Chow Julie C, Kyritsis Nia, Mills Micah, Godfrey Matthew H, Harms Craig A, Anderson Paul E, Shedlock Andrew M
Genome Center, University of California, Davis, CA 95616, USA.
Program in Bioinformatics, Franklin and Marshall College, Lancaster, PA 17604, USA.
Animals (Basel). 2021 Oct 20;11(11):3013. doi: 10.3390/ani11113013.
: Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. The sex of the endangered loggerhead sea turtle () is subject to temperature-dependent sex determination (TSD), a mechanism by which exposure to temperatures during embryonic development irreversibly determines sex. Higher temperatures produce mainly female turtles and lower temperatures produce mainly male turtles. Incubation temperature can have long term effects on the immunity, migratory ability, and ultimately longevity of hatchlings. We perform RNA-seq differential expression analysis to investigate tissue- and temperature-specific gene expression within brain ( = 7) and gonadal ( = 4) tissue of male and female loggerhead hatchlings. : We assemble tissue- and temperature-specific transcriptomes and identify differentially expressed genes relevant to sexual development and life history traits of broad adaptive interest to turtles and other amniotic species. We summarize interactions among differentially expressed genes by producing network visualizations, and highlight shared biological pathways related to migration, immunity, and longevity reported in the avian and reptile literature. : The measurement of tissue- and temperature-specific global gene expression of an endangered, flagship species such as the loggerhead sea turtle () reveals the genomic basis for potential resiliency and is crucial to future management and conservation strategies with attention to changing climates. Brain and gonadal tissue collected from experimentally reared loggerhead male and female hatchlings comprise an exceedingly rare dataset that permits the identification of genes enriched in functions related to sexual development, immunity, longevity, and migratory behavior and will serve as a large, new genomic resource for the investigation of genotype-phenotype relationships in amniotes.
数字转录组学正迅速成为一种强大的新技术，用于模拟不同谱系中适应性景观的环境动态。这在龟鳖类动物（龟鳖目）等分类群中尤其有价值，这些分类群中很大一部分濒危物种因人为对环境的影响而面临风险，包括污染、过度捕捞、栖息地退化和气候变化。特别是海龟（海龟科），需要采用基因组学方法来研究其显著的适应性进化组合。濒危蠵龟（Caretta caretta）的性别由温度依赖型性别决定（TSD）控制，即胚胎发育期间暴露于特定温度会不可逆地决定性别。较高温度主要产生雌性海龟，较低温度主要产生雄性海龟。孵化温度会对幼龟的免疫力、迁徙能力以及最终寿命产生长期影响。我们进行RNA测序差异表达分析，以研究蠵龟幼龟大脑（n = 7）和性腺（n = 4）组织中组织特异性和温度特异性基因表达。我们组装了组织特异性和温度特异性转录组，并鉴定出与海龟和其他羊膜动物广泛适应性相关的性发育和生活史特征相关的差异表达基因。我们通过生成网络可视化来总结差异表达基因之间的相互作用，并突出鸟类和爬行动物文献中报道的与迁徙、免疫和寿命相关的共同生物学途径。对濒危旗舰物种蠵龟（Caretta caretta）进行组织特异性和温度特异性全局基因表达测量，揭示了潜在恢复力的基因组基础，对于关注气候变化的未来管理和保护策略至关重要。从实验饲养的蠵龟雌雄幼龟收集的大脑和性腺组织构成了一个极其罕见的数据集，可用于鉴定在与性发育、免疫、寿命和迁徙行为相关的功能中富集的基因，并将作为研究羊膜动物基因型-表型关系的大型新基因组资源。
