We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater diversifying selection than autosomal and organellar genes. Interestingly, this is driven primarily by divergence of male-specific genes, while divergence of other sex-linked genes is similar to autosomal genes. Through analysis of sex-specific read coverage, we identify and validate genetic sex markers for M. inflexa, which will enable diagnosis of sex for non-reproductive individuals. To investigate dehydration tolerance, we capitalized on a difference between genetic lines, which allowed us to identify multiple dehydration associated genes two of which were sex-linked, suggesting that dehydration tolerance may be impacted by sex-specific genes.
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Genome sequencing was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants Program (grant no. RGPIN-2014-05820) grant to Q.C. Field work was funded by a University of Kentucky, Department of Biology’s Ribble grant to R.A.M. and the 2016 American Bryological and Lichenological Society’s Anderson and Crum Bryology Field Research Award to R.A.M. We thank the Flora Ribble Endowment, University of Kentucky, Department of Biology for a fellowship to R.A.M. that enabled this work.
The unprocessed sequence data associated with this study are available in GenBank (accession numbers: SRR7348360 and SRR7348361). This Whole Genome Shotgun project (M_inflexa_v1.1) has been deposited at DDBJ/ENA/GenBank under the accession QLSQ00000000. The version described in this paper is version QLSQ01000000. The complete mitochondrial and chloroplast sequences are available at FigShare (https://doi.org/10.6084/m9.figshare.6639209.v1).
Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-45039-9.
Marks, Rose A.; Smith, Jeramiah J.; Cronk, Quentin; Grassa, Christopher J.; and McLetchie, D. Nicholas, "Genome of the Tropical Plant Marchantia inflexa: Implications for Sex Chromosome Evolution and Dehydration Tolerance" (2019). Biology Faculty Publications. 177.