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Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing

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Rodrigues Jardim, B., Tran-Nguyen, L. T. T., Gambley, C., Rodoni, B. and Constable, F. E. (2022) Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing. Frontiers in Microbiology, 13 . ISSN 1664-302X

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Article Link(s): https://doi.org/10.3389/fmicb.2022.937648

Publisher URL: https://www.frontiersin.org/articles/10.3389/fmicb.2022.937648

Abstract

Obtaining complete phytoplasma genomes is difficult due to the lack of a culture system for these bacteria. To improve genome assembly, a non-ionic, low- and iso-osmotic iodixanol (Optiprep™) density gradient centrifugation method was developed to enrich for phytoplasma cells and deplete plant host tissues prior to deoxyribonucleic acid (DNA) extraction and high-throughput sequencing (HTS). After density gradient enrichment, potato infected with a ‘Candidatus Phytoplasma australasia’-related strain showed a ∼14-fold increase in phytoplasma HTS reads, with a ∼1.7-fold decrease in host genomic reads compared to the DNA extracted from the same sample without density gradient centrifugation enrichment. Additionally, phytoplasma genome assemblies from libraries equalized to 5 million reads were, on average, ∼15,000 bp larger and more contiguous (N50 ∼14,800 bp larger) than assemblies from the DNA extracted from the infected potato without enrichment. The method was repeated on capsicum infected with Sweet Potato Little Leaf phytoplasma (‘Ca. Phytoplasma australasia’-related strain) with a lower phytoplasma titer than the potato. In capsicum, ∼threefold more phytoplasma reads and ∼twofold less host genomic reads were obtained, with the genome assembly size and N50 values from libraries equalized to 3.4 million reads ∼137,000 and ∼4,000 bp larger, respectively, compared to the DNA extracted from infected capsicum without enrichment. Phytoplasmas from potato and capsicum were both enriched at a density of 1.049–1.058 g/ml. Finally, we present two highly contiguous ‘Ca. Phytoplasma australasia’ phytoplasma reference genomes sequenced from naturally infected Solanaceae hosts in Australia. Obtaining high-quality phytoplasma genomes from naturally infected hosts will improve insights into phytoplasma taxonomy, which will improve their detection and disease management.

Item Type:Article
Business groups:Horticulture and Forestry Science
Keywords:Host DNA contamination, unculturable bacteria, phytopathogen, Natural host, OptiPrep, Density gradient centrifugation, high throughput sequencing,16SrII phytoplasma
Subjects:Science > Microbiology
Plant culture
Plant culture > Vegetables
Plant pests and diseases > Plant pathology
Deposited On:13 Sep 2022 02:32
Last Modified:13 Sep 2022 02:32

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