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

Bianca Rodrigues Jardim; Lucy T T Tran-Nguyen; Cherie Gambley; Brendan Rodoni; Fiona E Constable

doi:10.3389/fmicb.2022.937648

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

Front Microbiol. 2022 Aug 12:13:937648. doi: 10.3389/fmicb.2022.937648. eCollection 2022.

Authors

Bianca Rodrigues Jardim^{1

2}, Lucy T T Tran-Nguyen³, Cherie Gambley⁴, Brendan Rodoni^{1

2}, Fiona E Constable^{1

2}

Affiliations

¹ School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.
² Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora, VIC, Australia.
³ Plant Health Australia, Deakin, ACT, Australia.
⁴ Horticulture and Forestry Science, Department of Agriculture and Fisheries, Maroochy Research Facility, Nambour, QLD, Australia.

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.

Keywords: 16SrII phytoplasma; OptiprepTM; density gradient centrifugation; high-throughput sequencing; host DNA contamination; natural host; phytopathogen; unculturable bacteria.