Talk:PLOS/Holocentric chromosomes

Review by František Zedek

I reviewed the article‘s version with an ID=8096.

Major comment:

1. The main suggestion I have, which I admit may rather be an issue of a personal taste, is to reconsider the outline of the article. Although holocentric chromosomes are somewhat different in arthropods, nematodes and plants, they are nevertheless the feature that all these groups have in common. Due to the possession of holocentric chromosomes, they can, therefore, be expected to have experienced similar evolutionary pathways and selective contexts and to have faced similar problems. I think that the article would benefit from the discussion of more general topics regarding holocentric chromosomes (e.g., selective advantages and disadvantages of holocentrism – tolerance to fragmentation, telomere healing, suppression of centromere drive, meiotic problems; discussion og selective contexts that may have favored holocentrism; structure of holocentric chromosomes; occurrence of holocentric chromosomes) that would use the appropriate examples from different groups rather than discussing holocentric chromosomes in arthropods, nematodes and plants separately. I think that with such an approach, the article would benefit by gaining a backbone that could be easily followed and the authors would also avoid repeating themselves (e.g., in which groups do holocentric chromosomes occur or how they may stabilize hybrids and structural heterozygotes in plants and animals etc.).

Minor comments:

2. Regarding the occurrence of holocentric chromosomes, there is evidence that they also occur in millipedes and centipedes (Ogawa 1953), entire plant family Droseraceae (Kolodin et al. 2018) and in an entire spider superfamily Dysderoidea (Král et al. 2019), which contains Segestridae, Dysderidae and three other families. Moreover, based on the molecular evidence of Drinnenberg et al. (2014), the presence of holocentric chromosomes in Ephemeroptera is at least questionable.

3. In Future directions you name the kinetochore genes/proteins in C. elegans that are also known from monocentric organisms. I think it should be mentioned (not necessarily here) and discussed that CENP-A and CENP-C, previously considered essential for kinetochore function, are actually missing in holocentric insects (Drinnenberg et al. 2014).

Literature cited:

• Drinnenberg IA, DeYoung D, Henikoff S, Malik HS. 2014. Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLlife 3: e03676.
• Kolodin P, Cempírkova H, Bures P, Horova L, Veleba A, Francova J, et al. 2018. Holocentric chromosomes may be an apomorphy of Droseraceae. Plant Syst Evol 304: 1289–1296.
• Kral J, Forman M, Korinkova T, Lerma ACR, Haddad CR, Musilova J, et al. 2019. Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes. Sci Rep 9: 3001.
• Ogawa K. 1953. Chromosome studies in the Myriapoda V. A chromosomal survey in some Chilopods with a cyto-taxonomic considerations. Jpn J Genet 28:12–18.

Fzedek (talk) 01:31, 3 September 2019 (PDT)

Author response to Referee

We are very grateful for the positive comments and precious suggestions that we accepted almost entirely with an exception related to the organization of the text. In particular, we:

1. revised the section related to holocentric chromosomes in arthropods adding the citation of their presence in millipedes and centipedes, Droseraceae and spiders. At the same time we edited our text about the presence of holocentric chromosomes in Ephemeroptera since it is at present questionable.
2. added a sentence explaining that highly studied proteins homologues of CENP-C and CENP-A, which are highly conserved structural component of the kinetochore in eukaryotes, are actually absent in insect holocentric chromosomes.
3. revised our section about the evolution of holocentrism, also in accordance with the suggestions of other referees. Even if we still prefer the current organization of the text based on a “taxonomical order” in place on a functional one, we agree that it could be useful to elucidate common advantages of holocentrism

Review by Chris Wheat

Suggested set of direct edits

Author response to Referee

We are very grateful for the improvement of our text and the editing made by the Referee.

Review by Jason Hill

The authors comprehensively addressed the topic of holocentric chromosomes, especially in the description of the functional and mechanistic aspects that differentiate holocentric from monocentric chromosomes. Aside from a few grammatical changes that I changed directly in the text I have only one comment that could be addressed by the authors in further drafts.

The section describing the evolutionary history of emphasizes the uncertainly about the adaptive significance of holocentric chromosomal structure and while indications that adaptive explanations exist are cited, none are listed explicitly. In later sections when the authors describe the function of holocentric chromosomes within clades of species the advantage of holocentric vs. monocentric chromosomes is explored in more detail. It may make sense to list some of those advantages which are shared among clades in the earlier section to highlight what is common among species that share holocentric organization. Jasonplos (talk) 11:05, 30 November 2019 (PST)

Author response to Referee

We are very grateful for the improvement of our text and the editing made by the Referee. We edited our text in order to better explain that, despite the presence of differences in the specific factors that favoured the evolution of holocentrism, some general and recurrent benefits are present (related to responses to clastogenic damage).

Final Wikification

As a last step, please look though and see if there are any additional hyperlinks that could usefully be added. For instance, [[w:kinetochore|kinetochores]] renders to kinetochores.

Please add the figure legends that are currently missing.

The version added to Wikipedia will omit the final "future directions" section and subheadings will be shortened (e.g. from "Evolution and structure of holocentric chromosomes" to just "Evolution and structure"). T Shafee (talk) 19:36, 22 February 2020 (PST)

Author replies to Final wikification

According to these requests, we added additional hyperlinks that could be useful for readers and we also added captions of the two figures. We agree with changes suggested by the Editors to the final Wikipedia page.