Abstract Detail

Phylogenomics

Burke, Sean [1], Ungerer, Mark [2], Duvall, M [3].

Differential Decay of an Ancient Mitochondrial Insertion in the Plastid Genomes of Paspalum (Poaceae).

The grass family (Poaceae), ca. 12075 species, has been a focal point of many recent studies that aim to use complete plastomes to reveal and substantiate relationships within the family. The use of Next Generation Sequencing technology has allowed for the full and partial recovery of the genomes in plants, specifically intricate details in many Poaceae plastomes. The transfer of DNA from between these genomes, such as from plastomes to nuclear and mitochondrial genomes, was a common occurrence and was consistently recorded. The lack of information for the reverse situation led people to conclude that plastomes never or rarely acquired foreign DNA. This conclusion changed with the discovery of mitochondrial inserts in the plastome of Daucus carota and Asclepias syriaca, and with the eventual discovery of more mitochondrial inserts found within grasses. This study investigates the trnI - trnL intergenic spacer region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae. Note that in other land plant plastomes a large protein coding sequence is normally found in this spacer, but has been lost to the grass plastome. 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 trnI - trnL inserts were determined to be of mitochondrial origin. In conclusion, a hypothetical ancestral insert, 17685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2809 bp, was found in the same region for Paraneurachne muelleri (Paniceae). Comparing these inserts to previous inserts found in this region, there are no similarities, suggesting independent events. The primary mechanism for changes in this insert region was determined to be intrastrand deletion between dispersed repeats. The differences among the Paspalum inserts were due to at least seven different intrastrand deletion events throughout the lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, the origin of the insert in the Paspalum lineage was likely recombination between plastid and mitochondrial DNA.

1 - Northern Illinois University, Biological Sciences, 1425 W. Lincoln Hwy, DeKalb, IL, 60115, United States
2 - Kansas State Univeristy, Biology, 426 Ackert Hall, Manhattan, KS, 66506, USA
3 - Northern Illinois University, Plant Molecular And Bioinformatics Center And Department Of Biology, 1425 W Lincoln Hwy, Dekalb, IL, 60115, United States

Keywords:
Poaceae
Paspalum
mtDNA
ptDNA
molecular evolution
inserts
Next generation sequencing
Grasses.

Presentation Type: Oral Paper
Session: 11, Phylogenomics II
Location: 114/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 2:00 PM
Number: 11003
Abstract ID:459
Candidate for Awards:None