Abstract Detail

Seed-free Plants at the Genomic Scale

Der, Joshua P. [1], Koppers, Nils [2], Simenc, Mathew [1], Cheng, Shifeng [3], Liu, Xin [3], Wong, Gane Ka-Shu [4], Brautigam, Andrea [5], Schluepmann, Henriette [6], Pryer, Kathleen [7], Li, Fay-Wei [7].

The genome and annotation of Azolla filiculoides.

Azolla filiculoides is a fast growing aquatic fern capable of fixing nitrogen via symbiosis with cyanobacteria. Azolla has been used for centuries as a biofertilizer in cultivation with rice and has potential for use in phytoremediation of contaminated water, as a nitrogen-rich animal feedstock, and in the generation of alternative biofuels. A heterosporous fern with a small genome size, we have sequenced and annotated the nuclear genome of Azolla to bridge an important gap in genome information in land plants. We used a whole genome shotgun approach using high-coverage PacBio long read sequencing data, combined with extensive transcriptome support. Transposons and other repetitive sequences were extensively annotated using a multifaceted approach. Protein coding genes were annotated using the MAKER-P pipeline. I will provide an overview of our assembly, the repeat content and gene annotations, and will describe some of the ongoing comparative and functional analyses of the genome.

1 - California State University, Fullerton, Biological Science, Fullerton, CA, USA
2 - Heinrich Heine Universität Düsseldorf, Dusseldorf, Germany
3 - BGI-Shenzhen, Shenzhen, China
4 - University of Alberta, Department of Biological Sciences, CW405, Biological Sciences Bldg. , Edmonton, AB, AB T6G 2E9, Canada
5 - Leibniz-Institute of Plant Genetics and Crop Plant Research, Stadt Seeland, Germany
6 - Utrecht University, Utrecht, Netherlands
7 - Duke University, Durham, NC, USA

Keywords:
fern
genome
transposon
de novo assembly
Transcriptome
heterospory
evolution.

Presentation Type: Colloquium Presentations
Session: C4, Seed Free Plants at the Genomic Scale
Location: Chatham Ballroom - C/Savannah International Trade and Convention Center
Date: Wednesday, August 3rd, 2016
Time: 5:00 PM
Number: C4015
Abstract ID:830
Candidate for Awards:None