Impacts of seasonality on gene expression in the Chinese horseshoe bat

Abstract

Seasonality can cause changes in many environmental factors which potentially affects gene expression. Here, we used a bat species ( Rhinolophus sinicus ) from eastern China as a model to explore the molecular mechanisms of seasonal effects, in particular during phenological shifts in the spring and autumn. Based on the analysis of 45 RNA‐seq samples, we found strong seasonal effects on gene expression, with a large number of genes identified as either specific or biased to each season. Weighted gene co‐expression network analysis also identified multiple modules significantly associated with each season. These seasonal genes were further enriched into different functional categories. Consistent with effects of phenological shifts on bats, we found that genes related to promoting food intake were highly expressed in both autumn and spring. In addition, immunity genes were also highly expressed in both seasons although this seasonal immune response had tissue specificity in different seasons. In female bats, genes related to the delay of ovulation (e.g., NPPC , natriuretic peptide precursor type C) were highly expressed in October, while genes associated with the promotion of reproduction (e.g., DIO2 , iodothyronine deiodinase 2) were biasedly expressed in April. Lastly, we found multiple known core clock genes in both October‐biased and April‐biased expressed genes, which may be involved in regulating the start and end of hibernation, respectively. Overall, together with studies in other land and aquatic animals, our work supports that seasonal gene expression variations may be a general evolutionary response to environmental changes in wild animals.

Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat

“…Here, we obtained 16 tissue samples of RNA-seq data from Chen & Mao (2022) with an average of 39,217,309 filtered pair reads per sample and an overall alignment rate of 98.11% to the reference genome ( Table S1 ). Based on these data, we identified and characterized the differentially expressed genes and spliced genes between males and females.…”

“…However, we still cannot confidently determine whether the sampled individuals were at the same age. To reduce the effect of age on gene expression, we only used adult bats in this study ( Chen & Mao, 2022 ). In the future, we can first determine the age of bats using DNA methylation profiles which use noninvasive sampling ( Wilkinson et al, 2021 ).…”

“…All samples used in this study were obtained from Chen & Mao (2022) and raw sequencing reads were available from the NCBI Sequence Read Archive (SRA) under Bioproject accession number PRJNA763734 . Briefly, bats were captured using mist nets in Jiangsu, China in April ( Fig.…”

“…Following Chen & Mao (2022) , raw sequencing reads from each sample were processed using TRIMMOMATIC version 0.38 ( Bolger, Lohse & Usadel, 2014 ) with the parameters of SLIDINGWINDOW:4:20. We further trimmed reads to 120 bp and removed those with <120 bp in order to meet the requirement of rMATs (see below) that all input reads should be of equal length.…”

Adapting to stress: The effects of hibernation and hibernacula temperature on the hepatic transcriptome of Rhinolophus pusillus

“…Additionally, immune‐related genes are upregulated, enhancing resistance against pathogens 15 . Seasonal changes also play a role in gene expression during hibernation, with several core clock genes regulating the initiation and conclusion of hibernation in R. sinicus 16 . However, for animals lacking a reference transcriptome, relying solely on RNA sequencing technology for research may lead to inaccurate findings due to limitations in sequence reading length and errors resulting from sequence splicing.…”