Research Interests:
My research interests intersect between molecular genetics and evolutionary biology. My lab’s research includes aspects of molecular evolution, genome evolution, evolution of gene regulation and splicing patterns, gene expression and epigenetics, and organellar genome evolution. We study how gene structures, expression, splicing patterns, and regulation evolve. We use molecular techniques and bioinformatics analyses to test hypotheses and answer questions. Projects center around genes duplicated by polyploidy, other types of duplicated genes, allelic expression in interspecific hybrids, and alternative intron splicing.

Expression, silencing, and alternative splicing of genes duplicated by polyploidy

Most eukaryotes have a large number of duplicated genes, many of which appear to have arisen from one or more cycles of genome doubling. Polyploidy has been especially common in flowering plants, with most plants being ancient polyploids that have been diploidized, followed by recent rounds of polyploidy in many plant species. Allopolyploidy is a prominent mode of speciation in angiosperms. Polyploids can display novel phenotypes, leading to morphological evolution, and hybrid vigor is often observed. Polyploidy is a dynamic process that is associated with considerable and rapid genomic reorganization in some plants and changes in gene expression including gene silencing.

We are studying the consequences of polyploidy on expression, silencing, and alternative splicing of duplicate genes, using polyploid cotton and canola as study systems. We determined that silencing of duplicated genes can be organ-specific and developmentally regulated, and that expression levels between the two copies can vary widely by organ type and developmental stage (Adams et al., 2003; Liu and Adams, 2007). Expression of the two duplicates can be partitioned between different organs (i.e., one copy is silenced in some organs and the other copy is silenced in other organs). Such reciprocal silencing of duplicated genes is indicative of qualitative subfunctionalization and suggests that both duplicates will be retained. We have been studying the effects of environmental stress on expression of genes duplicated by polyploidy. We discovered that expression of a duplicated gene pair can vary extensively in response to various abiotic stresses and that reciprocal silencing of duplicated genes can occur in response to two different stresses indicating subfunctionalization in response to stress (Liu and Adams, 2007). Current research is aimed to further understand the effects of environmental stress on expression of duplicated genes. In addition we are studying alternative splicing patterns in duplicated genes in canola to examine the effects of gene duplication on alternative splicing.

Expression of genes duplicated by ancient polyploidy events: To examine the long term evolutionary effects of whole genome duplication on gene expression we have been studying genes duplicated by an ancient polyploidy event (25 - 40 mya) during the evolutionary history of Arabidopsis and Brassica (the Brassicaceae family). We found that the duplicated genes show extensive divergence in alternative splicing patterns including organ and abiotic stress-specific differences (Zhang et al, submitted). Also we have been analyzing expression patterns of the duplicated genes using microarray data sets including a large developmental data set and stress data sets. Another project is a study of structural evolution of the gene pairs.

Effects of interspecific hybridization on gene expression

It has become apparent from recent studies of allopolyploids that hybridization between two species has a greater effect than chromosome doubling on gene expression. We have examined allelic expression patterns of a set of 30 genes in interspecific F1 hybrids of Populus trichocarpa x P. deltoides that display strong hybrid vigor (Zhuang and Adams, 2007). A large majority of genes showed unequal allelic expression, some of which appears to be caused by inter-species hybridization. The paternal copy of one gene was silenced in the hybrid. Also we have been studying alternative splicing patterns of genes in the hybrid compared with its parents.

Other research areas

Another line of research in the lab is a study of gene regulation in native vs. invasive populations of Canada thistle. Genes whose expression is up or down regulated in the native vs. invasive populations are being studied to infer the mode of regulation (cis or trans) that is responsible. This project is part of a larger collaborative project with Loren Rieseberg, Sally Otto, and Jeannette Whitton.

Transfers of mitochondrial genes to the nucleus: The transfer of mitochondrial genes to the nucleus is a duplicative process because the transferred nuclear copy must become functional before the organellar copy is deleted. A small number of cases exist where a gene for the same organellar protein is present and expressed in both the organelle and nucleus representing a special type (trans-compartmental) of gene duplication, for example in Choi et al. (2006). We performed comparative analyses of gene structures and sequence evolution of 77 genes transferred to the nucleus in various angiosperms to reveal the frequency and origins of numerous chimeric transferred genes and to analyze sequence evolution of the transferred genes (Liu et al. 2009). Also we have studied sequence and expression evolution in organellar rps13 genes in which the product of a duplicated nuclear gene is targeted to mitochondria (Liu and Adams, 2008). We are not currently pursuing projects on this topic.

I am interested in advising new graduate students. Contact me at the email address listed at the top of this page.

Zhang P, Huang S, Pin A-L, and Adams KL. 2009. Extensive divergence in alternative splicing patterns following gene and genome duplication. Submitted.

Liu S-L*, Zhuang Y*, Zhang P, and Adams KL. 2009. Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus. Molecular Biology and Evolution, 26: 875-891. *equal contributions

Liu S-L and Adams KL 2008. Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evolutionary Biology 8: 25 (15 pages).

Adams KL 2008. Insights into the evolution of duplicated gene expression in polyploids from Gossypium. Botany 86: 827-834.

Liu Z and Adams KL 2007. Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Current Biology 17: 1669-1674.
Dispatches article about the paper: Hegarty, M., and Hiscock, S. Polyploidy: Doubling up for evolutionary success. Current Biology, 17: R927-929.

Adams KL 2007. Evolution of duplicate gene expression in polyploid and hybrid plants. Journal of Heredity, 98: 136-141.

Zhuang Y and Adams KL 2007. Extensive allelic variation in gene expression in Populus F1 hybrids. Genetics 177: 1987-1996.

Choi C, Liu Z, and Adams KL 2006. Evolutionary transfers of mitochondrial genes to the nucleus in the Populus lineage and co-expression of nuclear and mitochondrial Sdh4 genes. New Phytologist 172: 429-439.
Article highlighting the paper: Bonen L. 2006. Mitochondrial genes leave home. New Phytologist 172: 379-381.

Adams KL and Wendel JF. 2005. Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8: 135-141.

Adams KL and Wendel JF. 2005. Allele-specific, bi-directional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 171: 2139-2142.

Adams KL and Wendel JF 2005. Novel patterns of gene expression in polyploid plants. Trends in Genetics 21: 539-543.

Selected publications: 2004 and earlier

Adams KL, Percifield, R., and Wendel JF. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217–2226.

Adams KL, Cronn R, Percifield R, and Wendel JF. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100: 4649-4654.

Bergthorsson U., Adams KL, Thomason B, and Palmer JD. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197-201.

Adams KL, Qiu Y-L, Stoutemyer M, and Palmer, JD. 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. USA 99: 9905-9912.

Adams KL, Daley DO, Qiu YL, Whelan J, and Palmer JD. 2000. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408: 354-357.

Additional papers that I have published can be found by doing a PubMed search at http://www.ncbi.nlm.nih.gov/sites/entrez