Transcriptomic study of evolution and gene expression in diploid and allotetraploid glycine subgenus glycine

The genus Glycine is divided into two subgenera, subgenus Soja and subgenus Glycine. One of the member species of subgenus Soja, soybean (Glycine max) is an important crop plant that has been extensively studied. Unlike soybean, the perennial wild relatives in subgenus Glycine are less well known even though they possess both an interesting evolutionary history of speciation and polyploidization, and a possible potential as a source of diversity to expand the current soybean gene pool. Most studies on the member species of subgenus Glycine have focused on either their taxonomic aspects or the history of polyploidization within this subgenus. In this thesis we try to expand the scope of the studies in the member species of the subgenus Glycine by looking at the evolution and expression of their genes. We first look at the evolutionary forces that drive the speciation between soybean and its perennial wild relatives. We leveraged the use of de novo transcriptome assembly to gain access to the transcriptome of the perennial wild relatives of soybean. Using 2,430 orthologous genes shared between soybean and the perennial wild Glycine we perform test to detect signature of selection acting on the protein coding sequence. We found five genes that show signatures of selection in this study. One of the genes that we found, Glyma02g00320 showed positive selection in the soybean lineage. Along with several nucleotide variants, we also found a 24-base-pair sequence deleted in the 5’-region containing the putative signal peptide. Glyma02g00320 encodes for a BolA4-like protein, a protein with known conservation across the three different domains of life, Archaea, Bacteria, and Eukaryote. In silico prediction on the subcellular localization of soybean BolA4-like protein suggested a dual targeting nature between chloroplast and mitochondria. A similar BolA protein in Arabidopsis thaliana has been implicated in the mediation of redox homeostasis. Changes in distribution of this BolA4-like protein due to the 24-base-pair deletion in the soybean lineage would likely make this protein differently distributed in soybean compared to its perennial wild relatives. Whether the predicted changes does have effect on soybean redox homeostasis compared to wild perennial Glycine is still an open question that merits further investigation. We also look at the changes in gene expression on an allotetraploid species and its diploid progenitors species in the subgenus Glycine following exposure to high light stress. We compared the overall expression of homeologous gene pairs (duplicated genes due to whole genome duplication) with the expression of its homologous genes in its diploid progenitors. We observed that a majority of the genes observed showed equal level of expression between the allotetraploid Glycine and its diploid progenitors, with only a small fraction of the genes observed showing unequal expression levels. We also found that the homeologous gene pairs in allotetraploid Glycine displayed differential pattern of homeolog expression bias after exposure to high light stress across hundreds of genes. The extent of the observed differential pattern of homeolog expression bias across hundreds of genes suggests a regulatory mechanism that acts on a group of genes, one possible example mechanism involving the maintenance of DNA methylation level of said genes. The promoters of soybean orthologs of the genes showing differential pattern of homeolog expression bias were enriched for two distinct, non-overlapping subsets of known cis-regulatory motifs related to light and / or hormone response. Taken together, this would suggest that expression sub-functionalization achieved through differential pattern of homeolog expression bias may have an important role in the increase adaptability of allotetraploid species to a wider range of environmental conditions