Abstract
Old and young duplicate genes have been reported in some organisms. However, little is known about the properties of old and young duplicate genes in Arachis. Here, we have identified old and young duplicate genes in Arachis duranensis, and analyzed the evolution, gene complexity, gene expression pattern, and functional divergence between old and young duplicate genes. Our results showed different evolutionary, gene complexity and gene expression patterns, as well as differing correlations between old and young duplicate genes. Gene ontology results showed that old duplicate genes play a crucial role in lipid and amino acid biosynthesis and the oxidation–reduction process and that young duplicate genes are preferentially involved in photosynthesis and response to biotic stimulus. Transcriptome data sets revealed that most old and young duplicate genes had asymmetric function, and only a few duplicate genes exhibited symmetric function under drought and nematode stress. We found that old duplicate genes are preferentially involved in lipid and amino acid metabolism and response to abiotic stress, while young duplicate genes are likely to participate in photosynthesis and response to biotic stress. This work provides a better understanding of the evolution and functional divergence of old and young duplicate genes in A. duranensis.
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Funding
This study was supported by the Forage Industrial Innovation Team, Shandong Modern Agricultural Industrial and Technical System (SDAIT-23-01), China Agriculture Research System (CARS-34) and Natural Science Foundation of Shandong Province, China (ZR2019QC017).
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438_2019_1574_MOESM1_ESM.tif
Fig. S1 Correlation analysis of gene-expression level, gene-expression breadth, gene complexity, and substitution rate between old and young duplicate genes in A. duranensis. The figure was constructed using the gplots package in R. (TIFF 1660 kb)
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Fig. S2 Comparisons of the number of gene ontology terms between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate genes based on the sequencing name. The figure was constructed using the ggpubr package in R. (TIFF 573 kb)
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Fig. S3 Old and young duplicate genes distributed on 10 chromosomes in A. duranensis. A. Old duplicate gene locations on the 10 chromosomes. B. Young duplicate gene locations on the 10 chromosomes. A red line indicates duplicate gene pairs in a chromosome. Grey line indicates duplicate gene pairs in a different chromosome. The chromosomal location of A. duranensis genes has been documented on https://peanutbase.org/gbrowse_aradu1.0. We extracted the chromosomal location of each old and young duplicate gene based on the sequencing name. The figure was constructed using Circos 9.0. (TIFF 1275 kb)
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Table S1 Young and old duplicate genes in A. duranensis. Ks: synonymous substitution rate per synonymous site; Ka: nonsynonymous substitution rate per nonsynonymous site; Ka/Ks: nonsynonymous to synonymous substitution ratio (XLSX 118 kb)
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Table S2 Specific gene ontology terms for cell components between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate gene based on the sequencing name. (XLSX 12 kb)
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Table S3 Specific gene ontology terms for molecular functions between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate gene based on the sequencing name (XLSX 13 kb)
438_2019_1574_MOESM7_ESM.xlsx
Table S4 Specific gene ontology terms for biological processes between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate gene based on the sequencing name (XLSX 13 kb)
438_2019_1574_MOESM8_ESM.xlsx
Table S5 Common gene ontology terms for cell components between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate genes based on the sequencing name (XLSX 8 kb)
438_2019_1574_MOESM9_ESM.xlsx
Table S6 Common gene ontology terms for molecular functions between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate genes based on the sequencing name (XLSX 10 kb)
438_2019_1574_MOESM10_ESM.xlsx
Table S7 Common gene ontology terms for biological processes between old and young duplicate genes in A. duranensis. Gene ontology (GO) of A. duranensis sequences has been released. We extracted the GO terms of each old and young duplicate genes based on the sequencing name (XLSX 8 kb)
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Song, H., Sun, J. & Yang, G. Old and young duplicate genes reveal different responses to environmental changes in Arachis duranensis. Mol Genet Genomics 294, 1199–1209 (2019). https://doi.org/10.1007/s00438-019-01574-8
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DOI: https://doi.org/10.1007/s00438-019-01574-8