Eric H Lyons
Publications
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
Abstract:
The flowering plants, also known as the angiosperms, are the most diverse group of plants. The basal flowering plant lineages diverged at very early stage in flowering plant evolution, followed by rapid diversification of the magnoliids, the eudicots and the monocots. Genomic comparisons within and across plant lineages help identify the critical events that occurred during the evolution of major groups of flowering plants. In this chapter, we first review the basic concepts and analytic methods for studying ancient polyploidy-a prominent feature during plant evolution. We then highlight recent progress on the dating of deep polyploidies in the eudicot and monocot lineage, respectively. With a clear knowledge of genomic history, we can effectively compare the eudicot genomes to monocot genomes, which promise to bridge functional equivalence between genes of the two well-studied groups. Finally, we deduce the composition and structure of the 'ancestral genome' on the basis of the arrangements of genes in the extant species. The in silico reconstruction of the ancestral genome provides an integrated framework under which conservation of modern plant genomes can be systematically studied. © 2014 Elsevier Ltd.
PMID: 18269575;Abstract:
There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text. © 2008 The Authors.
Chaining is a major problem in constructing gene families.
PMID: 18836034;PMCID: PMC2593585;Abstract:
Previous to this work, typical genes were thought to move from one position to another infrequently. On the contrary, we now estimate that between one-fourth and three-fourths of the genes in Arabidopsis transposed in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited a median frequency of 5% transposed genes. In contrast, other gene families were composed largely of transposed genes: NB-LRR disease-resistance genes, genes encoding MADS-box and B3 transcription factors, and genes encoding F-box proteins. A unique method involving transposition-rich regions of genome allowed us to obtain an indirect estimate of the positional stability of the average gene. The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition. ©2008 by Cold Spring Harbor Laboratory Press.