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Gene family construction

SD Shanshan Dong
ML Min Liu
YL Yang Liu
FC Fei Chen
TY Ting Yang
LC Lu Chen
XZ Xingtan Zhang
XG Xing Guo
DF Dongming Fang
LL Linzhou Li
TD Tian Deng
ZY Zhangxiu Yao
XL Xiaoan Lang
YG Yiqing Gong
EW Ernest Wu
YW Yaling Wang
YS Yamei Shen
XG Xun Gong
HL Huan Liu
SZ Shouzhou Zhang
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Protein and nucleotide sequences from M. biondii and five other angiosperms (A. trichopoda, A. thaliana, C. kanehirae, L. chinense, Vitis vinifera) were used to construct gene families using OrthoFinder72 (https://github.com/davidemms/OrthoFinder) based on an all-versus-all BLASTP alignment with an e-value cutoff of 1e − 5. Potential gene pathways were obtained via gene mapping against the KEGG database, and Gene Ontology (GO) terms were extracted from the corresponding InterProScan or Pfam results (Fig. ​(Fig.22).

a Number of genes in various plant species, showing a high gene number for M. biondii compared to a model species (Arabidopsis thaliana) and other species (Amborella trichopoda, Cinnamomum kanehirae, Liriodendron chinense, and Vitis vinifera). b Venn diagram showing overlaps of gene families between M. biondii, L. chinense, A. trichopoda, A. thaliana, and V. vinifera

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