|Figure 1 from Pollock et al. 2000|
We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.AND
We describe here the approach, the type of sequence data it generates, the procedure to recover mitochondrial genomes without external tagging, and some potential uses. We perform an in-silico validation test based on the analysis of a simulated dataset with read lengths of two different sizes to represent average read length of three 2nd generation desktop sequencing platforms, Illumina Mi-Seq, 454 GS junior and Ion Torrent PGM. Thus we can contrast their relative efficiencies for the experimental protocol proposed here.Sounds great. Except I wrote a paper with David Pollock, Norman Doggett, and Michael Cummings published in 2000 proposing the same thing. Our paper: Pollock DD, Eisen JA, Doggett NA, Cummings MP. Mol Biol Evol. 2000 Dec;17(12):1776-88. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.
Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.
And not any mention of our paper in this new one. I could do a detailed side by side comparison but I am too angry right now.
UPDATE 11 AM 12/22: I got carried away with anger when I wrote the last few sentences crossed out above. Upon further, more rational consideration, I do not think the authors or editors did anything really wrong here. Yes, they missed some prior literature on the topic and our prior paper is indeed quite similar to theirs. But our prior paper is pretty hard to find by literature searches (see comments/discussion) and they clearly came up with their ideas independently. I truly regret the aggressive, obnoxious tone of my post and sincerely apologize to the authors of the new paper.
PS. I wish to thank @DrShmoo on Twitter for knocking some sense into me
@phylogenomics you support women in science but your aggressive stance is the kind of thing that makes women leave in droves.Comment?
— Louise Allcock (@DrShmoo) December 20, 2012
@drshmoo ouch - not sure I completely agree but fair point and will try to temper self— Jonathan Eisen (@phylogenomics) December 20, 2012
@drshmoo you too ... thanks for the watchful eye and pointers ...
— Jonathan Eisen (@phylogenomics) December 20, 2012