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Title: The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers

item Phillips, Wendy
item BROWN, AMANDA - Oregon State University
item HOWE, DANA - Oregon State University
item Peetz, Amy
item BLOK, VIVIAN - The James Hutton Institute
item DENVER, DEE - Oregon State University
item Zasada, Inga

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2016
Publication Date: 9/5/2016
Citation: Phillips, W.S., Brown, A.M., Howe, D.K., Peetz, A.B., Blok, V., Denver, D., Zasada, I.A. 2016. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. Biomed Central (BMC) Genomics. 17:706-719. doi: 10.1186/s12864-016-3047-x.

Interpretive Summary: The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida occur worldwide and can cause over 80% yield loss of potato. Both of these nematodes are regulated pests in the U.S. Recently, a very similar nematode to PCN, G. ellingtonae was found in Oregon and Idaho. Little is known about the molecular biology of G. ellingtonae. The focus of this research was to explore the mitochondrial genomics of G. ellingtonae. Mitochondria are organelles found in animal cells which generate most of the chemical energy in a cell. It was discovered that the mitochondrial genome in G. ellingtonae is found in two circles; normally in animals it is arranged in one circle. It appears that this two circle arrangement may allow this nematode to independently express sets of genes found on each circle. These results are significant because they help us better understand the relationship of this nematode to PCN and may provide a unique target for management or diagnostics. The data from this project will be freely shared with the other scientists to allow for further exploration into nematode mitochondrial genomics.

Technical Abstract: The evolution of animal mitochondrial (mt) genomes has yielded a highly conserved structure: a single circular chromosome approximately 14 to 20 kb long. Within the last two decades, exceptions to this conserved structure have been reported in a diverse set of organisms. One such exception is the division of mt genomes into multiple, or multipartite, chromosomes. We report on the multipartite two circle mt genome of a newly described cyst nematode, Globodera ellingtonae. Partially assembled mtDNA was obtained from de novo assembly of Illumina MiSeq genomic reads, and the complete sequence of both circles was obtained by PCR amplification and Sanger sequencing. The genetic content of the genome is disproportionately divided between the two circles, with one circle (mtDNA-I) containing ten protein-coding genes and two tRNA genes, whereas the second circle (mtDNA-II) contains just two protein-coding genes but 20 tRNA genes and both rRNA genes. Such segregation of gene types to different circles could provide benefit by localizing gene functional types to independent transcriptional units. Perhaps correlated to this division of genetic content, the copy number of mtDNA-II is more than four-fold that of mtDNA-I in individual nematodes. The differential in copy number increases between second-stage and fourth-stage juveniles, necessitating a mechanism by which copy ratio is reset in the next generation. The G. ellingtonae circles, which share a ~6.8 kb non-coding region, are larger than any other multipartite circular mt chromosome yet reported, and both are larger than the singular mt circle of the model organism Caenorhabditis elegans.