Trivellone, V.; Cao, Y.; Dietrich, C.H. Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors. Biology2022, 11, 977.
Trivellone, V.; Cao, Y.; Dietrich, C.H. Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors. Biology 2022, 11, 977.
Trivellone, V.; Cao, Y.; Dietrich, C.H. Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors. Biology2022, 11, 977.
Trivellone, V.; Cao, Y.; Dietrich, C.H. Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors. Biology 2022, 11, 977.
Abstract
Despite several decades’ effort to detect and identify phytoplasmas (Tenericutes: Mollicutes) using PCR and Sanger sequencing focusing on diseased plants, knowledge of phytoplasma biodiversity and vector associations remains highly incomplete. To improve protocols for documenting phyto-plasma diversity and ecology, we used DNA extracted from phloem-feeding insects and com-pared traditional Sanger sequencing with a next-generation sequencing method, Anchored Hy-brid Enrichment (AHE) for detecting and characterizing phytoplasmas. Among 22 of 180 leaf-hopper samples that initially tested positive for phytoplasmas using qPCR, AHE yielded phyto-plasma 16Sr sequences for 20 (19 complete and 1 partial sequence) while Sanger sequencing yield-ed sequences for 16 (11 complete and 5 partial). AHE yielded phytoplasma sequences for an addi-tional 7 samples (3 complete and 4 partial) that did not meet the qPCR threshold for phytoplasma positivity or yielded non-phytoplasma sequences using Sanger sequencing. This suggests that AHE is more efficient for obtaining phytoplasma sequences. Twenty-three samples with sufficient data were classified into eight 16Sr subgroups (16SrI-B, I-F, I-AO, III-U, V-C, IX-J, XI-C, XXXVII-A), three new subgroups (designated as 16SrVI-L, XV-D, XI-G) and three possible new groups. Our results suggest that screening phloem-feeding insects using qPCR and AHE sequencing may be the most efficient method for discovering new phytoplasmas.
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