title: The First Complete Plastid Genome from Joinvilleaceae (J. ascendens; Poales) Shows Unique and Unpredicted Rearrangements.
abstract: Joinvilleaceae is a family of tropical grass-like monocots that comprises only the genus Joinvillea. Previous studies have placed Joinvilleaceae in close phylogenetic proximity to the well-studied grass family. A full plastome sequence was determined and characterized for J. ascendens. The plastome was sequenced with next generation methods, fully assembled de novo and annotated. The assembly revealed two novel inversions specific to the Joinvilleaceae lineage and at least one novel plastid inversion in the Joinvilleaceae-Poaceae lineage. Two previously documented inversions in the Joinvilleaceae-Poaceae lineage and one previously documented inversion in the Poaceae lineage were also verified. Inversion events were identified visually and verified computationally by simulation mutations. Additionally, the loss and subsequent degradation of the accD gene in order Poales was explored extensively in Poaceae and J. ascendens. The two novel inversions along with changes in gene composition between families better delimited lineages in the Poales. The presence of large inversions and subsequent reversals in this small family suggested a high potential for large-scale rearrangements to occur in plastid genomes.
authors.affiliation: Center for Data Intensive Sciences, University of Chicago, 5454 South Shore Dr., Chicago, IL 60615, United States of America.|Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America.
authors.forename: William P
authors.identifier: http://orcid.org/0000-0002-4069-8517
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America.
authors.forename: Sean V
authors.initials: SV
authors.lastname: Burke
authors.affiliation: Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America.
authors.forename: Wesley D
authors.initials: WD
authors.lastname: Swingley
authors.affiliation: Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall