BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session


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9
Comparative Genomics

Room: Salon 3, Marriott Hotel

10:50 - 12:40

Moderator: Guojie Zhang, BGI-Shenzhen & University of Copenhagen



9.1  11:00  CRISPR and the functional genomics of crustaceans and butterflies - two crucibles of morphological diversification. Martin A*, The George Washington University

Exploring the generative mechanisms of morphological diversification requires a routine manipulation of genomes in a comparative context. However, beyond traditional model organisms, few organisms permit this research program to date. The recent CRISPR revolution has clearly changed this ordeal. Here, I present how current work using CRISPR mutagenesis has allowed to decipher developmental mechanisms that may have driven the diversification of two spectacular examples of morphological systems: the specialized limbs of crustaceans, and the color wing patterns of butterflies. In a model of crustacean development, I generated CRISPR-induced gene knock-outs for 7 Hox genes, which resulted in drastic re-organisations of the antero-posterior limb type sequence of evolutionary relevance. I also demonstrate the incorporation of a green fluorescent molecule using a scarless homologous-repair strategy in this animal. In butterflies, CRISPR genome editing can be routinely performed to induce wing both pattern and color modifications at high-efficiency. I notably describe the phenotypic effects of WntA in 5 species, and illustrate how this signaling molecule has been essential for both pattern formation and exploration fo the morphospace on the butterfly wing. I will discuss the potential of CRISPR to explore previously inaccessible questions in comparative functional genomics.


9.2  11:20  The origin and evolution of RNA editing in metazoans. Li Q*, BGI-Shenzhen; Zhang P, BGI-Shenzhen; Yu H, BGI-Shenzhen; Zhan X, BGI-Shenzhen; Zhou Y, BGI-Shenzhen; Martin M, UC Berkeley; Meritxell AS, Pompeu Fabra University; Garcia L, University of Copenhagen; Gilbert MT, University of Copenhagen; Zhang G, BGI-Shenzhen

The central dogma of molecular biology emphasizes how genetic information passes faithfully from DNA, to RNA, to proteins. However, this dogma has recently been challenged by the phenomenon of RNA editing, which is a post-transcriptional-processing mechanism that can recode RNA sequences by insertion, deletion or substitution of specific nucleotides while producing transcripts that are not encoded in the genome. In metazoa, the most prevalent form of RNA editing is the deamination of adenosine (A) to inosine (I), which particularly affects neural function. Although it is now widely acknowledged that A-to-I RNA editing provides an important source of additional genetic diversity that might contribute considerably to animal phenotypic plasticity, fundamental questions relating to the origin and evolution of RNA editing in metazoans remain to be explored. Our current knowledge of metazoan RNA editing is restricted largely to a few model organisms such as humans, mice, fruit flies and C. elegans. A fundamental understanding of how RNA editing emerged in our branch of life, and how its regulatory targets changed as metazoan lineages evolved, is essential for obtaining a thorough grasp of the cellular functions of RNA editing for animal functionality and human health. We therefore systemically investigate the prevalence of RNA editing across 22 selected species encompassing the key transitions in metazoan evolution, including four unicellular species which are the closest outgroups of metozoa and the most basal animals ctenophore and sponge. Our preliminary analyses provide some interesting insights into the origin and evolution of RNA editing in metazoans.


9.3  11:40  Comparative genomics of ant communication. McKenzie SK*, The Rockefeller University; Kronauer DJC, The Rockefeller University

Ants live in complex societies and require communication to coordinate behaviors among colony members. Ants primarily communicate via pheromones- chemical messages emitted from glands on the signaler and detected by the olfactory system of the receiver. Several large gene families are known to be involved in insect olfaction, however the specific genetic architecture of social insect pheromone perception has eluded researchers. We have used comparative genomics, transcriptomics, evolutionary analyses, functional genetics, and neuroanatomy to elucidate the molecular basis of pheromone perception in the ants. All of these lines of evidence implicate one particularly interesting clade of genes in the odorant receptor (OR) family- the 9e-alpha ORs. This clade underwent massive expansion in the ancestors of ants, expanding from one or a few copies in the most recent common ancestor of the ants and bees to 60-180 copies in extant ants. Transcriptomic and neuroanatomical data suggest that these genes are expressed in hydrocarbon-sensitive sensilla and may therefore function in perception of pheromones used in colony, species, and caste recognition as well as fertility signaling and reproductive division of labor. Corresponding changes can be seen in the ant olfactory neuroanatomy, and the next frontier will be to learn about the evolution and genetic basis of ant olfactory neurodevelopment.


9.4  12:00  Discovering the genomic basis underlying species� phenotypic differences. Hiller M*, Max Planck Institute

The rapidly growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: What is the genomic basis that underlies phenotypic differences between species? Previously, we developed a macroevolutionary association method called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes with changes in independent lineages. First, I will present a new Forward Genomics method that controls for the phylogenetic relatedness between the species of interest and takes differences in their evolutionary rates into account. We have applied this approach to discover genomic loci that underlie the degeneration of the visual system in independent blind subterranean mammals. This genome-wide screen identifies many genes related to eye development and the perception of light as well as loci associated with eye diseases in human. Furthermore, Forward Genomics identifies divergence in many regulatory regions that are also enriched for lens-related functions and overlap functional enhancers in these tissues. Second, I will present our work on detecting differences in the gene repertoire between species. We have developed a genomics pipeline to accurately detect losses of ancestral coding genes. Using a multiple genome alignment of 145 vertebrates, we applied this approach to obtain catalogs of inactivated genes of 70 placental mammals. These catalogs provide the basis to systematically explore how gene loss affects phenotypic change and I will present new associations to physiological and morphological adaptations in mammals. These comparative genomics approaches can be applied to predict the genomic basis underlying other phenotypic differences in mammals and other clades. Understanding which genomic changes underlie phenotypic changes will contribute our understanding of how nature's phenotypic diversity has evolved.


9.5  12:20  Comparative genomics, multigene families, and physiological evolution. Storz J, University of Nebraska

When integrated with experimental studies of protein expression and protein function, comparative genomic studies of multigene families can provide important insights into mechanisms of physiological evolution. Here I describe comparative genomic analyses of the vertebrate globin gene family that have led to surprising discoveries regarding the evolution of blood-oxygen transport and the developmental regulation of hemoglobin synthesis. For example, using genomic sequence data for birds and nonavian reptiles, we documented physiological consequences of recurrent gene losses by integrating analyses of gene turnover in the globin gene family with measures of hemoglobin isoform expression and experimental measures of isoform-specific oxygenation properties. We also discuss the role of genomic data in facilitating microevolutionary studies of physiological adaptation




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