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Sequencing the Green Sturgeon Genome to Identify a Genetic Sex Marker

Sequencing the Green Sturgeon Genome to Identify a Genetic Sex Marker

Background and Significance

The green sturgeon, Acipenser medirostris, is a diadromous sturgeon species inhabiting the Pacific Coast of North America. Like all sturgeons, green sturgeon have experienced significant population declines due to numerous anthropogenic disturbances, including habitat loss, overharvest, and climate change. Recent research has indicated that there are two genetically distinct population segments of green sturgeon, the northern and southern DPSs (Israel et al. 2004, 2009). The northern DPS currently spawns in the Klamath and Rogue rivers and occasionally the Columbia River (Schreier et al. 2016) while the southern DPS spawns only in the Sacramento-San Joaquin drainage (Brown 2007; Poytress et al. 2012; Seesholtz et al. 2015). The northern DPS is considered a species of special concern while the southern DPS is listed as threatened under the federal Endangered Species Act (ESA) due to low abundance and existence of only a single viable spawning site in the upper Sacramento River (NMFS 2006).

The southern DPS of green sturgeon is monitored by Interagency Ecological Program agencies to ensure persistence of the species and ecosystem resilience in the Sacramento-San Joaquin Delta. However, green sturgeon monitoring is currently constrained by an inability to non-invasively determine an individual’s sex; males and females are morphologically indistinguishable unless they are actively spawning. Invasive methods, such as visual inspection of gonads or gonad biopsy, are undesirable for a listed DPS. Though hormones can be measured from a blood sample, this method can only sex mature adults. Without basic biological information such as sex, it is impossible to accurately estimate important metrics such as sex ratios and migration timing which are critical for effective species management and evaluation of drought effects (Beccio et al. 2015). For greatest monitoring accuracy and efficiency, we need a method that would allow biologists to determine the sex of green sturgeon at any age and without taking invasive samples. A genetic sex marker would satisfy this need.

Unlike many organisms, sturgeon don’t have sex chromosomes and though molecular biologists researchers in Europe identified a small region of chromosome 4 in the sterlet (Acipenser ruthenus) that seems to be associated with female sex (Kuhl et al. 2021), this marker has only been tested widely in Atlantic clade species. Preliminary testing by our lab found in Pacific clade white sturgeon (Acipenser transmontanus) found that the marker was found in both males and females of Sacramento River origin. Therefore, the sex marker may not be diagnostic for Pacific clade species. To find a diagnostic sex marker to improve monitoring of sDPS green sturgeon, we are sequencing the nDPS green sturgeon genome.

Preliminary Results

We have successfully performed long read sequencing on one male and one female green sturgeon held at the UC Davis Center for Aquaculture and Aquatic Biology (CABA) for conservation research. These fish have been generously provided by the Yurok Tribe to co-PI Dr. Nann Fangue for conservation-oriented studies. The estimated genome size from the assembled genome matches what we’ve observed from flow cytometry and Coulter counter analyses and the gene set present in both the male and female genomes is highly complete. Phase Genomics performed HiC on the genomes and currently the genomes are being scaffolded. We will then compare the male and female genomes to look for any differences on the sequence or structural level. Then we will test whether any candidate sex specific differences are found in a larger sample and known male and female green sturgeon from both DPS’s.


Dr. Daphne Gille from the California Department of Water Resources and Dr. Fangue are co-PIs on this project. This project is proceeding alongside an effort to sequence the lake sturgeon genome, led by  Dr. Matt Thorstensen , a GVL alum and now post-doc at the University of Manitoba in Dr. Gary Anderson’s lab.

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