A chromosome level genome assembly of the marine flowering plant, Torrey's surfgrass (Phyllospadix Torreyi) reveals an exceptionally large Y-chromosome - PubMed (original) (raw)
. 2026 May 6;117(3):566-576.
doi: 10.1093/jhered/esaf097.
Malia L Moore 2 3, Merly Escalona 4, Courtney Miller 5, Noravit Chumchim 6, Oanh Nguyen 6, Mohan P A Marimuthu 6, Colin W Fairbairn 7, Eric Beraut 7, William E Seligmann 7, Samuel Sacco 7, Erin Toffelmier 5, H Bradley Shaffer 5, Todd P Michael 2 3 8, Scott Hodges 1
Affiliations
- PMID: 41269242
- PMCID: PMC13147172
- DOI: 10.1093/jhered/esaf097
A chromosome level genome assembly of the marine flowering plant, Torrey's surfgrass (Phyllospadix Torreyi) reveals an exceptionally large Y-chromosome
Jason Johns et al. J Hered. 2026.
Abstract
Phyllospadix spp. (surfgrass) are flowering plants and keystone species in the rocky intertidal and subtidal environments of the North Pacific Ocean. Here we report a chromosome level assembly for P. torreyi, which occurs along the coast of California, sometimes in sympatry with P. scouleri. Both of these species and their putative hybrids are being studied as part of the California Conservation Genomics Project. Phyllospadix are dioecious, and males are exceptionally rare compared to females. Using high throughput, long reads (PacBio) and chromatin capture (Omni-C), we assembled a chromosome level genome for a male individual and a contig level assembly for a female individual. Comparison between the male and female assembly confirmed that the male is the heterogametic sex and has a massive Y chromosome at 124.8 megabases, which encompasses over 27% of the male genome. We also compared the male P. torreyi assembly to a genome from its sister genus, the monoecious Zostera marina, and found relatively high levels of synteny, that syntenic gene blocks on the P. torreyi sex chromosomes align to a single chromosome of Z. marina, and an estimated divergence time of ca. 25 million years ago. The Phyllospadix genome will be a powerful tool for studying marine dispersal, sex ratios, genetic diversity, sex chromosome evolution, and other dynamics in a keystone marine species.
Keywords: Y-chromosome; dioecious; genome; intertidal; seagrass; subtidal.
© The Author(s) 2025. Published by Oxford University Press on behalf of The American Genetic Association.
Figures
Fig. 1
Photographs and ranges of Phyllospadix (surfgrass) species. A) P. scouleri and B) P. (male individual with inflorescences). Border colors around photos in A & B correspond to the color of the dots in C. C) Map of California showing the locations of sites for both species of Phyllospadix found in coastal California visited by the authors. The collection points of P. Torreyi tissue used for the male (♂) and female (♀) genome assemblies are indicated.
Fig. 2
Overview of genome assembly metrics for P. Torreyi. A) K-mer spectrum output of male PacBio HiFi data without adapters, generated using GenomeScope2.0. K-mers at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes. B) Hi-C contact map for the primary genome assembly of the male genome generated with PretextSnapshot. Hi-C contact maps translate proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation. C,D) Snail plots for the primary (C) male and consensus (D) female genome assembly showing a graphical representation of the quality metrics in Table S2 for the primary assembly. The circle represents the full size of the assembly. From the inside-out, the central plot displays length-related metrics. The red line represents the longest scaffold; other scaffolds are ordered by size moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs mark the scaffold N50 and N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of ns in the assembly the dark versus light blue area around it shows mean, maximum, and minimum GC versus AT content at 0.1% intervals (Challis et al. 2020).
Fig. 3
Alignment of genome assemblies. A) Dot plot alignment comparing P. Torreyi male primary assembly and female consensus assembly. 11 chromosomes/contigs are labeled for each assembly. Chromosome 1 (Y chromosome; Pt.1) is unique to the male except for the putative PAR with the X chromosome (circled on both Pt.1 and Pt.5/Pt.3 female). B) Gene synteny blocks shared between P. Torreyi scaffolds and Z. Marina chromosomes. Yellow syntenic blocks denote genes occurring on the P. Torreyi X chromosome, and orange on the Y. Chromosomes (1–6 for Z. Marina, and 1–11 for P. Torreyi) scale by presence of gene coding regions and therefore do not reflect relative chromosome size.
References
- Bush D, Hollbrook S, Schmitt, Reed D, Hodges S. Male-specific AFLP markers reveal extreme female-biased sex-ratios in the surfgrass Phyllospadix torreyi (Zosteraceae). Minerals Management Service, Final Study Report MMS 2006–049. 2006;1:1–5
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