Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae)

Abstract

Background: The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae.

Results: Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6 Ma, with the insert arising at 8.7 Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA.

Conclusions: A hypothetical ancestral insert, 17,685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808 bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.

Keywords: Grasses; Inserts; Next generation sequencing; Paspalum; Poaceae; mtDNA; ptDNA.

Fig. 1

Chronogram of Poaceae species with support values (ML / BI) for nodes that did not recover maximum support. All other nodes are maximally supported. Highlighted branches depict different taxonomic groups with similar inserts in the trnI - trnL IGS. Letters in the Paspalum lineage designate IDEs (Table 2)

Fig. 2

The inserts compared among Paspalum species and across generalized subfamilies. Aligned subregions are differentiated with alternating blue and green bars. These subregions are flanked by red bars representing trnI (left) and trnL (right). IDEs are represented with overlapping colored bars and their designated letter (Table 2)

Fig. 3

ESOM of mtDNA and partitions of ptDNA sequences based on tetranucleotide frequency. The mtDNA is in blue with the ptDNA divided into LSC (green), SSC (red), IR (orange), and the Paspalum inserts (yellow). High ‘elevations’ are in white visualizing major distances in tetranucleotide frequency, while ‘low elevations’ are in darker grays showing similarity in tetranucleotide frequency