Shawn Starkenburg, Ph.D. is the Group Leader for Genomics and Bioanalytics within the Bioscience Division at Los Alamos National Laboratory (LANL). His Group is focused on deployment and advancement of genome sequencing technologies and analysis tools to tackle a plethora of bioenergy, climate, biosurveillance and biosecurity challenges.
Shawn has led over 25 genome projects throughout his career and continues to lead and support several DOE sponsored programs that utilizes genomic, functional genomic, metagenomic, and multi-omics information to characterize and improve the performance of algal feedstocks. Most recently, Shawn is leading a multi-disciplinary program at LANL to re-envision what it means to ‘sequence’ a genome by constructing 4-dimensional genome analysis tools to decipher chromosome-level genome structure-function relationships.
TITLE: Assembly and analysis of the 100% complete genome and methylome of Scenedesmus obliquus UTEX 3031
Authors: Shawn R. Starkenburg1*, Thomas C. Biondi1, Colin P.S. Kruse1, Samuel I. Koehler1, Taehyung Kwon1, Yuliya Kunde1, Cheryl D. Gleasner1, Jim Umen3, Juergen Polle2,, Blake T. Hovde1, Erik R. Hanschen1
Los Alamos National Laboratory, Bioscience Division, United States of America
Department of Biology, Brooklyn College of the City University of New York, Brooklyn, NY 11210, USA
Danforth Plant Science Center
ABSTRACT: Scenedesmus has been a model organism for fundamental photosynthesis research and was instrumental in the discovery of the Calvin Cycle. Nevertheless, we still lack detailed knowledge of the Scenedesmus sexual cycle and its genetic and functional diversity, limiting the potential for genetic engineering and breeding to further improve and identify industrially relevant traits. To accelerate domestication and trait mapping, we initiated a genome finishing project to fully assemble the genome of Scenedesmus obliquus. In this talk, I will present the methodology and analysis of a 100% complete, gapless, phased, telomere-to-telomere ‘diploid’ genome assembly of S. obliquus DOE0152z (UTEX3031). Comparative analysis of the resolved chromosome pairs revealed large genomic rearrangement between haplotypes, suggesting the haplotypes are actively evolving specialized functions. Furthermore, new evidence supporting sexual recombination was found, candidates for sex chromosomes were identified, and CpG methylation information was used to inform differential gene activation between haplotypes. Additional analysis of these and other fully phased and complete non-haploid genomes will contribute to our understanding of genetic diversity, structural variation, and enable the ability to decipher the full range of genome variation/functional diversity that have evolved in single celled algae.