Wysocki William P, Burke Sean V, Swingley Wesley D, Duvall Melvin R
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.
PLoS One. 2016 Sep 22;11(9):e0163218. doi: 10.1371/journal.pone.0163218. eCollection 2016.
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.
沼金花科是一类热带草状单子叶植物科，仅包含沼金花属。先前的研究已将沼金花科置于与已充分研究的禾本科在系统发育上密切相关的位置。已测定并表征了上升沼金花的完整质体基因组序列。该质体基因组采用下一代方法进行测序，完全从头组装并注释。组装结果揭示了沼金花科谱系特有的两个新倒位以及沼金花科 - 禾本科谱系中至少一个新的质体倒位。沼金花科 - 禾本科谱系中两个先前记录的倒位以及禾本科谱系中一个先前记录的倒位也得到了验证。通过视觉识别倒位事件，并通过模拟突变进行计算验证。此外，在禾本科和上升沼金花中广泛探索了禾本目accD基因的丢失及随后的降解。这两个新倒位以及科间基因组成的变化更好地界定了禾本目中的谱系。这个小科中存在大的倒位及随后的反转表明质体基因组中发生大规模重排的可能性很高。
