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. 2024 Nov 1;16(11):evae238.
doi: 10.1093/gbe/evae238.

Chromosome-Level Genome Assembly of the Australian Rainforest Tree Rhodamnia argentea (Malletwood)

Stephanie H Chen  1   2   3 , Ashley Jones  4 , Patricia Lu-Irving  2 , Jia-Yee S Yap  2 , Marlien van der Merwe  2 , Jason G Bragg  2 , Richard J Edwards  1   5
Affiliations

Chromosome-Level Genome Assembly of the Australian Rainforest Tree Rhodamnia argentea (Malletwood)

Stephanie H Chen et al. Genome Biol Evol. .

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 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.

Keywords: Rhodamnia; Myrtaceae; genome assembly; long-reads; myrtle rust.

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Figures

Fig. 1.
Fig. 1.
Rhodamnia argentea (malletwood), photo (c) Stephanie Chen. a) Diploid status estimated by Smudgeplot. b) Juicebox Hi-C contact map with 11 chromosomes. c) Genome assembly workflow.
See this image and copyright information in PMC

References

    1. Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, et al. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol. 2024:25(1):60. 10.1186/s13059-024-03198-7. - DOI - PMC - PubMed
    1. Berthon KA, Fernandez Winzer L, Sandhu K, Cuddy W, Manea A, Carnegie AJ, Leishman MR. Endangered species face an extra threat: susceptibility to the invasive pathogen Austropuccinia psidii (myrtle rust) in Australia. Australas Plant Pathol. 2019:48(4):385–393. 10.1007/s13313-019-00640-4. - DOI
    1. Boetzer M, Pirovano W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics. 2014:15(1):211. 10.1186/1471-2105-15-211. - DOI - PMC - PubMed
    1. Brandies P, Peel E, Hogg CJ, Belov K. The value of reference genomes in the conservation of threatened species. Genes (Basel). 2019:10(11):846. 10.3390/genes10110846. - DOI - PMC - PubMed
    1. Breitwieser FP, Salzberg SL. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics. 2020:36(4):1303–1304. 10.1093/bioinformatics/btz715. - DOI - PMC - PubMed