Keith Adams

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Research Interest

My research interests intersect among molecular genetics, genomics, and molecular evolution. My lab’s research is in the areas of genome evolution, molecular evolution, and gene expression – transcriptomics. We study how gene expression patterns, regulation, alternative splicing, and functions evolve. We focus on genes duplicated by whole genome duplication (polyploidy) and other duplication mechanisms at different evolutionary time scales.  We use molecular techniques and bioinformatics analyses of large sequence and expression data sets (RNA-seq – Illumina and PacBio) to test hypotheses and answer questions.

Some of the major questions that we study include:

– How do duplicated genes change in expression patterns and alternative splicing patterns?

– How do duplicated genes change in functions and in subcellular localizations?

– How does gene expression and alternative splicing change upon allopolyploidy, as well as over evolutionary time in a polyploid plant?

– How does duplicate gene expression vary by organ/tissue type and developmental stage and what impacts does that have on gene retention and function?

– How is duplicate gene expression and alternative splicing affected by abiotic (environmental) stress and biotic (pathogen) stress conditions?

– How extensive are copy number variants (CNVs) in plant genomes and what are their effects on gene expression?

To answer those questions we have been studying polyploid Brassica napus (canola) along with its diploid progenitors B. rapa and B. oleracea. We use Arabidopsis thaliana and other flowering plants for questions about the longer-term fates of duplicated genes. We use Populus trichocarpa (cottonwood) for questions about copy number variants and introgression. In addition, we have studied alternative splicing in Cannabis sativa RNA-seq data sets.  New directions for the lab include studies of nuclear architecture (TADs – topologically associating domains; A and B compartments), as well as experimental studies of polyploids using two species of duckweed as experimental systems.

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Selected Publications

De Jong G and Adams KL. 2023. Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors. Plant Journal,114:142-158. https://doi.org/10.1111/tpj.16127

Severson TF and Adams KL. 2022. Transcriptome-wide characterization of alternative splicing in five drug-type cultivars of Cannabis sativa. Botany: https://doi.org/10.1139/cjb-2022-0099

Cardoso-Silva CB, Aono AH, Mancini MC, Sforça DA, da Silva CC, Pinto LR, Adams KL, de Souza AP. 2022. Taxonomically Restricted Genes are Associated with Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.). Frontiers in Plant Science, 13: 923069.

Šola K., Dean GH, Li Y, Lohmann J, Movahedan M, Gilchrist EJ, Adams KL, Haughn GW. 2021. Expression Patterns and Functional Characterisation of Arabidopsis GALACTOSE OXIDASE-LIKE (GOXL) Genes Suggest Specialised Roles for Galactose Oxidases in Plants. Plant and Cell Physiology 62: 1927-1943.

Lee J.S. and Adams KL. 2020. Global insights into duplicated gene expression and alternative splicing in polyploid Brassica napus under heat, cold, and drought stress. Plant Genome 13: e20057.

Nitta Y., Qiu Y, Yaghmaiean H, Zhang Q, Huang J., Adams KL, and Zhang Y. 2020. MEKK2 inhibits activation of MAP kinases in Arabidopsis. Plant Journal 103: 705-714.

Qiu Y, Tay YV, Ruan Y and Adams KL. 2020. Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization. New Phytologist 225: 1011-1022. 

Yu K, Feng M, Yang G, Sun L, Qin Z, Cao J, Wen J, Li H, Zhou Y, Chen X, Huiru P, Yao Y, Hu Z, Guo W, Sun Q, Ni Z, Adams KL, and Xin M. 2020. Changes in Alternative Splicing in Response to Polyploidization and Domestication in Wheat. Plant Physiology 184: 1955-1968.

Qiu Y, Liu S-L, and Adams KL. 2017. Concerted divergence after gene duplication in polycomb repressive complexes. Plant Physiology, 174: 1192-1204.

Arsovski AA, Pradinuk J, Guo X, Wang S, Adams KL. 2015. Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant Physiology169: 2982-2991.

Wang S and Adams KL. 2015. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis andBrassica. Genome Biology and Evolution, 7: 646–655.

Tack DC, Pitchers WR, and Adams KL. 2014. Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana. Genetics 198:1473-1481.

Liu S-L, Pan A, and Adams KL. 2014. Protein subcellular relocalization of duplicated genes in Arabidopsis. Genome Biology and Evolution 6: 2501-2515.

Qiu Y, Filipenko S, Darracq A, and Adams KL. 2014. Expression of a transferred nuclear gene in a mitochondrial genome. Current Plant Biology 1: 68-72.

Chalhoub B, Denoeud F … Adams KL (author #72 out of 82). 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345: 950-953. Leader of a working group.

Qiu Y, Liu S-L, and Adams KL. 2014. Frequent changes in expression patterns and accelerated sequence evolution of duplicated imprinted genes in Arabidopsis. Genome Biology and Evolution, 6:1830–1842.

Adams KL. 2013. Genomic clues to the ancestral flowering plant. Science 342: 1456-1457

Darracq A, and Adams KL. 2013. Features of evolutionarily conserved alternative splicing events between Brassica and Arabidopsis. New Phytologist 199: 252-263. 

De Smet R, Adams KL, Vandepoele K, Van Montagu, MCE, Maere S, and Van de Peer Y. 2013. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. PNAS 110: 2898-2903.

Bell G, Kane N, Rieseberg LH, and Adams KL. 2013. RNA-Seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biology and Evolution 5:1309-1323.

Adams KL and Wendel JF. 2013. Dynamics of Duplicated Gene Expression in Polyploid Cotton. In Polyploid and Hybrid Genomics (Z. J. Chen and J. A. Birchler, Eds). John Wiley & Sons, Inc., pp. 187-194.

Lai Z, Kane N, et al. 2012. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany, 99: 209-218.

Zhou R, Moshgabadi N, and Adams KL. 2011. Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids. PNAS, 108: 16122-16127.

Liu S-L, Baute G, and Adams KL. 2011. Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biology and Evolution 3: 1419-1436.

Dong S, and Adams KL. 2011. Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids. New Phytologist, 190: 1045–1057.

Liu S-L, and Adams KL. 2010. Dramatic change in function and expression pattern of a gene duplicated by polyploidy created a paternal effect gene in the Brassicaceae. Molecular Biology and Evolution, 27: 2817–2828.

Scascitelli M, Cognet M, and Adams KL. 2010. An interspecific plant hybrid shows novel changes in parental alternative splice forms of genes for splicing factors. Genetics, 184: 975-983. Featured in Issue Highlights at the time of publication.

Zhang PG, Huang S, Pin A-L, and Adams KL. 2010. Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis. Molecular Biology and Evolution, 27: 1686-1697.

Additional papers that I published since 1998 can be found by doing a PubMed search at http://www.ncbi.nlm.nih.gov/sites/entrez