Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris

Abstract

Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

Figure 1.

Annotation Results of Chromosome Segments from Soybean (Gm8 and Gm15) and Phaseolus (Pv5). The two soybean homoeologous regions, Gm8 and Gm15, and orthologous Phaseolus region, Pv5, are shown. Black bars are sequence contigs. Gm8 has two physical gaps, and Pv5 has one. Pentagons represent genes. Orange genes have homoeologs and/or orthologs (collinear genes), connected by black lines. Yellow genes do not have homoeologs and orthologs (noncollinear genes). Triangles represent transposons: blue triangles are intact LTR retrotranspsons, pink triangles are solo LTRs, cyan triangles are truncated LTR retrotransposons, and green triangles are non-LTR retrotransposons. Shaded boxes show the duplication events: green boxes show segmental duplications. The purple box shows a tandem duplication. Black numbers are the gene number from annotation results. Insertion times of intact LTR retrotransposons are shown in red. Regions between the two pink dotted lines are physical gaps in Gm8 and their corresponding intervals in Gm15.

Figure 2.

Distribution of Ks Values of Genes in Both Soybean Homoeologs and Phaseolus. Blue circles are Ks values from Pv5-Gm8; green triangles are Ks values from Pv5-Gm15; red boxes are Ks values from Gm8-Gm15. Different zones show the Ks from different homoeologous and orthologous counterparts. Zone I shows the Ks from the pairwise comparison of the two soybean homoeologs and one Phaseolus ortholog. Zone II shows the Ks from the sequence comparisons of Pv5 orthologs and Gm8 homoeologs. Zone III shows the Ks from Pv5 orthologs and Gm15 homoeolog comparisons. Zone IV shows the Ks from homoeologs between Gm8 and Gm15. Numbers below the plot are the annotated gene numbers. Ks value of gene114 (Pv5-Gm15) is ~2.8 due to extensive variation outside the conserved protein domain, and it is not shown here.

Figure 3.

Heat Maps of Relative Transcript Abundance of Homoeologous Genes on Gm8 and Gm15 for Seven Different Tissue Types. The relative positions of 29 tested genes (top to bottom) are shown as colored rectangles along the Gm8 and Gm15 contigs. The numbers on the left are gene annotation results of the 29 tested genes. The transcription level of each gene is indicated as high (red) or low (blue) relative to the respective homoeologous counterpart. Homoeologs with approximately equal transcription levels are shown as black. The scale on the right indicates the coloration used to depict relative transcript proportions between homoeologous copies.

Figure 4.

Assessment of Tissue-Specific Transcriptional Divergence between Homoeolog Pairs. The relative transcriptional proportions of the Gm8 homoeologs are shown for 29 tested gene pairs. The mean Gm8 proportion across two biological replicates is shown in the plot for each gene pair across seven tissue types. The percentage of statistically significant (P < 0.05) tissue × tissue differences detected in a factorial pairwise comparison of the homoeolog proportions among seven tissue types is shown below each gene pair number. There was a wide range (2 to 67%) of transcription variations among homoeolog pairs. The genes are ordered from lowest to highest percentage of tissue × tissue differences among the seven tissue types. Therefore, the gene pairs on the left infrequently exhibited significant tissue-specific transcriptional variation, and the genes on the right frequently exhibited significant tissue-specific transcriptional variation. The red number shown below each percentage indicates the number of informative assays for each homoeolog pair.