Diversity and characterization of oomycetes associated with corn seedlings in Michigan

This repository contains data, code and results for the analysis of oomycetes associated with corn seedlings from Michigan collected in 2011 and 2012.

Contents

1. Corn production in Michigan and locations sampled
2. Community analysis
3. Pathogenicity and virulence in corn seedlings

Database for OTU assignment

• coxI genes and taxonomy files generated based on BOLD (http://www.boldsystems.org/) are available at the folder COI_reference_files

Citation

Rojas, J.A. et al. (XXX). Diversity and characterization of oomycetes associated with corn seedlings in Michigan. Phytobiomes Journal.

Please use the following DOI to cite this data and associated functions/analyses.

Session Info

R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biom_0.4.0         gtable_0.2.0       ggrepel_0.8.0      ggtree_1.10.5      treeio_1.2.2       vegan_2.5-3       
 [7] lattice_0.20-38    permute_0.9-4      ape_5.2            phyloseq_1.25.2    ggcounty_0.1       maptools_0.9-4    
[13] sp_1.3-1           mapproj_1.2.6      maps_3.3.0         bindrcpp_0.2.2     here_0.1           stringr_1.3.1     
[19] cowplot_0.9.3      FactoMineR_1.41    reshape2_1.4.3     magrittr_1.5       MASS_7.3-51.1      dplyr_0.7.8       
[25] tidyr_0.8.2        knitr_1.21         lsmeans_2.30-0     emmeans_1.3.0      lme4_1.1-19        Matrix_1.2-15     
[31] plyr_1.8.4         gridExtra_2.3      RColorBrewer_1.1-2 ggplot2_3.1.0     

loaded via a namespace (and not attached):
 [1] nlme_3.1-137         rprojroot_1.3-2      tools_3.4.4          backports_1.1.2      utf8_1.1.4           R6_2.3.0            
 [7] mgcv_1.8-26          lazyeval_0.2.1       BiocGenerics_0.24.0  colorspace_1.3-2     ade4_1.7-13          withr_2.1.2         
[13] tidyselect_0.2.5     compiler_3.4.4       cli_1.0.1            Biobase_2.38.0       flashClust_1.01-2    sandwich_2.5-0      
[19] labeling_0.3         scales_1.0.0         mvtnorm_1.0-8        digest_0.6.18        foreign_0.8-71       minqa_1.2.4         
[25] rmarkdown_1.11       XVector_0.18.0       base64enc_0.1-3      pkgconfig_2.0.2      htmltools_0.3.6      highr_0.7           
[31] rlang_0.3.0.1        rstudioapi_0.8       bindr_0.1.1          zoo_1.8-4            jsonlite_1.6         leaps_3.0           
[37] biomformat_1.7.0     fansi_0.4.0          Rcpp_1.0.0           munsell_0.5.0        S4Vectors_0.16.0     scatterplot3d_0.3-41
[43] stringi_1.2.4        multcomp_1.4-8       yaml_2.2.0           RJSONIO_1.3-1.1      zlibbioc_1.24.0      rhdf5_2.22.0        
[49] parallel_3.4.4       crayon_1.3.4         Biostrings_2.46.0    gpclib_1.5-5         splines_3.4.4        multtest_2.34.0     
[55] pillar_1.3.0         igraph_1.2.2         estimability_1.3     codetools_0.2-15     stats4_3.4.4         glue_1.3.0          
[61] packrat_0.5.0        evaluate_0.12        data.table_1.11.8    nloptr_1.2.1         foreach_1.4.4        purrr_0.2.5         
[67] assertthat_0.2.0     xfun_0.4             xtable_1.8-3         coda_0.19-2          survival_2.43-3      tibble_1.4.2        
[73] rvcheck_0.1.3        iterators_1.0.10     IRanges_2.12.0       cluster_2.0.7-1      TH.data_1.0-9 ```