Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Dolby, Greer A.; Morales, Matheo; Webster, Timothy H.; DeNardo, Dale F.; Wilson, Melissa A.; Kusumi, Kenro

doi:10.1093/gbe/evaa016

Cited by 10 publications

(6 citation statements)

References 48 publications

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“…Gene duplication events can facilitate the evolution and expansion of a gene family's function, specialized sub-functionalization, or differences in gene expression [175][176][177]. However, gene loss through mutations or pseudogenization can also be an adaptive evolutionary force depending on gene dispensability, mutational robustness, and environmental conditions [178]. The genomic diversity of TLRs in non-model species is a very interesting area of research, indicating evolution through both positive and negative selection because of infectious or environmental pressure.…”

Section: Toll-like Receptorsmentioning

confidence: 99%

Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running

Nash

Ryan

2023

Animals

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The immune system of sea turtles is not completely understood. Sea turtles (as reptiles) bridge a unique evolutionary gap, being ectothermic vertebrates like fish and amphibians and amniotes like birds and mammals. Turtles are ectotherms; thus, their immune system is influenced by environmental conditions like temperature and season. We aim to review the turtle immune system and note what studies have investigated sea turtles and the effect of the environment on the immune response. Turtles rely heavily on the nonspecific innate response rather than the specific adaptive response. Turtles’ innate immune effectors include antimicrobial peptides, complement, and nonspecific leukocytes. The antiviral defense is understudied in terms of the diversity of pathogen receptors and interferon function. Turtles also mount adaptive responses to pathogens. Lymphoid structures responsible for lymphocyte activation and maturation are either missing in reptiles or function is affected by season. Turtles are a marker of health for their marine environment, and their immune system is commonly dysregulated because of disease or contaminants. Fibropapillomatosis (FP) is a tumorous disease that afflicts sea turtles and is thought to be caused by a virus and an environmental factor. We aim, by exploring the current understanding of the immune system in turtles, to aid the investigation of environmental factors that contribute to the pathogenesis of this disease and provide options for immunotherapy.

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Section: Toll-like Receptorsmentioning

confidence: 99%

Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running

Nash

Ryan

2023

Animals

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“…Indeed, we found many general immune-related responses to be enriched among experimental immune groups, including GO:0002275 (myeloid cell activation involved in immune response), GO:0009410 (response to xenobiotic stimulus), and GO:0002252 (immune effector process). Previous studies on turtles revealed expression of immune-related genes [2,31,38,[58][59][60][61][62][63]] associated with both innate and adaptive immune functions. We expected differential expression of cytokines (e.g.…”

Section: Plos Onementioning

confidence: 99%

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii

Dolby

Drake

et al. 2020

PLoS ONE

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The immune system of ectotherms, particularly non-avian reptiles, remains poorly characterized regarding the genes involved in immune function, and their function in wild populations. We used RNA-Seq to explore the systemic response of Mojave desert tortoise (Gopherus agassizii) gene expression to three levels of Mycoplasma infection to better understand the host response to this bacterial pathogen. We found over an order of magnitude more genes differentially expressed between male and female tortoises (1,037 genes) than differentially expressed among immune groups (40 genes). There were 8 genes differentially expressed among both variables that can be considered sex-biased immune genes in this tortoise. Among experimental immune groups we find enriched GO biological processes for cysteine catabolism, regulation of type 1 interferon production, and regulation of cytokine production involved in immune response. Sex-biased transcription involves iron ion transport, iron ion homeostasis, and regulation of interferon-beta production to be enriched. More detailed work is needed to assess the seasonal response of the candidate genes found here. How seasonal fluctuation of testosterone and corticosterone modulate the immunosuppression of males and their susceptibility to Mycoplasma infection also warrants further investigation, as well as the importance of iron in the immune function and sexbiased differences of this species. Finally, future transcriptional studies should avoid drawing blood from tortoises via subcarapacial venipuncture as the variable aspiration of lymphatic fluid will confound the differential expression of genes.

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“…Yet, the hybrid zone between these species indicates they have not yet reached complete reproductive isolation, offering an opportunity to assess to what degree genomic reinforcement mechanisms have developed in this lineage pair. To do this we developed a chromosome-scale reference genome for G. morafkai and performed comparative genomic analyses with the published reference genome for G. agassizii 23 .…”

Section: Introductionmentioning

confidence: 99%

Strong signatures of selection on genes underlying core reinforcement mechanisms in speciating desert tortoises

Baty,

Araya-Donoso,

Paulsen

et al. 2024

Preprint

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Genomic reinforcement and differential ecological adaptation are thought to be fundamental mechanisms of speciation. In this study we investigate the genomic basis of adaptation and reinforcement between two desert tortoise species of North America that occupy desert habitats with differing seasonal rainfall patterns and have considerable behavioral and reproductive differences yet maintain a narrow hybrid zone. We generated a chromosome-scale reference genome for Gopherus morafkai and performed analysis of synteny, genes under positive selection, and environmental niche modeling. Results show extensive positive selection (422 genes) including related to eye development and function that may relate to environmental differences, as well as prezygotic isolation mechanisms such as sperm-egg recognition, and postzygotic reinforcement mechanisms such as the spindle assembly checkpoint, and sister chromatid pairing. Together, results offer strong genetic support for the role of these classic processes in shaping reproductive isolation and lineage divergence of speciating tortoises.

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Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Cited by 10 publications

References 48 publications

Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running

Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii

Strong signatures of selection on genes underlying core reinforcement mechanisms in speciating desert tortoises

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