Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai–Tibetan plateau

Yu, Xiaolei; Wei, Pei; Zhao, Shuqi; Chen, Zhuyifu; Li, Xinzhong; Zhang, Wencai; Liu, Chenlai; Yang, Yujiao; Li, Xiaoyan; Liu, Xing

doi:10.1007/s00299-023-03005-w

Cited by 4 publications

(2 citation statements)

References 82 publications

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“…This indicates that the divergence in genome expression is subjected to stabilizing selection under nonstressful conditions, and the evolution trends in expression variation levels are consistent with sequence variation levels [9]. However, when populations are subjected to environmental stress, epigenetic modifications (e.g., DNA methylation) and gene expression can be changed, leading to faster adaptation to new growth environments compared to sequence mutations [36][37][38][39]. Changes in the expression of one gene can affect other related genes, so genome-wide expression regulation might evolve more rapidly than nucleotide variation [34,39].…”

Section: Divergence Between Indica and Japonica Rice At Both Dna Sequ...mentioning

confidence: 81%

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Wang,

Huang,

Kou

et al. 2023

Genes

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Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world’s most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.

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Section: Divergence Between Indica and Japonica Rice At Both Dna Sequ...mentioning

confidence: 81%

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Wang,

Huang,

Kou

et al. 2023

Genes

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“…High-altitude areas such as the Qinghai-Tibetan Plateau are often accompanied by extreme weather conditions of low temperature, hypoxia, and strong ultraviolet radiation, which are usually unsuitable for the growth and development of biological organisms (Yu et al, 2023 ). However, organisms such as mammals and ruminants have evolved some strategies to adapt to high-altitude environments (Friedrich and Wiener, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats

et al. 2023

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The gut microbiota affects the health and overall fitness of bumblebees. It can enhance the host's ecological range by leveraging their metabolic capacities. However, the diversity of the gut microbiota and adaptive functional evolution in high-altitude regions remain unclear. To explore how the gut microbiota helps the host adapt to high-altitude environments, we analyzed the differences in diversity and function of the gut microbiota between high- and low-altitude regions through full-length 16S rRNA sequencing. Our results show that high-altitude regions have a lower abundance of Fructobacillus and Saccharibacter compared to low-altitude regions. Additionally, some individuals in low-altitude regions were invaded by opportunistic pathogens. The gut microbiota in high-altitude regions has a greater number of pathways involved in “Protein digestion and absorption” and “Biosynthesis of amino acids,” while fewer carbohydrate pathways are involved in “digestion and absorption” and “Salmonella infection.” Our finding suggests that plateau hosts typically reduce energy metabolism and enhance immunity in response to adverse environments. Correspondingly, the gut microbiota also makes changes, such as reducing carbohydrate degradation and increasing protein utilization in response to the host. Additionally, the gut microbiota regulates their abundance and function to help the host adapt to adverse high-altitude environments.

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Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation

Lai,

Hsu,

Futschik

et al. 2024

Preprint

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The phenomenon of parallel evolution, whereby similar genomic and phenotypic changes occur across replicated pairs of population or species, is widely studied. Nevertheless, the determining factors of parallel evolution remain poorly understood. Theoretical studies have proposed that pleiotropy, the influence of a single gene on multiple traits, is an important factor. In order to gain a deeper insight into the role of pleiotropy for parallel evolution from standing genetic variation, we characterized the interplay between parallelism, polymorphism and pleiotropy. The present study examined the parallel gene expression evolution in 10 replicated populations of Drosophila simulans , which were adapted from standing variation to the same new temperature regime. The data demonstrate that parallel evolution of gene expression from standing genetic variation is positively correlated with the strength of pleiotropic effects. The ancestral variation in gene expression is, however, negatively correlated with parallelism. Given that pleiotropy is also negatively correlated with gene expression variation, we conducted a causal analysis to distinguish cause and correlation and evaluate the role of pleiotropy. The causal analysis indicated that both direct (causative) and indirect (correlational) effects of pleiotropy contribute to parallel evolution. The indirect effect is mediated by historic selective constraint in response to pleiotropy. This results in parallel selection responses due to the reduced standing variation of pleiotropic genes. The direct effect of pleiotropy is likely to reflect a genetic correlation among adaptive traits, which in turn gives rise to synergistic effects and higher parallelism.

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Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai–Tibetan plateau

Cited by 4 publications

References 82 publications

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Potential role of the gut microbiota of bumblebee Bombus pyrosoma in adaptation to high-altitude habitats

Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation

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