School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia.
Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney, Sydney, NSW 2000, Australia.
Genome Biol Evol. 2024 Nov 1;16(11). doi: 10.1093/gbe/evae238.
Myrtaceae are a large family of woody plants, including hundreds that are currently under threat from the global spread of a fungal pathogen, Austropuccinia psidii (G. Winter) Beenken, which causes myrtle rust. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mb and BUSCO completeness 98.0%) with 99.0% of the 347 Mb assembly anchored to 11 chromosomes (2n = 22). The R. argentea genome will inform conservation efforts for Myrtaceae species threatened by myrtle rust, against which it shows variable resistance. We observed contamination in the sequencing data, and further investigation revealed an arthropod source. This study emphasizes the importance of checking sequencing data for contamination, especially when working with nonmodel organisms. It also enhances our understanding of a tree that faces conservation challenges, contributing to broader biodiversity initiatives.
桃金娘科是木本植物的一个大科，其中有数百种目前正受到真菌病原体 Austropuccinia psidii (G. Winter) Beenken 全球传播的威胁，这种病原体可引起桃金娘锈病。本研究从澳大利亚本土雨林树种银叶树 Rhodamnia argentea Benth.（马利筋木）的牛津纳米孔技术长读段、10x Genomics Chromium 连接读段和 Hi-C 数据组装了参考基因组（N50 = 32.3 Mb，BUSCO 完整性 98.0%），347 Mb 组装中有 99.0%锚定到 11 条染色体（2n = 22）。银叶树基因组将为受桃金娘锈病威胁的桃金娘科物种的保护工作提供信息，因为这些物种对锈病表现出不同程度的抗性。我们在测序数据中观察到了污染，进一步的调查揭示了这种污染的来源是节肢动物。本研究强调了检查测序数据污染的重要性，特别是在处理非模式生物时。它还增强了我们对面临保护挑战的树木的理解，为更广泛的生物多样性倡议做出了贡献。
