A great leap forward in solving the long-standing mystery of sex determination in lampreys
In our recent paper in Nature Communications Biology, we describe a detailed transcriptomic analysis of sex and stage specific changes in sea lamprey gonad development that provides insights into the long-standing mystery of sex determination in lampreys.
Lampreys, ancient jawless vertebrates, have earned the nickname “vampires of the deep” because of their parasitic feeding habit. They have a round suctorial disc armed with teeth that they use to attach to other fishes while drinking their blood. Akin to fictional vampires, the lamprey lineage is also incredibly long-lived, having survived four mass extinction events in their ~500-million-year history, including the most recent one that led to the extinction of dinosaurs. Lampreys have retained a highly conserved body plan for the past 350 million years, providing biologists with invaluable insights into events that occurred at the dawn of vertebrate evolution (Docker et al., 2015).
Although lampreys are important parts of the ecosystem and are highly valued for food where they occur naturally (Docker et al., 2015), the sea lamprey has become an invasive pest in the Laurentian Great Lakes when canals allowed it to gain access from the Atlantic Ocean. Exploiting the great abundance of host fishes in the Great Lakes and a shortage of predators, sea lamprey numbers exploded following invasion, resulting in devastation of the commercial fishery. The sea lamprey control program, administered by the Great Lakes Fishery Commission, has successfully reduced sea lamprey numbers to ~10% of their peak abundance, and it continues to search for control methods that exploit the unique vulnerabilities of this ancient vertebrate (Great Lakes Fishery Commission, 2022).
The sea lamprey life cycle starts with a prolonged larval stage followed by a dramatic metamorphosis, during which the blind and toothless larvae—which live burrowed in stream beds feeding on detritus and algae—transform into the formidable parasitic juveniles. The juveniles migrate out to the lake, where they feed on lake trout and other fishes for ~1 year, before becoming sexually mature during their migration back into rivers where they will spawn and die.
An unusual feature of lamprey development is the very long period during which the single elongated gonad remains undifferentiated. In sea lamprey, a recognizable ovary is not apparent until larvae are ~2–3 years old, and the gonad of future males remains undifferentiated for several more years; a recognizable testis does not develop until metamorphosis at ~5–7 years (Docker et al., 2019). When and how the future sex of the lamprey gonad is determined has been a deep-rooted mystery for lamprey researchers. Because sea lamprey sex ratios shifted from ~75% male to ~75% female following initiation of sea lamprey control, environmental sex determination (which has been observed in some fishes and many reptiles) was suggested previously, and a systematic and exhaustive analysis of the sea lamprey somatic genome, led by Dr. Phil Grayson (second author on this paper), found no evidence of genomic differences between males and females (Grayson et al., 2022).
For the first time, our research now suggests that the germline-specific region of the genome—the part jettisoned from somatic cells—holds the key to sea lamprey sex differentiation, and we propose a mechanism for how environmental and genetic factors might work together to control lamprey gonadal development.
This research project was initiated by Dr. Margaret Docker, a world expert on the biology of lampreys, who has been studying these fascinating animals for >35 years. Lead author, doctoral student Tamanna Yasmin, started working on this project in 2016 when there were only a handful of genomic resources available for sea lamprey. Then comes Dr. Sara Good’s contribution to the study. Earlier in her career, Dr. Good worked on molecular population and evolutionary genetics of both animals and plants, but since 2016 has been collaborating with Dr. Docker to study the genes underlying gonadogenesis in lampreys using transcriptomic and comparative approaches. She was the bioinformatics lead on this study and a previous study identifying genes underlying gonadogenesis in two native lamprey species (Ajmani et al., 2021).
Interestingly, sea lamprey undergo an unusual process called programmed genome rearrangement (PGR) during which ~20% of the genome, representing 12 micro-chromosomes, are jettisoned from somatic cells 3 days post-fertilization (Smith et al., 2009; Timoshevskiy et al., 2016). Only the germ cells retain this portion of the genome, and previous research suggested that the genes in this germline-specific region (GSR) are essential for early embryonic development (Smith et al. 2012, 2018). Following from these insights, Tamanna Yasmin started working with the new Vertebrate Genomes Project (VGP) chromosome-level assembly, and employed a powerful reference-guided mapping algorithm which allowed us to generate deeper insights into the role of the GSR in sea lamprey gonadogenesis. With the help of Dr. Phil Grayson, an evolutionary biologist whose research combines developmental and computational biology with genetics and genomics to investigate the origin of complex phenotypes, we identified the limits of the GSR in the new VGP genome. This led to one of our most exciting findings—that the genes in the GSR showed highly male-biased expression compared to genes in the somatic genome. The next most exciting moment was to discover that chromosome 81 and many other unassembled scaffolds were part of the GSR.
