A genomic resource for ants, and more
Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: steppingstones towards genomic studies of hybridogenesis and thermal adaptation in desert ants
Recommendation: posted 05 July 2022, validated 12 July 2022
Ponts, N. (2022) A genomic resource for ants, and more. Peer Community in Genomics, 100017. https://doi.org/10.24072/pci.genomics.100017
The ant species Cataglyphis hispanica is remarkably well adapted to arid habitats of the Iberian Peninsula where two hybridogenetic lineages co-occur, i.e., queens mating with males from the other lineage produce only non-reproductive hybrid workers whereas reproductive males and females are produced by parthenogenesis (Lavanchy and Schwander, 2019). For these two reasons, the genomes of these lineages, Chis1 and Chis2, are potential gold mines to explore the genetic bases of thermal adaptation and the evolution of alternative reproductive modes.
Nowadays, sequencing technology enables assembling all kinds of genomes provided genomic DNA can be extracted. More difficult to achieve is high-quality assemblies with just as high-quality annotations that are readily available to the community to be used and re-used at will (Byrne et al., 2019; Salzberg, 2019). The challenge was successfully completed by Darras and colleagues, the generated resource being fully available to the community, including scripts and command lines used to obtain the proposed results.
The authors particularly describe that lineage Chis2 has 27 chromosomes, against 26 or 27 for lineage Chis1, with a Robertsonian translocation identified by chromosome conformation capture (Duan et al., 2010, 2012) in the two Queens sequenced. Transcript-supported gene annotation provided 11,290 high-quality gene models. In addition, an ant-tailored annotation pipeline identified 56 different families of repetitive elements in both Chis1 and Chis2 lineages of C. hispanica spread in a little over 15 % of the genome. Altogether, the genomes of Chis1 and Chis2 are highly similar and syntenic, with some level of polymorphism raising questions about their evolutionary story timeline. In particular, the uniform distribution of polymorphisms along the genomes shakes up a previous hypothesis of hybridogenetic lineage pairs determined by ancient non-recombining regions (Linksvayer, Busch and Smith, 2013).
I recommend this paper because the science behind is both solid and well-explained. The provided resource is of high quality, and accompanied by a critical exploration of the perspectives brought by the results. These genomes are excellent resources to now go further in exploring the possible events at the genome level that accompanied the remarkable thermal adaptation of the ants Cataglyphis, as well as insights into the genetics of hybridogenetic lineages.
Beyond the scientific value of the resources and insights provided by the work performed, I also recommend this article because it is an excellent example of Open Science (Allen and Mehler, 2019; Sarabipour et al., 2019), all data methods and tools being fully and easily accessible to whoever wants/needs it.
Allen C, Mehler DMA (2019) Open science challenges, benefits and tips in early career and beyond. PLOS Biology, 17, e3000246. https://doi.org/10.1371/journal.pbio.3000246
Byrne A, Cole C, Volden R, Vollmers C (2019) Realizing the potential of full-length transcriptome sequencing. Philosophical Transactions of the Royal Society B: Biological Sciences, 374, 20190097. https://doi.org/10.1098/rstb.2019.0097
Darras H, de Souza Araujo N, Baudry L, Guiglielmoni N, Lorite P, Marbouty M, Rodriguez F, Arkhipova I, Koszul R, Flot J-F, Aron S (2022) Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants. bioRxiv, 2022.01.07.475286, ver. 3 peer-reviewed and recommended by Peer community in Genomics. https://doi.org/10.1101/2022.01.07.475286
Duan Z, Andronescu M, Schutz K, Lee C, Shendure J, Fields S, Noble WS, Anthony Blau C (2012) A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods, 58, 277–288. https://doi.org/10.1016/j.ymeth.2012.06.018
Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS (2010) A three-dimensional model of the yeast genome. Nature, 465, 363–367. https://doi.org/10.1038/nature08973
Lavanchy G, Schwander T (2019) Hybridogenesis. Current Biology, 29, R9–R11. https://doi.org/10.1016/j.cub.2018.11.046
Linksvayer TA, Busch JW, Smith CR (2013) Social supergenes of superorganisms: Do supergenes play important roles in social evolution? BioEssays, 35, 683–689. https://doi.org/10.1002/bies.201300038
Salzberg SL (2019) Next-generation genome annotation: we still struggle to get it right. Genome Biology, 20, 92. https://doi.org/10.1186/s13059-019-1715-2
Sarabipour S, Debat HJ, Emmott E, Burgess SJ, Schwessinger B, Hensel Z (2019) On the value of preprints: An early career researcher perspective. PLOS Biology, 17, e3000151. https://doi.org/10.1371/journal.pbio.3000151
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2022.01.07.475286
Version of the preprint: 1
Author's Reply, 11 May 2022
Decision by Nadia Ponts, posted 21 Feb 2022
Thank you for submitting to PCI Genomics.
After careful examination of your manuscript and the corresponding external reviews, the value of the paper and the work performed is unanimously recognized. The comments and remarks formulated by the reviewers should nonetheless be addressed prior recommendation. Notably, as noted by both reviewers, discussion putting the findings back in perspective with current biological knowledge and questions is lacking.
As an additional specific comment, considering the level of bioinformatics performed, a schematic drawing of the pipeline describing the sequential analyses performed would be very much welcome as supplemental data for example.
You are kindly invited to submit a revised version of your manuscript addressing all comments and remarks formulated.