TaxonOMICS of Australian Chenopods: a multifaceted study to resolve one of Australia’s most challenging plant families

澳大利亚藜类分类组学：一项多方面的研究，旨在解决澳大利亚最具挑战性的植物家族之一

• 批准号: 350360458
• 负责人: Professorin Dr. Gudrun Kadereit
• 金额: --
• 依托单位: Bereich Systematik, Biodiversität & Evolution der Pflanzen
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/350360458?language=en
• 关键词: TaxonOMICS; Australian; Chenopods; multifaceted; study

Our project focuses on universal molecular and bioinformatics methods for a simplified exploration and description of biodiversity. So far, we have developed a modified RADseq approach for the phylogenetic analysis of rapidly and recently radiated species complexes. This allows, in addition to widely used SNP based approaches, the application of two-step coalescent-based summary methods for species tree inference. We overcame several hurdles of classical RAD data by sequencing libraries with several thousand loci of 300-600 bp length. Furthermore, we developed a comprehensive target group specific data analysis approach to ensure an accurate assembly process, complemented by comparative phylogenetic analyses. This approach has not only been tested successfully for our study group, the Australian Camphorosmeae, but also worked for a broad variety of plant lineages in our lab. The molecular approach is accompanied by the development of an image classification tool to facilitate identification of taxa in the field. So far, we performed a promising pilot study to test the performance of different neural network architectures using the morphologically diverse Australian Camphorosmeae as a trial group. Together with our international collaboration network of phylogenetics, bioinformatics and taxonomy experts we are now set to tackle even more diversity of the Australian Chenopodiaceae during the second SPP Taxon-Omics round. We will extend our study group to the species-rich and cryptic genera Atriplex and Tecticornia, covering nearly 80% of Australian chenopods. In addition to the varying needs of our study groups, we will also extend the spectrum of molecular approaches for species delimitation. Our modified llddRADseq approach will be further refined by incorporating the capturing principle of hyRAD (Suchan et al. 2017) for lineage delimitation in Atriplex and the Camphorosmeae. Extending the RAD based methods, we will utilize a Hyb-Seq approach specially designed for Australian Angiosperm lineages to unravel the species complexes of the enigmatic Tecticornia. Both approaches will then be suitable for phylogenomics of degraded DNA samples aiming at the comprehensive biodiversity resources stored at museums. Besides further refinements for the Camphorosmeae, our image classification approach will be extended for a pilot study in Atriplex using specimen and field imagery. This image-based resource will be implemented alongside already available online keys including detailed descriptions and imagery. However, these keys must first be taxonomically updated based on our phylogenetic species delimitation approaches. In combination, the molecular and bioinformatics approaches will not only reveal the complex evolutionary histories of our study groups and unravel challenging species complexes within, but also serve as a sustainable resource for the next generation of taxonomists targeting the stunning diversity of life in Australia.

我们的项目侧重于通用分子和生物信息学方法，以简化生物多样性的探索和描述。到目前为止，我们已经开发了一种改进的 RADseq 方法，用于快速和最近辐射的物种复合体的系统发育分析。除了广泛使用的基于 SNP 的方法之外，这还允许应用基于两步合并的摘要方法进行物种树推断。我们通过对具有数千个长度为 300-600 bp 的基因座的文库进行测序，克服了经典 RAD 数据的几个障碍。此外，我们开发了一种全面的针对特定目标群体的数据分析方法，以确保准确的组装过程，并辅以比较系统发育分析。这种方法不仅在我们的研究小组澳大利亚樟树中得到了成功的测试，而且还适用于我们实验室的多种植物谱系。分子方法伴随着图像分类工具的开发，以促进现场分类单元的识别。到目前为止，我们进行了一项有前途的试点研究，以形态多样的澳大利亚樟树作为试验组来测试不同神经网络架构的性能。与我们的系统发生学、生物信息学和分类学专家的国际合作网络一起，我们现在准备在第二轮 SPP 分类组学中解决澳大利亚藜科的更多多样性问题。我们将把我们的研究小组扩展到物种丰富且神秘的 Atriplex 属和 Tecticornia 属，覆盖澳大利亚近 80% 的藜类动物。除了我们研究小组的不同需求之外，我们还将扩展物种界定的分子方法的范围。我们修改后的 llddRADseq 方法将通过结合 hyRAD (Suchan et al. 2017) 的捕获原理进一步完善，用于 Atriplex 和 Camphorosmeae 的谱系界定。扩展基于 RAD 的方法，我们将利用专为澳大利亚被子植物谱系设计的 Hyb-Seq 方法来解开神秘的 Tecticornia 的物种复合体。这两种方法都将适用于针对博物馆存储的综合生物多样性资源的降解 DNA 样本的系统发育学。除了对 Camphorosmeae 进行进一步改进外，我们的图像分类方法还将扩展到利用标本和现场图像对滨藜进行试点研究。这种基于图像的资源将与已有的在线密钥（包括详细描述和图像）一起实施。然而，这些键必须首先根据我们的系统发育物种界定方法进行分类学更新。结合起来，分子和生物信息学方法不仅将揭示我们研究小组复杂的进化历史并解开其中具有挑战性的物种复合体，而且还可以为下一代分类学家提供可持续的资源，以澳大利亚令人惊叹的生命多样性为目标。