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The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution
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Summary: The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome‐scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TE s), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene‐ and TE‐rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono‐centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein‐coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via si RNA mediated silencing. Structure‐based detection methods show that the genome evolved via two rounds of whole genome duplications (WGD s), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant‐specific cell growth and tissue organization. The P. patens genome lacks the TE‐rich pericentromeric and gene‐rich distal regions typical for most flowering plant genomes. More non‐seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Metadata
- Authors
- Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., Piednoel, M., Gundlach, H., Van Bel, M., Meyberg, R., Vives, C., Morata, J., Symeonidi, A., Hiss, M., Muchero, W., Kamisugi, Y., Saleh, O., Blanc, G., Decker, E. L., van Gessel, N., Grimwood, J., Hayes, R. D., Graham, S. W., Gunter, L. E., McDaniel, S. F., Hoernstein, S. N. W., Larsson, A., Li, F., Perroud, P., Phillips, J., Ranjan, P., Rokshar, D. S., Rothfels, C. J., Schneider, L., Shu, S., Stevenson, D. W., Thümmler, F., Tillich, M., Villarreal Aguilar, J. C., Widiez, T., Wong, G. K., Wymore, A., Zhang, Y., Zimmer, A. D., Quatrano, R. S., Mayer, K. F. X., Goodstein, D., Casacuberta, J. M., Vandepoele, K., Reski, R., Cuming, A. C., Tuskan, G. A., Maumus, F., Salse, J., Schmutz, J., & Rensing, S. A.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2018-01-19
- Volume
- 93
- Issue
- 3
- Pages
- 515-533
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W2772246790
- Cited by
- 423
- References
- 85
- FWCI
- 31.82
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
