Chromosome-level genome assembly of the Australian rainforest tree Rhodamnia argentea (malletwood).

IF 3.2 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Genome Biology and Evolution Pub Date : 2024-11-02 DOI:10.1093/gbe/evae238

Stephanie H Chen, Ashley Jones, Patricia Lu-Irving, Jia-Yee S Yap, Marlien van der Merwe, Jason G Bragg, Richard J Edwards

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引用次数: 0

Abstract

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 (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp 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 emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of a tree that faces conservation challenges, contributing to broader biodiversity initiatives.

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澳大利亚热带雨林树种红木（Rhodamnia argentea）的染色体级基因组组装。

桃金娘科（Myrtaceae）是一个木本植物大家族，其中有数百种植物目前正受到一种真菌病原体 Austropuccinia psidii (G.Winter) Beenken 在全球传播的威胁，这种病原体会导致桃金娘锈病。澳大利亚原生雨林树 Rhodamnia argentea Benth.(malletwood) 的参考基因组，该基因组由牛津纳米孔技术公司（ONT）的长读数、10 倍基因组学 Chromium 链接读数和 Hi-C 数据（N50 = 32.3 Mbp，BUSCO 完整性 98.0%）组装而成，347 Mbp 组装的 99.0% 固定在 11 条染色体上（2n = 22）。R. argentea 的基因组将为受到桃金娘锈病威胁的桃金娘科物种的保护工作提供信息，桃金娘锈病对该物种表现出不同的抗性。我们在测序数据中发现了污染，进一步调查发现了节肢动物的来源。这项研究强调了检查测序数据污染的重要性，尤其是在研究非模式生物时。这项研究还增进了我们对一种面临保护挑战的树种的了解，为更广泛的生物多样性计划做出了贡献。

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来源期刊

Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY

CiteScore

5.80

自引率

6.10%

发文量

169

审稿时长

1 months

期刊介绍： About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.