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Genomic insights into Raffaelea lauricola pathogenesis

Citation

Rollins, Jeffrey; Zhang, Yucheng (2020), Genomic insights into Raffaelea lauricola pathogenesis, Dryad, Dataset, https://doi.org/10.5061/dryad.05qfttf14

Abstract

Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated from Asia; however, there is no report of laurel wilt causing widespread mortality on native Lauraceae trees in Asia. To gain insight into why R. lauricola is a tree-killing plant pathogen in North America, we generated and compared high quality draft genome assemblies of R. lauricola and its closely related non-pathogenic species R. aguacate. Relative to R. aguacate, the R. lauricola genome uniquely encodes several small-secreted proteins that are associated with virulence in other pathogens and is enriched in secondary metabolite biosynthetic clusters, particularly polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit significant differences in secreted proteins including CAZymes that are associated with polysaccharide binding including the chitin binding CBM50 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and in vitro-grown fungal cultures further revealed a number of secreted protein genes, secondary metabolite clusters and alternative sulfur uptake and assimilation pathways that are coordinately up-regulated during infection. Through these comparative analyses we have identified potential adaptations of R. lauricola that may enable it to colonize and cause disease on susceptible hosts. How these adaptations have interacted with co-evolved hosts in Asia, where little to no disease occurs, and non-co-evolved hosts in North America, where lethal wilt occurs, requires additional functional analysis of genes and pathways.

Methods

These data represent whole genome shotgun assemblies and gene predictions of Raffaelea lauricola RL4 (CBS 127349) and R. aguacate PL1004 (CBS 141672) . Sequencing was performed on the Ion Torrent Personnel Genome machine (PGM) and by Illumina Hiseq technology. Ion torrent reads were assembled using the de Bruijn algorithm implemented in the CLC Genomics Workbench version 5.0.1, MIRA 4, and Spades 3.7.1. The Illumina reads were assembled using the ALLPATHS-LG assembler. Assemblies generated from Ion Torrent and Illumina reads were merged using Metassembler to achieve final assemblies. These Whole Genome Shotgun projects have been deposited at DDBJ/ENA/GenBank under accessions JACBXF000000000 and JACCPH000000000.   Raffaelea spp. genes were predicted through two cycles of the Maker pipeline using the Uniprot reveiwed protein database for protein evidence, and transcripts from PASA pipeline as additional EST evidence for gene prediction.

Data files with "RL4" designations are from Raffaelea lauricola RL4 (CBS 127349)

Data files with "Rsp272" designations are genetrated from Raffaelea aguacate PL1004 (CBS 141672)

Funding

National Institute of Food and Agriculture, Award: 2015*51181-24257