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Open Access Highly Accessed Research article

Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean

Shanshan Chu12, Jiao Wang2, Hao Cheng2, Qing Yang1* and Deyue Yu2*

Author Affiliations

1 College of Life Sciences, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China

2 National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China

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BMC Genetics 2014, 15:76  doi:10.1186/1471-2156-15-76

Published: 24 June 2014



Previous studies suggest that the metabolic pathway structure influences the selection and evolution rates of involved genes. However, most of these studies have exclusively considered a single gene copy encoding each enzyme in the metabolic pathway. Considering multiple-copy encoding enzymes could provide direct evidence of gene evolution and duplication patterns in metabolic pathways. We conducted a detailed analysis of the phylogeny, synteny, evolutionary rate and selection pressure of the genes in the isoflavonoid metabolic pathway of soybeans.


The results revealed that 1) only the phenylalanine ammonia-lyase (PAL) gene family most upstream from the pathway preserved all of the ancient and recent segmental duplications and maintained a strongly conserved synteny among these duplicated segments; gene families encoding branch-point enzymes with higher pleiotropy tended to retain more types of duplication; and genes encoding chalcone reductase (CHR) and isoflavone synthase (IFS) specific for legumes retained only recent segmental duplications; 2) downstream genes evolved faster than upstream genes and were subject to positive selection or relaxed selection constraints; 3) gene members encoding enzymes with high pleiotropy at the branching points were more likely to have undergone evolutionary differentiation, which may correspond to their functional divergences.


We reconciled our results with existing controversies and proposed that gene copies at branch points with higher connectivity might be under stronger selective constraints and that the gene copies controlling metabolic flux allocation underwent positive selection. Our analyses demonstrated that the structure and function of a metabolic pathway shapes gene duplication and the evolutionary constraints of constituent enzymes.

Isoflavonoid phytoalexin pathway; Duplication pattern; Evolution divergence; Multiple copies; Soybean