This is an interesting article because it reviews an area of work that has barely been born - the 4 or so key papers in the field, all by the authors, have appeared in the last year or so. I struggle to decide what to make of this. On one hand, an interested party could just read those 4 papers and be as aware as they could by reading this one. Similarly there are real issues with the limits and critical appraisal of this field that aren't answered in this paper, and indeed aren't answerable until more studies are done. The authors make this point themselves at several junctions. On the other hand it is a truly promising approach, corrects some of the larger overreach of the original CO1 metabarcoding approaches and does summarize the key findings from those papers pretty efficiently. So on the question of significance of this review I am genuinely undecided. So here are some suggestions for the improvement of a pretty good paper and I'll let the editor decide on significance.

1) There are issues with barcoding and metabarcoding that go well beyond just the length of the sequence and relate to the unique evolutionary history of mitochondria. Sequencing the whole mt genome for these questions doesn't skirt that and so I think a fairer review of the utility of mt based barcoding in the introduction highlighting at least some of these mt-centric objections to barcoding would improve the balance of the paper.

2) While you can find at least one paper that uses the term "mitogenomics" citation [16] for your approach (P4, line 9), I can find hundreds that use the term for almost anything to do with mitochondrial genomics - genome descriptions, genome phylogenies, comparative genomics etc. Given how frequently poorly phrased statements get cited for years to come as incontrovertible facts in this field, please, I beg you don't continue with the misuse of a general term for a specific application. MMG is part of the broader mitogenomics field that efficiently and precisely describes what you are doing, leave it at that.

3) Ease of assembly vs PCR constraints (P5, line 2). While I don't disagree with the general thrust of this argument, none of the published examples of PCR-free mt genome sequencing that I have read have actually attempted taxa that were hard/impossible to sequence via a PCR-based approach. In truth most examples, including the three cited papers [25-27], concerned taxa for which close relatives had already been sequenced by PCR-based approaches without commentary on how hard it was. The physical genomic issues that make PCR hard in some taxa- such as genome fragmentation, heteroplasmy or rampant rearrangements, also make assembly hard in those same taxa. This argument (and you aren't the first to make it) is a bit of a straw man - unarguably PCR-free is quicker but it hasn't ever been demonstrated to get something easily, that would be otherwise impossible. In my experience that which is impossible with PCR-based (like say lice) are still very very hard with PCR free.

4) Criteria for a complete mt genome (P8, line 25). While I understand that previous authors may have differed on what they did in individual papers this isn't an issue that needs any discussion. The animal mt genome is 37 genes in size - they are all 37 genes in size. The only wiggle room regards whether a complete control region is assembled or not, and as they aren't typically used in phylo- or pop genetics "near-complete" means all 37 genes but an incomplete control region. This isn't nuclear genome sequencing when there is usually some lack of certainty about real genome size or gene complement - if you get the 37 genes it is complete, if not it isn't. One of the reasons the statistics on "genome completeness" from bulk samples aren't comparable is because the authors didn't tackle this issue head on and use the actual objective measure of completeness - all 37 genes or at least all 15 protein-coding plus rRNA genes. This is an area of the manuscript where flaws in previous studies could be meaningfully critiqued and so move this field forward rather than mutely accept that different forms of a categorically incorrect statement "a genome with 8/10 genes is complete" have been made.

5) Assembly algorithms for circular organelle genomes (P9, line 60). I found this section confusing. Such algorithms exist - Geneious has one in its standard release and MitoBIM was explicitly written as a mt genome assembler. Indeed you mention MitoBIM several lines later. I am confused as to why you seem to make a distinction between whatever Coissac personally communicated to you and the existing software/pipelines that do exactly what you seem to be saying is still being developed?

6) Mitochondrial isolation. Just for laughs could you please find the last time someone actually used a CsCl gradient to isolate mtDNA? I can't find any that are younger than 30 years ago. CsCl is super toxic and the papers that used it are almost older than I - and even then the authors typically bemoan how hard it is. It didn't die off because PCR was a little better - but because PCR was almost unbelievably better. I don't think it is reasonable to even present this as an option without some firm statement about how this is basically a "dead" method nobody knows how to use anymore.

7) On a related front the capture of mt reads by hybrid enrichment is a genuinely exciting move. There are papers showing poor capture of mt reads in arrays with mixed nuclear and mt baits (Hancock-Hanser et al. 2013 Mol Ecol 13: 254) probably because of DNA competition on the baits. I'd almost be inclined to suggest that this review wait until that paper is published and the results can be fully dissected and discussed in the review because it is such a potentially major advance in this realm. At a bare minimum reviewing the modest number of papers that have attempted mtDNA enrichment through hybrid capture is in order.

8) General point - at too many instances you refer to "pers comm" or "in prep" or "in review" rather than available publications. This seriously undermines a worthy paper's utility as a review because you know lots of things, we readers can't access. Please think hard about whether you need to make these statements, whether other papers could be cited or whether this whole review could be better shelved for a year until the field pans out more.

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