Using Fluorescence In Situ Hybridization (FISH) in the Evolutionary Reference Plant Amborella to Verify Genome Sequence Assembly and Generate a Karyotype

Lan, Tianying

Tianying Lan , University at Buffalo, Amherst, NY

Andre Chanderbali , University of Florida, Gainesville, FL

Tien-Hao Chang , Department of Biological Sciences, University at Buffalo, NY

Alex Powell , University of Florida, Gainesville, FL

Nestor Santiago , Florida Museum of Natural History, Gainesville, FL

Greg Traub , Florida Museum of Natural History, Gainesville, FL

Nico Cellinese , ncellinese@flmnh.ufl.edu, Gainesville, FL

Srikar Chamala , University of Florida, Gainesville, FL

Jamie Estill , University of Georgia, Athens, GA

Seunghee Lee , Arizona Genomics Institute, University of Arizona, Tucson, AZ

Paula Ralph , Penn State University

Lynn P. Tomsho , Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, PA

Brandon Walts , University of Florida, Gainesville, FL

Yeisoo Yu , Arizona Genomics Institute, University of Arizona, Tucson, AZ

Joshua P. Der , Penn State University, University Park, PA

Claude dePamphilis , Penn State University, University Park, PA

Jim Leebens-Mack , University of Georgia, Athens, GA

Hong Ma , The Pennsylvania State University, University Park, PA

Jeff Palmer , University of Indiana

Steve Rounsley , University of Arizona/Dow Agrosciences, Indianapolis, IN

Stephan C. Schuster , Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, PA

Susan Wessler , University of California, Riverside

Rod A. Wing , Arizona Genomics Institute, University of Arizona, Tucson, AZ

Douglas E. Soltis , University of Florida, Gainesville, FL

Pamela S. Soltis , University of Florida, Gainesville, FL

Victor A. Albert , University at Buffalo, Buffalo, NY

The sister species to all extant angiosperms, Amborella trichopoda, occupies an evolutionary position that makes it a crucial reference for all genomic studies in plant biology. Our complete genome sequence underway will help in understanding the evolution of key angiosperm traits and provide a baseline to examine genome organization throughout angiosperms. We have developed a Fluorescence In Situ Hybridization (FISH) system for locating physically mapped BACs directly on Amborella’s chromosomes. Probes for nuclear DNA localization were selected on the basis of weak to moderate Southern hybridization signals using an Amborella nDNA probe against a panel of BACs. Three main types of FISH signals were found: dispersed/GISH-like signals, centromeric signals, and strong single-locus signals marking specific chromosome arms. BACs with characteristics of the latter two categories were used to construct a partial karyotype that to-date identifies 6 out of 13 chromosome pairs. To assess the quality of our genome assembly, FISH was used to localize BACs mapped to different ends of in silico determined scaffolds. Finally, FISH using mtDNA and cpDNA BAC probes was applied to assess the possibility of large inserts of organellar DNA into the Amborella nuclear genome. We have also constructed a chromosome module for the TOLKIN (Tree of Life Knowledge and Information Network) web-based application, which provides informatics support for phylodiversity and biodiversity research projects.

P0236 Using Fluorescence In Situ Hybridization (FISH) in the Evolutionary Reference Plant Amborella to Verify Genome Sequence Assembly and Generate a Karyotype