Phylogenetic Analysis of Rosid Genomes

Except for pecan and Chinese hickory, V. vinifera and 10 other genome-sequenced representatives from the Rosids (J. regia, G. max, Medicago truncatula, P. persica, Morus notabilis, Carica papaya, Gossypium hirsutum, Theobroma cacao, Betula pendula, and Populus trichocarpa), along with A. thaliana, were selected for constructing the phylogenetic tree (J. regia genome data were downloaded from [99 ]; others were downloaded from Phytozome [100 (link)] [v12]). The protein set of each species was obtained and filtered as follows: (i) only the longest isoform was considered for further analysis if a gene encoded several isoforms; (ii) proteins of <30 amino acids were filtered out. The similarity relation between homologous proteins in all species was obtained through BLASTp with the E-value 1e–5. All the protein datasets of the 14 species were clustered into paralogous and orthologous using the program OrthoMCL [101 (link)] with the inflation parameter 1.5. Finally, 170 single-copy-gene–encoded proteins were used for the phylogenetic analysis. The protein sequences from all species were then aligned by MUSCLE (MUSCLE, RRID:SCR_011812) [102 (link)] and a super alignment matrix was generated by combining all the alignment results. A phylogenetic tree containing 14 species was constructed using RAxML (RAxML, RRID:SCR_006086) [103 (link)] with the ML method and 1,000 bootstraps. Finally, the MCMCtree program implemented in phylogenetic analysis by maximum likelihood (PAML) (PAML, RRID:SCR_014932) [104 (link)] was applied to infer the divergence time on the basis of the phylogenetic tree. The MCMCtree running parameters were as follows: burn-in, 5,000,000; sample-number, 1,000,000; sample-frequency, 50. The calibration times of divergence between A. thaliana and C. papaya (54–90 MYA), G. hirsutum and T. cacao (32–99 MYA), A. thaliana and P. trichocarpa (107–109 MYA), G. max and M. truncatula (46–60 MYA), M. notabilis and P. persica (73–90 MYA), and A. thaliana and G. max (107–111 MYA) were obtained from the TimeTree database [105 (link)].

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Huang Y., Xiao L., Zhang Z., Zhang R., Wang Z., Huang C., Huang R., Luan Y., Fan T., Wang J., Shen C., Zhang S., Wang X., Randall J., Zheng B., Wu J., Zhang Q., Xia G., Xu C., Chen M., Zhang L., Jiang W., Gao L., Chen Z., Leslie C.A., Grauke L.J, & Huang J. (2019). The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. GigaScience, 8(5), giz036.

Publication 2019

Amino acids Betula pendula Cacao Chinese Gene Gene proteins Genome Gossypium hirsutum Isoforms Medicago truncatula Morus Muscle Papaya Pecan Populus Protein Protein sequences

Corresponding Organization : Zhejiang A & F University

Other organizations : Novogene Bioinformatics Institute, United States Department of Agriculture, Agricultural Research Service, New Mexico State University, Zhejiang University, Fujian Agriculture and Forestry University, Kunming Institute of Botany, Institute of Botany, University of California, Davis

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Variable analysis

independent variables

Selection of genome-sequenced representatives from the Rosids (V. vinifera, J. regia, G. max, Medicago truncatula, P. persica, Morus notabilis, Carica papaya, Gossypium hirsutum, Theobroma cacao, Betula pendula, and Populus trichocarpa), along with A. thaliana

dependent variables

Phylogenetic tree constructed using 170 single-copy-gene-encoded proteins

control variables

Pecan and Chinese hickory were excluded from the phylogenetic tree construction
Only the longest isoform was considered for each gene
Proteins with less than 30 amino acids were filtered out
Homologous proteins were identified using BLASTp with E-value 1e-5
Paralogous and orthologous proteins were clustered using OrthoMCL with inflation parameter 1.5
Protein sequences were aligned using MUSCLE
Phylogenetic tree was constructed using RAxML with the ML method and 1,000 bootstraps
Divergence time was inferred using MCMCtree program implemented in PAML with the following parameters: burn-in, 5,000,000; sample-number, 1,000,000; sample-frequency, 50
Calibration times were obtained from the TimeTree database

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