specifically designed to facilitate the data exchange and population genomics in Camellia. Collectively, TPIA2 provides diverse updated valuable genomic resources and powerful functions, and will continue to be an important gateway for functional genomics and population genetic studies in Camellia.
山茶属约有 200 个种，其中包括许多经济上重要的种，广泛用于制茶、观赏花卉和食用油。在这里，我们通过整合更多新颖的大规模基因组、转录组、代谢和遗传变异数据集以及各种有用的工具，为山茶基因组学（TPIA2；http://tpia.teaplants.cn）提供了一个更新的茶树信息档案。具体来说，TPIA2 承载了所有现有的、组装良好的 10 个山茶基因组及其来自山茶三个主要部分的综合注释。从 350 个不同茶树品系的大规模基因组重测序中收集了 1500 万个 SNP 和 950950 个小型插入缺失，随后实现了一个新的“变异”模块，以方便检索和分析功能注释的变异组。此外，还新组装并添加了 116 个山茶转录组，从而大大扩展了山茶基因的表达谱，达到 13 个发育阶段和 8 个非生物/生物处理。还实现了一个更新的“表达”功能，为山茶提供了一个全面的基因表达图谱。两个新的分析工具（例如 Gene ID Convert 和种群遗传分析）专门设计用于促进山茶中的数据交换和群体基因组学。总的来说，TPIA2 提供了多样化的更新的有价值的基因组资源和强大的功能，将继续成为山茶功能基因组学和群体遗传学研究的重要门户。
