Transcriptomic thermal plasticity underlying gonadal development in a turtle with ZZ/ZW sex chromosomes despite canalized genotypic sex determination

Abstract

Understanding genome‐wide responses to environmental conditions during embryogenesis is essential for discerning the evolution of developmental plasticity and canalization, two processes generating phenotypic variation targeted by natural selection. Here, we present the first comparative trajectory analysis of matched transcriptomic developmental time series from two reptiles incubated under identical conditions, a turtle with a ZZ/ZW system of genotypic sex determination (GSD), Apalone spinifera, and a turtle with temperature‐dependent sex determination (TSD), Chrysemys picta. Results from our genome‐wide, hypervariate gene expression analysis of sexed embryos across five developmental stages revealed that substantial transcriptional plasticity in the developing gonads can persist for >145 Myr, long after the canalization of sex determination via the evolution of sex chromosomes, while some gene‐specific thermal sensitivity drifts or evolves anew. Such standing thermosensitivity represents an underappreciated evolutionary potential harbored by GSD species that may be co‐opted during future adaptive shifts in developmental programing, such as a GSD to TSD reversal, if favored by ecological conditions. Additionally, we identified novel candidate regulators of vertebrate sexual development in GSD reptiles, including sex‐determining candidate genes in a ZZ/ZW turtle.

Cross-species genomic survey reveals a single origin of the soft-shelled turtles

“…sinensis , combining Oxford Nanopore sequencing, Illumina, and Hi-C technologies, with the genome size of 2.36 Gb and the scaffold N50 124.95 Mb, which is larger than the reported Trionychidae species P . sinensis (Wang et al ., 2013), A. spinifera (Gessler et al, 2023), R. swinhoei (Ren et al ., 2022), and P. cantorii (Liu et al, 2023) genomes and even other hard-shelled turtles including Trachemys scripta (Brian Simison et al, 2020), Chelonia mydas , and Dermochelys coriacea , providing an invaluable genetic resource for the origin and evolution of Trionychidae. The assembled P .…”

“…Moreover, P . sinensis and A. spinifera currently only have draft genomes (Gessler et al ., 2023; Wang et al ., 2013).…”

“…A. spinifera (Gessler et al, 2023), R. swinhoei (Ren et al, 2022), and P. cantorii (Liu et al, 2023) genomes and even other hard-shelled turtles including Trachemys scripta (Brian Simison et al, 2020), Chelonia mydas, and Dermochelys coriacea, providing an invaluable genetic resource for the origin and evolution of Trionychidae. The assembled P. sinensis genome has 32 autosomes, and complete Z and W sex chromosomes, which directly demonstrated that P. sinensis turtle has a ZW-type GSD system, matching with previous studies (Liang et al, 2019;Mu et al, 2015).…”

Understanding the role of environmental temperature on sex determination through comparative studies in reptiles and amphibians

“…In addition, genes related to epigenetic modifications, such as Lysine (K)‐specific demethylase 6B ( KDM6B ; also called Jumonji domain‐containing protein‐3 , JMJD3 ) and Jumonji and AT‐rich interaction domain containing 2 ( JARID2 ), were upregulated at female‐producing temperatures (Yatsu et al, 2016). Subsequently, gonadal transcriptome analyses (RNA‐seq) have been conducted in various TSD and GSD testudines during sex determination periods, including studies involving TSD T. scripta (Czerwinski et al, 2016), comparisons between the western pond turtle (TSD Chrysemys picta ) and the spiny softshell turtle (GSD Apalone spinifera ) (Bista et al, 2021; Gessler et al, 2023; Radhakrishnan et al, 2017), a comparison between GSD and sex‐reversed individuals of the central bearded dragon ( Pogona vitticeps ) (Whiteley, Holleley, et al, 2022), and a comparison between TSD T. scripta and TSD A. mississippiensis (Toyota et al, 2023). In amphibians, transcriptome analysis (microarray) during the sex determination period has also been conducted in X. laevis tadpoles (Piprek et al, 2018).…”

Müllerian Duct Development and Regression in Reeves' Turtles, Mauremys reevesii, Under Female- and Male-Producing Temperatures

“…All crocodilians and snakes exhibit TSD and genotypic sex determination (GSD), respectively, but evolutionary transitions between TSD and GSD have occurred multiple times in lizard and turtle lineages. Species in these lineages offer opportunities to investigate the mechanisms of evolutionary transitions in sex determination systems through comparisons between TSD and/or GSD turtles, such as studies on Painted Turtles (Chrysemys picta - TSD) and Spiny Softshells (Apalone spinifera – GSD [Radhakrishnan et al, 2017; Bista et al, 2021; Gessler et al, 2023]). In the family Geoemydidae, M. reevesii is the only species whose genome has been determined at the chromosomal level to date (Liu et al, 2022).…”