Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

Abstract

With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and differential evolutionary pressures over time and across different gene families. In this report, we trace the changes that have occurred in 12 surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current Glycine max genome: a genome triplication before the origin of the rosids (~130 to 240 million years ago), a genome duplication early in the legumes (~58 million years ago), and a duplication in the Glycine lineage (~13 million years ago). Patterns of gene retention following the genome triplication event generally support predictions of the Gene Balance Hypothesis. Finally, we find that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity and that the enrichment of these highly connected genes in the 12 highly conserved homoeologous segments may in part explain their retention over more than 100 million years and repeated polyploidy events.

Evolutionary Patterns and Coevolutionary Consequences of MIRNA Genes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

“…The results also suggest that MIR2118 and the MIR1510 were generated by a duplication seemingly predating the split of soybean and common bean from a common ancestor. Because MIR1510 was also found in M. truncatula ( Figure 5C; Zhai et al, 2011), it is thus reasonable to deduce that the duplication of the MIR2118 and MIR1510 lineages occurred prior to the divergence of soybean/common bean and M. truncatula (Bertioli et al, 2009;Severin et al, 2011). However, because the genomic regions harboring MIR2118 and MIR1510 did not show clear syntenic relationships in either soybean/common bean or M. truncatula, while the MIR2118 region in common bean is syntenic to a genomic region without MIR1510 (Schmutz et al, 2014), suggesting that the duplication event producing these two MIRNAs may not be the WGD shared by the soybean/common bean and M. truncatula lineages proposed to have occurred ;50 to 60 MYA.…”

“…A MIRNA superfamily composed of the MIR482 family and the MIR2118 family target NB-LRRs at the encoded and conserved P-loop motif and is highly conserved among divergent plant species including Arabidopsis, tomato (Solanum lycopersicum), Medicago truncatula, soybean, and even the grasses (Lu et al, 2006;Subramanian et al, 2008;Szittya et al, 2008;Zhai et al, 2011;Shivaprasad et al, 2012). In addition, a third, related family, MIR1510, was recently identified in legumes such as M. truncatula and soybean (Subramanian et al, 2008;Szittya et al, 2008;Zhai et al, 2011;Arikit et al, 2014;Zhao et al, 2015), indicating the existence of this MIRNA family prior to the divergence of these two species from a common ancestor ;50 MYA (Bertioli et al, 2009;Severin et al, 2011). As expected, MIR1510 was also found in common bean ( Figures 5A and 5B).…”

Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean

“…Analysis of the duplicated regions in the soybean genome has revealed extensive genomic rearrangements (Schmutz et al, 2010;Severin et al, 2011). It is obvious that those rearrangements have substantially reshaped the landscape of the soybean genome in the past 13 million years, leading to dramatic differentiation of genomic features between duplicated regions over evolutionary time (Schmutz et al, 2010), including transitions from euchromatin (e.g., chromosomal arms) to heterochromatin (e.g., pericentromeric regions) or vice versa (Figure 1).…”

Identification of new QTLs for seed mineral, cysteine, and methionine concentrations in soybean [Glycine max (L.) Merr.]

“…is one of the most widely grown legume crops in the world. Soybean has a fully sequenced genome (Schmutz et al 2010) and results from soybean studies may be translated to other legumes due to extensive synteny (Bordat et al 2011;Lucas et al 2011;McClean et al 2010;Severin et al 2011). Soybean seed has approximately 40% protein in commercial cultivars (Kim et al 2012).…”