Genetic basis of drought tolerance in loblolly pine
Bark beetle genomics
Bark beetles are common forest pests responsible for the annual loss of millions of conifers and other trees in the United States. Dendroctonus frontalis, also known as the Southern pine beetle (SPB), is the most damaging forest pest in the southeastern United States, having caused losses estimated at more than $1.5 billion. SPB outbreaks have primarily affected loblolly pine, which forms 80% of the planted forestland and over one-half of the standing volume in the southern U.S. SPB is increasingly threatening pine forests across Central and North America and has recently colonized previously unaffected areas north of its historical range due to climate change (i.e. higher average winter temperatures). To better understand the biology and evolution of this pest, we are sequencing and analyzing the genome and transcriptome of the SPB in collaboration with Dr. Heath Blackmon, Department of Biology @TAMU and Prof. Lynne Rieske-Kinney at the University of Kentucky.
Evolution and phenotypic impact of de novo genes
New protein-coding genes can evolve from scratch from noncoding DNA sequences. These so-called de novo genes (DNGs) have been found in a number of species and are implicated in the emergence of novel phenotypes, for instance resistance to low water temperature in artic and antartic fish. Some strategies used to identify DNGs have proven somewhat inaccurate (Casola 2018). We are developing new tools to find DNGs and to assess their phenotypic impact both computationally and experimentally.
Gene copy-number variants (CNVs) in loblolly pine
Many genes in a genome can be present in 0,1 or >1 copies in different individuals of a given population or species. Variations in the number of copies of these genes are called copy-number variants or CNVs. In plants, hundreds to thousands of CNVs have been discovered, with at least some of these CNVs involved in important traits such as disease resistance and adaptation to harsh environmental conditions. We have recently developed a new CNV simulation tools, SECNVs in collaboration with Prof. Alan Dabney in the Department of Statistics @ TAMU and Prof. Clare Gill in the Department of Animal Science @TAMU. Using SECNVs, we are optimizing strategies to detect CNVs in the loblolly genome.
Comparative genomics of conifers
Comparative analyses of conifer genomes have shown that a large fraction of genes in these species have no detectable homologs in angiosperms or other eukaryotes. While the origin of these conifer-specific genes is still largely unexplained, there are several known mechanisms that could have contributed to generating new genes in this group of plants. My group is developing computational tools to determine the possible role of gene duplication and other processes in the emergence of lineage-specific genes in conifers. We have recently determined that, contraty to the nucleotide substitution rate, conifers experience a comparable frequency of gene duplication and loss compared to flowering plants (Casola and Koralewski 2018). In collaboration with other forest genomic groups across the country, we have deciphered the evolutionary dynamics of gene families in other conifer genomes (Neale et al. 2017). Finally, we have investigated the interplay between genome size evolution and recombination in conifers and other plants (Cossu, Casola et al. 2018), and the evolutionary origin of the Penelope family of transposable elements in conifers (Lin et al. 2018).