Abstract Detail

Comparative Genomics/Transcriptomics

Ramsey, Adam [1], Phan, Vinthuy [2], Pham, Diem-Trang [2], Melton, Caroline [3], Daigle, Bernie [4], Mandel, Jennifer [4].

Identifying sequence heteroplasmy across entire organellar genomes of Daucus carota using whole genome sequence data.

Heteroplasmy, a state in which cells or individuals contain multiple, but distinguishable, mitochondrial or plastid genomes, is increasingly recognized as a common state of organellar genomes. Heteroplasmy has been found in numerous and diverse taxa including bed bugs, Drosophila, humans, Saccharomyces, Arabidopsis, maize, and carrot. In plants, the genomes of mitochondria and plastids may each be found in the heteroplasmic state, although the structural complexity found within mitochondrial genomes tends to make it more prone to heteroplasmy. As the development of molecular techniques have improved over the last several decades, the detection of structural and sequence heteroplasmy has increased. Sanger sequencing, quantitative-PCR, and fragment length analysis, among others, allow for the detection of heteroplasmy as single nucleotide variants, indels, and structural rearrangements, limited to small regions of the genome. Yet with the explosion of whole genome sequencing, interest has turned towards discovering sequence heteroplasmy across entire genomes. Bioinformatic pipelines have been developed to do so (e.g., MitoBamAnnotator, MitoChip, MitoRS, and MToolBox), but such programs have limitations (e.g., species-specific and sequence data format requirements), and they do not allow for detection of plastid heteroplasmy. Our interest in genome-wide heteroplasmy extends to the maintenance of heteroplasmy across generations and the evolutionary outcomes of heteroplasmy in the context of cyto-nuclear interactions. Here, we report the results of a new bioinformatic pipeline with the ability to 1) detect heteroplasmy in mitochondrial and plastid genomes of any species and 2) visualize heteroplasmic sites from multiple individuals aligned to a reference genome. Such a pipeline enables us to discover regions of organellar genomes commonly found in the heteroplasmic state and test hypotheses relating to those regions. Further, once identified, heteroplasmic regions can be analyzed for signatures of selection and analyzed for geographic structuring of heteroplasmy. In this study, we carried out whole genome sequencing on 48 carrot individuals from North America, Europe, North Africa, and Southwest Asia. After being processed through our pipeline, we find heteroplasmy common in both organellar genomes, and it is present in coding and non-coding regions. Moreover, coding regions contain heteroplasmic variants which alter the amino acid sequences of proteins.

1 - University Of Memphis, Department Of Biological Sciences, 3700 Walker Avenue, 104 Ellington Hall, Memphis, TN, 38111, United States
2 - University of Memphis, Department of Computer Science, Memphis, TN, 38152, United States
3 - University of Memphis, Department of Biological Sciences, 3700 Walker Avenue, Memphis, TN, 38152, United States
4 - University of Memphis, 3700 Walker Avenue, Memphis, TN, 38152, United States

Keywords:
carrot
mitochondria
chloroplast
SNP
bioinformatic pipeline
NGS.

Presentation Type: Oral Paper
Session: 21, Comparative Genomics and Transcriptomics I
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 11:45 AM
Number: 21015
Abstract ID:112
Candidate for Awards:Margaret Menzel Award