The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

Abstract

The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank-an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.

Keywords: Marine Microbial Eukaryotic Transcriptome Sequencing Project; genome sequencing; microbial diversity; mitochondrial genome; mitochondrial transcriptome.

Figure 1

Complete mitochondrial genome sequences in GenBank. (A) Annual number deposited since 2003. (B) Total number of sequences (5319) as of 5 February 2015. Statistics from the National Center for Biotechnology Information Organelle Genome Resources [53]. (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)

Figure 2

Annual number of peer-reviewed journal articles describing mitochondrial genome sequences. Statistics based on PubMed papers with the words ‘complete mitochondrial genome’, ‘complete mitochondrial DNA’, ‘entire mitochondrial genome’ or ‘mitochondrial genome sequence’ in their title or abstract. These search criteria do not capture all of the published mitochondrial genome sequences per year, but still provide reasonable insights into annual mtDNA publication rate, particularly its large increase over the past 3 years.