MtDNA

From AAAWiki

Contents 1 People working on this project 2 mtDNA assemblies and alignments 3 mtDNA annotations 4 mtDNA evolutionary genetic analyses 5 Our intent for publication 6 Resources 7 Discussion

People working on this project

• Kristi Montooth
  
• Dawn Abt
  
• Jeffrey Hofmann
  
• David Rand
  

mtDNA assemblies and alignments

• The major mtDNA types within D. melanogaster, D. simulans, D. sechellia, D. mauritiana and D. yakuba have been sequenced [Ballard, J.W. (2000) J Mol Evol 51, 48-63]. We have assembled the mitochondrial genomes of D. erecta, D. ananassae, D. persimilis, D. willistoni, D. mojavensis, D. virilis, and D. grimshawi from the trace archives of each species. Most assemblies resulted in a single nearly-complete 15kb mtDNA sequence and we sequenced any remaining gaps.
  
• Complete mtDNAs were aligned in ClustalX and checked by hand. Assemblies will be made available shortly on the Rand Lab Homepage.
  
  

mtDNA annotations

• We have annotated the complete proteome, tRNAs and rRNAs based on previous annotations of the D. melanogaster and D. yakuba sequences, as well as using programs such as DOGMA.
  
• An annotated complete assembly and individual annotations of each genome in NCBI format will be made available shortly on the Rand Lab Homepage.
  
  

mtDNA evolutionary genetic analyses

• molecular evolution: mtDNA phylogeny, branch-specific rates of substitution, dn/ds-based analysis for each oxidative phosphorylation complex
  
• genomic patterns: base composition, codon bias
  
• genomic processes: compensatory evolution in tRNAs, co-evolution between proteins within complexes, evolution of intergenic spacer regions in mtDNA
  
• A poster from the fly meetings with results from preliminary analyses can be found here.
  
  

Our intent for publication

• We propose to submit a publication reporting these analyses as a companion to the 12 species genome paper, as well as contribute the most interesting results to the genome paper, if warranted. The 12 genomes paper will benefit greatly from a concrete effort of those in the community to contribute creative analyses and robust results.
  
  

Resources

• The genomes, in addition to providing a rich dataset towards understanding the evolutionary forces shaping mtDNA diversity, can be used for:
  

• Finding transpositions of mitochondrial-encoded genes into the nuclear genome
  
• Filtering mitochondrial sequence from nuclear genome assemblies
  
  

Discussion

• We find polymorphic sites at moderate frequency among traces for all of the mitochondrial genomes that we have assembled. What can we glean from this information?
  
• mtDNA have a strong AT-bias. Can we use these assemblies to help filter mtDNA sequence from nuclear genome assemblies?