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Yin-Long Qiu
Assistant Professor
yqiu@bio.umass.edu
Education
B.S., Nanjing Agricultural University, Nanjing, Jiangsu, China, 1984
Ph.D., University of North Carolina, Chapel Hill, 1993
Postdoctoral
1994-1997, Indiana University
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Research Interests
The research in my lab lies at the interface of organismal phylogenetics and evolutionary genomics. We employ molecular genetic techniques and bioinformatic tools to investigate evolution of genes and genomes, and use this information to infer phylogenetic history of organisms, in particular basal angiosperms and basal land plants.
Phylogeny of Basal Angiosperms
Tens of millions of base pairs in the cells hold many of life's secrets, including where they come from. Evolutionary biologists have been using information stored in these secret codes to understand how the life originated and what are the relationships among all of the living things on the earth. In my lab, we have been analyzing DNA sequences of several genes located in mitochondrial, chloroplast, and nuclear genomes from a large number of basal angiosperms, to reconstruct the early diversification patterns of angiosperms, which are the most dominant group in the modern earth's vegetation. We identified an assemblage of taxa called ANITA (Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya) as the earliest living angiosperms. Through an international collaboration with two other labs, we are currently amassing an even larger data set, nine genes in total and approximately 16 kb from ~100 species, to resolve the remaining issues in basal angiosperm phylogeny, in particular, the origins of eudicots and monocots. In addition, with so much sequence data collected across all three plant genomes and from a diverse and dense taxonomic sampling of basal angiosperms, many of which exhibit disjunct distribution patterns with well dated geological separation, we are exploring the crude molecular clocks to estimate the time of origin of angiosperms.
Phylogeny of Pre- and Early Land Plants and Organellar Genome Evolution
The emergence of land plants (embryophytes) approximately 480 million years ago was one of the major events in the history of life on earth, which led to major changes in the earth's environment (e.g. reduced atmospheric CO2 level and consequently lowered earth's surface temperature), initiated development of the entire terrestrial ecosystem, and set the stage for evolution of other terrestrial organisms, including ourselves. Yet, what represents the algal ancestor of land plants and how the extant basal land plant lineages (i.e. liverworts, mosses, hornworts, lycopods, Equisetum, Psilotaceae, ferns, and seed plant) are related to each other remain as unresolved issues. Here, we take a different approach than in the case of angiosperms to attack the problem - to search for rare events of genome structural evolution that occur at a larger scale than single nucleotide substitutions, such as gains and losses of introns, changes of intron splicing patterns, formations and disruptions of gene clusters, and losses of genes. This strategy takes advantage of the unique evolutionary histories of the chloroplast and mitochondrial genomes, which experienced dramatic structural changes during pre- and early land plant evolution. Previously, we have identified three introns that are present (with losses) in all land plant lineages but entirely absent in liverworts and green and red algae. Thus, these data suggest that liverworts had already diverged when the introns were gained in the common ancestor of all other land plants, and consequently they represent the earliest land plants. Currently, we are sequencing the entire mitochondrial genome from the hornwort Anthoceros agrestis Paton to identify whether many of the angiosperm specific introns are present at this early stage of land plant evolution. We are also interested in knowing whether many of the short repeat sequences (possibly related to retrotransposons) commonly found in angiosperm mitochondrial genomes are present in the hornwort genome. These short repeat sequences probably served as substrates for homologous recombination, which resulted in rapid genomic rearrangement and dramatic size variation in the mitochondrial genome evolution in land plants, something very unique in mitochondrial evolution throughout the entire eukaryotic kingdom. We are also trying to identify phylogenetic distribution patterns of the set of introns found in Marchantia mitochondrial genome. On the chloroplast side, we are investigating distribution of several gene clusters and their intron content in several species that represent major charophyte lineages. We hope that the data gathered here, in synergy with large scale DNA sequence analyses, will clarify diversification patterns before and after the emergence of land plants.
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Representative Publications
Qiu, Y.-L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen, V. Savolainen, & M. W. Chase. 2000. Phylogeny of basal angiosperms: analyses of five genes from three genomes. International Journal of Plant Science (in press).
Qiu, Y.-L. & J. Lee. 2000. Transition to a land flora: a molecular phylogenetic perspective. Journal of Phycology (in press).
von Balthazar, M., P. K. Endress, & Y.-L. Qiu. 2000. Molecular phylogenetics of Buxaceae based on nuclear ITS and plastid ndhF sequences. International Journal of Plant Science (in press).
Savolainen, V., M. W. Chase, S. B. Hoot, C. M. Morton, D. E. Soltis, C. Bayer, M. F. Fay, A. Y. de Bruijn, S. Sullivan, & Y.-L. Qiu. 2000. Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbcL gene sequences. Systematic Biology (in press).
Besendahl, A., Y.-L. Qiu, J. Lee, J. D. Palmer, & D. Bhattacharya. 2000. The endosymbiotic origin and vertical evolution of the plastid tRNALeu group I intron. Current Genetics 37: 12-23.
Qiu, Y.-L., J. Lee, F. Bernasconi-Quadroni, D. E. Soltis, P. S. Soltis, M. Zanis, E. A. Zimmer, Z. Chen, V. Savolainen, & M. W. Chase. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404-407.
Qiu, Y.-L. & J. D. Palmer. 1999. Phylogeny of basal land plants: insights from genes and genomes. Trends in Plant Science 4: 26-30.
Cho, Y., Y.-L. Qiu, P. Kuhlman, & J. D. Palmer. 1998. Explosive invasion of plant mitochondria by a group I intron. Proceedings of the National Academy of Sciences, USA 95: 14244-14249.
Qiu, Y.-L., M. W. Chase, S. Hoot, E. Conti, P. R. Crane, K. J. Sytsma, & C. R. Parks. 1998. Phylogenetics of the Hamamelidae and their allies: parsimony analyses of nucleotide sequences of the plastid gene rbcL. International Journal of Plant Sciences 159: 881-890.
Qiu, Y.-L., Y. Cho, J. C. Cox, & J. D. Palmer. 1998. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature 394: 671-674.
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