The results of our RNA-sequencing analyses reveal that the GSR contains genes that are highly expressed in all stages of male but not female gonad development, particularly in so-called prospective males that do not yet show histologically identifiable testes and in metamorphosing males that are actively producing spermatogonia. This indicates that expression of genes in the GSR is important for testicular development, and led to our working model that provides insights into how environmental and genetic factors might work together to influence sea lamprey sex differentiation. We proposed that, in response to environmental cues and somatic-GSR molecular cross-talk, a decision is made to either open the chromatin of the GSR, permitting expression of these genes, or let it remain predominantly silenced. If the GSR remains silent, the gonad will initiate development as a female, while if the GSR is opened, we propose that a cascade of signalling events ensue and the gonad will commit to develop into a testis.
We hope that the findings presented in this paper will open the door for future research understanding the role of PGR in sex determination in lampreys. This study may also guide research in support of sea lamprey control, perhaps eventually allowing for the species-specific manipulation of sea lamprey sex ratios or reproduction.
Authors (from left): Tamanna Yasmin, Dr. Phil Grayson, Dr. Margaret Docker, Dr. Sara Good.
Banner photo: Sea lamprey suctorial oral disc (left), used to attach to host fishes and to move rocks while building a nest prior to spawning (right). Photos © Great Lakes Fishery Commission.
Ajmani, N., Yasmin, T., Docker, M. F., & Good, S. V. Transcriptomic analysis of gonadal development in parasitic and non-parasitic lampreys (Ichthyomyzon spp.), with a comparison of genomic resources in these non-model species. G3 (Bethesda, Md.), 11(2), https://doi.org/10.1093/g3journal/jkab030 (2021).
Docker, M.F., Hume, J.B. & Clemens, B.J. Introduction: a surfeit of lampreys in: Lampreys: Biology, Conservation and Control, Vol 1. (ed. Docker, M. F.) 1–34, https://link.springer.com/chapter/10.1007/978-94-017-9306-3_1?msclkid=3489ad27d16b11eca8e287e6423b1887 (2015).
Docker, M. F., Beamish, F. W. H., Yasmin, T., Bryan, M. B. & Khan, A. The lamprey gonad in: Lampreys: Biology, Conservation and Control, Vol. 2. (ed. Docker, M. F.) 1–186, https://link.springer.com/chapter/10.1007/978-94-024-1684-8_1?msclkid=63b4970cd16b11eca98b8c0c1ce2b0cd (2019).
Great Lakes Fishery Commission. Sea Lamprey: A Great Lakes Invader, http://sealamprey.org/?msclkid=d4243133d13011ec8a7882f5a1579741 (2022).
Grayson, P., Wright, A., Garroway, C. J. & Docker, M. F. SexFindR: A computational workflow to identify young and old sex chromosomes. bioRxiv,
Smith, J. J., Antonacci, F., Eichler, E. E. et al. Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci U S A 106, 11212–11217, https://doi.org/10.1073/pnas.0902358106 (2009).
Smith, J.J., Baker, C., Eichler, E.E. et al Genetic consequences of programmed genome rearrangement. Curr Biol 22,1524–1529, https://doi.org/10.1016/j.cub.2012.06.028 (2012).
Smith, J. J. et al. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics 50, 270–277, https://doi.org/10.1038/s41588-017-0036-1 (2018).
Timoshevskiy, V. A., Herdy, J. R., Keinath, M. C. & Smith, J. J. Cellular and molecular features of developmentally programmed genome rearrangement in a vertebrate (sea lamprey: Petromyzon marinus). PLoS Genet 12, e1006103, https://doi.org/10.1371/journal.pgen.1006103 (2016).