About

Sergey Nuzhdin holds a Ph.D. in Evolution and Ecology and is affiliated with the College of Biological Sciences at the University of California, Davis. His office is located in 2320 Storer Hall. His research focuses on evolution and ecology, contributing to the understanding of biological processes through his academic work. As a faculty member, he is involved in teaching and research activities within the Department of Evolution and Ecology, supporting the university's mission to advance knowledge in biological sciences.

Research topics

• Environmental science
• Food science
• Agronomy
• Ecology
• Animal science
• Biology

Selected publications

• Differential transcriptomic and circadian regulation across giant kelp blades based on relative tissue age

  Journal of Phycology · 2026-02-21

  articleOpen access

  Kelps are ecologically and economically important organisms. Kelp biomass generates habitat structure and carbon flux and is increasingly harvested as a sustainable resource. Kelp blades grow through cell proliferation at the proximal meristem and erode from the distal end, resulting in a spatiotemporal map reflecting tissue development. Diel physiology, such as photosynthesis, respiration, and carbohydrate metabolism, changes across the growing blade, yet the interaction of the circadian clock with age / blade structure has not been explicitly tested. Here, we sampled the proximal and distal ends of giant kelp (Macrocystis pyrifera) blades over 48 h under constant lab conditions to compare differential transcriptomic and circadian regulation across the blade. Gene function was differentially enriched across the blade, with proliferative and protective pathways upregulated in the younger proximal tissue and carbon acquisition and metabolic pathways upregulated in older distal tissue. We identified candidate aging-related genes based on similarities to plant, animal, and fungal senescence-associated genes, which were enriched in the older, distal tissue. While ~13% of analyzed genes displayed consistent circadian regulation across the blade, ~2% displayed altered rhythmic parameters, with consistently lower amplitudes and longer periods in older distal tissue. This is evidence of variable circadian physiology across giant kelp anatomy. The interacting developmental and circadian influences on the giant kelp transcriptome evoked here are integral for understanding the coordination of physiology important to kelp growth and health.

  PublisherOA PDFDOI

• Assessing the effects of ocean acidification on larval Mediterranean mussels (Mytilus galloprovincialis) and California mussels (Mytilus californianus): growth, survival, and microbiome community composition

  Discover Oceans · 2025-12-23

  articleOpen accessSenior author

  Ocean acidification (OA) affects marine calcifying organisms in a variety of ways, including: growth, survival, disease resistance, microbial communities, and physiological functions. With oceanic pH projected to drop to 7.7 or lower by the year 2100, it is important to the aquaculture industry to characterize the affects of these environmental conditions on species of economic and ecological importance. Associated microbiota can have a strong impact on organismal health, however, the microbiomes of many aquaculture species are only beginning to be thoroughly investigated within the context of climate change. This study assessed the growth, survival, and microbial communities of two mussel species, the Mediterranean mussel Mytilus galloprovincialis and the California mussel Mytilus californianus in response to experimental low-pH exposure across larval development (2–21 days post-fertilization). We found that experimental exposure resulted in significant decreases in growth rates for both species, but did not strongly affect larval survival probability. Sequencing of the V3-V4 region of the 16S ribosomal subunit demonstrated that although microbial membership and relative abundance were similar between the two mussel species, diversity measures were significantly different. Following exposure, we found that reduced-pH during the larval stage resulted carry-over effects into adulthood of wet weight and total length in M. galloprovincialis mussels. The results suggest that OA exposure during the larval stage may exert stronger effects in M. galloprovincialis than in M. californianus and provide insights into the response of mussel microbial communities to future ocean conditions.

  PublisherOA PDFDOI

• Phytohormones in <i>Kappaphycus alvarezii:</i> Genomic Insights, Activation Thresholds, and Implications for Seaweed-derived Biostimulants

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21

  preprintOpen access

  Abstract The use of seaweed extracts in agriculture has gained significant attention in recent years, yet the genomic mechanisms underlying their activity remain poorly understood. Seaweeds such as Kappaphycus alvarezii synthesize diverse bioactive compounds, but their endogenous hormone pathways have been largely uncharacterized. Phytohormones, essential regulators of plant growth, reproduction, and stress responses, are central to the beneficial effects of these biostimulants. To uncover these mechanisms, we performed a genome-wide analysis of hormone biosynthesis and recognition pathways across thirteen algal species, focusing on nine classes of phytohormones. By integrating KEGG annotation, structural modeling, and eggNOG-based orthology, we assessed the completeness and conservation of hormone-associated pathways. Our results revealed consistent retention of key biosynthetic entry points, including IAM-related enzymes for auxin, TRIT1/CYP735A for cytokinins, GA oxidases for gibberellins, and pchA for salicylic acid, alongside divergent or absent canonical upstream enzymes. In parallel, partial but conserved signaling modules were identified for abscisic acid, ethylene, and other classes. This mosaic pattern, fragmented biosynthesis coupled with selectively retained signaling, suggests that algae employ noncanonical enzymatic routes or microbial complementation to sustain hormone activity. Expression profiling in K. alvarezii further revealed light-responsive regulation of auxin, cytokinin, GA, and ABA genes, highlighting their role in environmental adaptation. Together, these findings provide new genomic insights into algal hormone biology, establish the first structural and functional evidence for GA metabolism in red algae, and identify candidate phytohormones likely to contribute to the biostimulant activity of K. alvarezii extracts.

