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Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS.

Publication ,  Journal Article
Mower, JP; Case, AL; Floro, ER; Willis, JH
Published in: Genome biology and evolution
January 2012

Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multibranched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mitochondrial DNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage (~30×). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 transfer RNAs, and 3 ribosomal RNAs), 22 introns, 3 large repeats (2.7, 9.6, and 29 kb), and 96 small repeats (40-293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric open reading frames (ORFs) identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line.

Duke Scholars

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

January 2012

Volume

4

Issue

5

Start / End Page

670 / 686

Related Subject Headings

  • Sequence Analysis, DNA
  • Repetitive Sequences, Nucleic Acid
  • Plant Infertility
  • Molecular Sequence Data
  • Molecular Sequence Annotation
  • Mimulus
  • Introns
  • Genome, Mitochondrial
  • Genes, Plant
  • Developmental Biology
 

Citation

APA
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ICMJE
MLA
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Mower, J. P., Case, A. L., Floro, E. R., & Willis, J. H. (2012). Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS. Genome Biology and Evolution, 4(5), 670–686. https://doi.org/10.1093/gbe/evs042
Mower, Jeffrey P., Andrea L. Case, Eric R. Floro, and John H. Willis. “Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS.Genome Biology and Evolution 4, no. 5 (January 2012): 670–86. https://doi.org/10.1093/gbe/evs042.
Mower, Jeffrey P., et al. “Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS.Genome Biology and Evolution, vol. 4, no. 5, Jan. 2012, pp. 670–86. Epmc, doi:10.1093/gbe/evs042.
Journal cover image

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

January 2012

Volume

4

Issue

5

Start / End Page

670 / 686

Related Subject Headings

  • Sequence Analysis, DNA
  • Repetitive Sequences, Nucleic Acid
  • Plant Infertility
  • Molecular Sequence Data
  • Molecular Sequence Annotation
  • Mimulus
  • Introns
  • Genome, Mitochondrial
  • Genes, Plant
  • Developmental Biology