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Laboratory of Keith Adams

Gossypium tomentosum

Research Description

My lab's research is in the areas of molecular and genomic evolution. We study how gene structures, sequences, expression patterns and regulation evolve. We focus on gene and genome duplications (polyploidy) and the expression of duplicated genes.

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). Polyploidy has been especially common in flowering plants, with most plants being ancient polyploids and at least 50% of angiosperm species having experienced an episode of genome doubling in their recent evolutionary history. 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 interactions between genomes, considerable and rapid genomic reorganization in some plants, and changes in gene expression including gene silencing.

My lab is studying the consequences of polyploidy on the expression, silencing, and function of duplicate genes, including the immediate effects and the evolutionary consequences. Multiple genotypes of polyploid cotton (Gossypium) are used as a study system, including natural polyploids formed 1-2 million years ago and synthetic polyploids. Previously I surveyed ~2000 genes and studied in detail over 50 gene pairs that were duplicated by polyploidy in allotetraploid cotton (Adams et al., 2003; 2004). I found numerous cases of duplicate gene silencing, some of which were evident by the first generation after polyploidy. Surprisingly I found 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. Most significantly, silencing of the two duplicates of some genes is bi-directional in 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 shows that expression patterns can be partitioned between two gene duplicates; the process is suggestive of sub-functionalization and that both duplicates will be retained. I also showed that bi-directional, organ-specific silencing of parental gene copies can occur in response to hybridization without genome doubling, as seen in F1 diploid Gossypium hybrids (Adams et al., 2005).

Current research in my lab is aimed to study duplicate gene expression patterns and mechanisms of duplicate gene silencing in polyploids. We are studying the organ-specific expression patterns of genes duplicated by polyploidy and what types of duplicated genes are silenced or display altered expression patterns in polyploids. One project is focusing on a gene that has undergone subfunctionalization in polyploid cotton (Adams et al., 2003). Another project is exploring the coordination of nuclear and organellar gene expression in cotton polyploids by testing the hypothesis that there are alterations in expression levels and silencing of nuclear genes for organellar proteins in allopolyploids. We are examining the effects of environmental stress conditions on duplicate gene expression to determine if stress alters gene expression levels. We are doing experiments to test hypotheses about what molecular mechanisms, including potential epigenetic mechanisms (such as DNA methylation and changes in histone modifications), cause duplicate gene silencing, especially silencing that is organ-specific.

In addition to studies of duplicate gene expression in polyploid cotton we are studying expression of genes that were duplicated by an ancient polyploidy event (25 - 40 mya) during the evolutionary history of the Arabidopsis and Brassica family (Brassicaceae).

A second area of research in the lab is to study interspecific hybridization and its effects on gene expression. It has become apparent from recent studies of allopolyploids that hybridization has a greater effect than chromosome doubling on gene expression. My lab is examining allelic expression patterns of a set of genes (~30) in interspecific F1 hybrids of Populus trichocarpa × P. deltoides that display strong hybrid vigor, to determine if one allele is expressed more highly than the other allele. For genes that show strong expression biases towards one allele we are examining expression patterns of neighboring genes on the chromosome to determine if expression is affected by position on the chromosome.

A third area of research in the lab is to study organellar genes that have been transferred to the nucleus. The transfer of organelle 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. We have identified several transferred genes in the nuclear genome of Populus and studied their expression and sequence evolution. One gene shows co-expression of the nuclear and mitochondrial copies. We are currently examining the structural and sequence evolution of genes that have been transferred to the nucleus in several flowering plant species.

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

Lab Personnel

Additional Publications

Please note: publications indexed by PubMed are displayed here. Listed below are papers not indexed by PubMed.

Adams KL, Wendel JF
Exploring the genomic mysteries of polyploidy in cotton
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 82: 573-581. 2004.

Adams KL, Cronn R, Percifield R, Wendel JF
Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing.
PROC NATL ACAD SCI USA 100 (8): 4649-54 APR 15 2003, Epub 2003 Mar 28.

Adams KL, Palmer JD
Evolution of mitochondrial gene content: gene loss and transfer to the nucleus
MOLECULAR PHYLOGENETICS AND EVOLUTION 29: 380-395. 2003.

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

Adams KL, Daley DO, Whelan J, Palmer JD
Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts.
PLANT CELL 14 (4): 931-43 APR 2002

Adams KL, Qiu YL, Stoutemyer M, Palmer JD
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 (15): 9905-12 JUL 23 2002, Epub 2002 Jul 15.

Adams KL, Ong HC, Palmer JD
Mitochondrial gene transfer in pieces: Fission of the ribosomal protein gene rpl2 and partial to complete transfers to the nucleus.
MOLECULAR BIOLOGY AND EVOLUTION 18 (12): 2289-97 Dec 2001

Adams KL, Rosenbleuth M, Qiu YL, Palmer JD
Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during flowering plant evolution.
GENETICS 158 (3): 1289-300 Jul 2001

Adams KL, Daley DO, Qiu YL, Whelan J, Palmer JD
Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants.
NATURE 408 (6810): 354-7 2000 Nov 16.

Links

University of British Columbia Botanical Garden and Centre for Plant Research UBC Botanical Garden and Centre for Plant Research UBC Centre for Plant Research is part of the University of British Columbia Botanical Garden and Centre for Plant Research.

UBC Faculty of Land and Food Systems UBC Botanical Garden and Centre for Plant Research is a department of the University of British Columbia Faculty of Land and Food Systems.

University of British Columbia University of British Columbia The University of British Columbia is an internationally recognized educational institution based in Vancouver, Canada.