  PublisherDOI

• The mutation atlas of giant kelp (Macrocystis pyrifera): a mutation database resource for natural knockouts

  Frontiers in Plant Science · 2025-01-27

  articleOpen accessSenior authorCorresponding

  ) is a paramount species of immense ecological and economic importance. It forms dense underwater forests, providing crucial habitat and serving as a foundation species for diverse marine ecosystems. Understanding the genetics of giant kelp is essential for conservation and sustainable farming, safeguarding these valuable ecosystems and their benefits. By analyzing mutations based on their impact, we can gain insights into the potential functional consequences and implications for the organism, helping to identify critical genes or regions that may play a significant role in adaptation, development, and environmental response. To achieve this, we annotated the effects and impact of spontaneous mutations in 559 giant kelp individuals from four different populations. We found over 15.9 million mutations in genes of giant kelp, and classified them into modifier, low, moderate, and high impact depending on their predicted effects. The creation of this mutation effect database, attached to the seedbank of these individuals, offers several applications, including enhancing breeding programs, aiding genetic engineering with naturally occurring mutations, and developing strategies to mitigate the impact of environmental changes.

  PublisherOA PDFDOI

• Comparative Genomics of Sex‐Determination‐Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies

  Molecular Ecology · 2025-09-21 · 3 citations

  articleOpen access

  The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination-related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetically aware dataset of these SRGs, and we find support for the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterised systems, mammals and fruit flies (genus Drosophila). In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role as master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.

  PublisherOA PDFDOI

• The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-21 · 2 citations

  preprintOpen access

  Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80x of coverage and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Mb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

  PublisherOA PDFDOI

• Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing

  Genome Biology and Evolution · 2025-11-25

  articleOpen accessSenior author

  Chromosomal structural changes happen when genomic stability is compromised, such as in disease or in species hybrids. In these contexts, diminished control of repetitive elements has been reported, but the reasons for this are not yet well understood. There are causal associations between repetitive elements and phenotypes such as disease progression, leading us to the hypothesis that chromosomal structure may be affected by transposable elements (TEs). In an intraspecific hybrid Drosophila melanogaster cell line (PnM), the degree of pairing among trans homologous chromosomes was affected by the presence of nearby TEs, in particular, LINE and LTR elements, such as Baggins1 or Gypsy. Chromosomal pairing was significantly lower in windows containing TEs than in windows without any TEs. Pairing was also affected by TEs in mouse, which suggests a possible general association between TEs and pairing that is highly conserved.

  PublisherOA PDFDOI

• Insights from farming <i>Macrocystis pyrifera</i> offshore: phenotypic analysis, genome-wide association studies, genomic selection

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-24

  preprintOpen accessSenior author

  Abstract Seaweed farming, as a part of aquaculture, offers a sustainable alternative to modern agricultural practices; however, genetic enhancement and breeding programs for most species are underdeveloped. We aimed to advance seaweed domestication by focusing on giant kelp ( Macrocystis pyrifera ), the fastest-growing haplodiplontic brown alga, which has significant ecological and commercial importance. We analyzed phenotypic data from two offshore experimental farms conducted in 2019 and 2020, which involved hundreds of outplanted genetically diverse sporophytes. We found that outplanting season and farm design had significant effects on giant kelp biomass. Broad-sense heritability estimates showed moderate (0.27-0.50) genetic contributions to two phenotypes, carbon content and total biomass. Genome-wide association studies for these phenotypes resulted in three statistically significant SNPs, located near or within genes involved in carbohydrate metabolism and cytoskeletal functions. In addition, we applied genomic selection models that integrated sporophyte phenotypes and parental gametophyte genotypes. These models utilized reduced sets of GWAS-ranked SNPs obtained by a procedure based on linkage disequilibrium estimations. Model testing yielded cross-validation accuracy values of up to 0.84 and predictive accuracy values of up to 0.40, demonstrating the potential of marker-assisted breeding for phenotype improvement. Our results provide foundational genomic resources and tools for domesticating and breeding M. pyrifera , offering a basis for developing giant kelp varieties with desirable traits.

  PublisherOA PDFDOI

• Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima

  Frontiers in Genetics · 2025-05-14 · 3 citations

  articleOpen access

  Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica . While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.

  PublisherOA PDFDOI

• The reference genome for the northeastern Pacific bull kelp, <i>Nereocystis luetkeana</i>

  Journal of Heredity · 2025-10-11 · 2 citations

  articleOpen access

  Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and Macrocystis pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPase enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01MH100879

  NIH · $1.5M · 2017

• NIH Grant R01GM076643

  NIH · $1.2M · 2011

• NIH Grant R01GM098741

  NIH · $1.3M · 2016

• NIH Grant U01GM103804

  NIH · $1.5M · 2017

• Community Genomics of Local Adaptation in Medicago Truncatula

  NSF · $3.2M · 2008–2012

Frequent coauthors

• Peter L. Chang

  University of Southern California

  91 shared

• Konstantin Kozlov

  Peter the Great St. Petersburg Polytechnic University

  59 shared

• Eric von Wettberg

  52 shared

• Lauren M. McIntyre

  University of Ottawa

  46 shared

• Katrina Sherbina

  40 shared

• Alina I. Chernova

  Skolkovo Institute of Science and Technology

  40 shared

• Anupam Singh

  National Research Centre on Plant Biotechnology

  39 shared

• E. G. Pasyukova

  Kurchatov Institute

  39 shared

Education

• Ph.D., Animal Genetics

  Federal State Institution of Science Institute of Molecular Genetics, Russian Academy of Sciences

  1992