Domestication and divergence of Saccharomyces cerevisiae beer yeasts

Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today's industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains

A Comparative Genomics Study of Human and Chimpanzee Evolution: Natural Selection, Function, and Disease

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 19-06-0

Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion

Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study

Computational studies of origins of life scenarios

Understanding the origins of life on Earth is one of the most intriguing problems facing science today. In the research presented here, we apply computational methods to explore origins of life scenarios. In particular, we focus on the origins of the genetic code and the intersection between geochemistry and a primordial ``biochemistry" in which mononucleotides could form short oligoucleotide chains. We also apply quantum chemical methods to a modern biochemical reaction, the charging of tRNA by an aminoacyl-tRNA synthetase, in order to shed light on the possible chemistry one may want to consider in problems relating to the origins of life. The question of how codons came to be associated with specific amino acids in the present form of the genetic code is one fundamental part of gaining insight into the origins of life. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated to the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by the PR experiments. We also investigate the possible roles of inorganic mineral surfaces in catalysis and stabilization of reactions essential for early forms of replicating systems that could have evolved into biochemical processes we know today. We study a proposed origins of life scenario involving the clay montmorillonite, as well as a generalized form of a charged surface, and their catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D- chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite. Finally, we shift our perspective on the problem of the origins of life, by considering a modern biological reaction which is essential to all forms of life today: the charging of tRNA with correct amino acids according to their anticodons. These reactions are performed by amino-acyl tRNA synthetases (AARSs), and are essential for enforcing the genetic code. While studies involving the PR and code optimality apply to a more error-prone epoch of early biology, possibly forming ``statistical proteins" whose sequence is determined probabilistically by a loose mechanism of assignment of amino acids based on (possibly) PR, the mechanisms that charge tRNA today are highly refined to charge only the correct amino acid to a tRNA, and are thus essential for the high-fidelity translation mechanism present in all living cells. To gain some insight into how the charging reaction may have come about, we apply quantum chemical methods to a problem of modern biology to gain a further understanding of the mechanisms behind biochemical reactions

The phylogeny of coleoid cephalopods inferred from molecular evolutionary analyses of the cytochrome c oxidase I, muscle actin, and cytoplasmic actin genes

Although the fossil record of early cephalopods is rich and demonstrates the dominance of the group in Paleozoic times, the mainly soft-bodied coleoids (Cephalopoda: Coleoidea) are poorly represented. Therefore, little is known of the evolutionary history of coleoids through paleontology and current classifications of the subclass are based primarily on the morphology of extant representatives. A molecular phylogenetic analysis of the Coleoidea was therefore warranted. Phylogenetic relationships within the Coleoidea were constructed using molecular sequence data from one mitochondrial and two nuclear genes: cytochrome c oxidase I (COI) and two unlinked actin genes (Actin I and Actin II, respectively). A 657 base-pair portion of the COI gene was examined for 55 coleoid taxa encompassing a broad spectrum of diversity in the subclass. The COI gene exhibited the most rapid evolutionary rate among the three genes examined. Eighty-two sequences from a 784 base-pair portion of three paralogous actin genes were obtained from 44 terminal taxa. The Actin I gene was highly conserved and provided information for determining deep-level relationships. The Actin II gene was intermediately conserved and exhibited a broad range of sequence divergence than the COI and Actin I genes. The evolution of the actin gene family in cephalopods was compared to that in other molluscs, protostomes, and deuterostomes. Analyses of actin gene family evolution provided evidence that the Actin I gene encodes a muscle-type of actin, and that the Actin II gene encodes a cytoplasmic actin. These analyses also supported at least two independent derivations of muscle-type actins during the evolution of the protostome lineage. The following conclusions were drawn from the results of phylogenetic analyses: (1) the cephalopod subclass Coleoidea is monophyletic; (2) the order Octopoda is monophyletic and is sister group to the monotypic order Vampyromorpha; (3) the Decapodiformes, consisting of the orders Teuthoidea and Sepioidea, is monophyletic; (4) the orders Teuthoidea and Sepioidea are polyphyletic; (5) the teuthoid suborders Myopsida and Oegopsida are monophyletic and polyphyletic, respectively; (6) the Myopsida and the oegopsid families Chtenopterygidae and Bathyteuthidae are more closely related to the sepioid families Spirulidae, Sepiidae, and Sepiolidae, than they are to other teuthoid groups