Referee 1's review (Anthony Larkum):

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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication, the manuscript has been revised in light of these comments and to address other editorial requirements.
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Alessandro Alboresi, Stefano Caffarri, Fabien Nogue, Roberto Bassi and Tomas Morosinotto.

In Silico and Biochemical Analysis of Physcomitrella Patens Photosynthetic Antenna Allows Identification of Subunits Evolved upon Land Adaptation

This ms is of a high standard and reports new and interesting aspects of the photosynthetic apparatus and its evolution in early land plants, viz the moss Physcomitrella patens. The work is based on the recent whole genome data of this moss. The results are exciting and of general interest.

The methods are largely phylogenetic, comparing homologous gene sequences across a variety of algae and land plants. While one could argue for other methods, the methods used are sufficiently accurate, and well done, that few will dispute them. The results show that land palnts developed a number of new antenna proteins for dealing with the land environment, probably related to a) higher light intensities, b) increased red light, and c) enhanced near far red light under certain (shade) conditions. This work is therefore of general interest. It is backed up with biochemical and physiological evidence on the moss P. patens.

The work should be published.

Criticisms

These guys are not biologists! Even the title misuses the Linnean binomial: it should be Physcomitrella patens. Generic names are not once put in italics in the paper! And in the titles of references specific names are not italicised as they should be. All this makes one a little bit suspicious.

The major gap in the presentation however is over the evolution of green algae. Ever since the early work of Stewart and Mattox in the 1970s (Bot Rev,1975), it has been realized that there are two branches of green algae, only one of which led to lands plants. This was called the charophyte line by Stewart and Mattox. However, with further studies this has been pushed back to Mesostigma and renamed the streptophyte line. This line includes some prasinophytes, a number of filamentous green algae, including Spirogyra and coleochaetales, and true charophytes.

The real question then is when did the antenna genes come in. The present ms ignores this really interesting question and is a lesser paper in the result.

The ms also ignores some of the structural/biochemical issues. The big question here is how are the changes related to grana? It has been shown that changes in grana complexity and fluorescence match this evolutionary transition to land plants (Gunning and Schwartz, Austr J Pl Physiol. 26, 695).

Certainly a large gene base exists for Mesostigma. Probably also for Chara and Spirogyra etc. These pieces of the puzzle ought to be put in and mentioned. Another question although less relevant is how these antenna proteins relate to the newly discovered antenna proteins of Six et al? Are they there in Mesostigma. If so when did they die out. A side issue is that there is not very much point in detailed comparisons with Chlamydomonas.

Relevant references:
Lemieux et al 2000 Nature 403, 649.
Rodriguez et al 2007 MBE 24, 723.
Lemieux eta al 2007. BMC Jan 12.
Nedeleu et al 2006 MBE 23, 1011.
McCourt et al 2004. Charophyte algae and land plant origins, TREE 19, 661.

And would there be some point in discussing if any thing is known in liverworts and mosses?

Viridiplantae has been taken by some workers to mean green algae and land plants, but by others to mean red algae + green algae + land plants. So be careful!

The English is deficient in a number of places. The authors need to get the next draft read by a native English speaker with good scientific competency.

Without a better naming system the phylogenetic trees are very difficult to read.

Fig. 6 D. What happens after 5.5 min? Presumably the actinic light is turned off?