Comparative transcriptome analysis reveals molecular adaptations underlying distinct immunity and inverted resting posture in bats

Single-cell and Spatial Transcriptomics Illuminate Bat Immunity and Barrier Tissue Evolution

Bats have adapted to pathogens through diverse mechanisms, including increased resistance-rapid pathogen elimination, and tolerance-limiting tissue damage following infection. In the Egyptian fruit bat (an important model in comparative immunology), several mechanisms conferring disease tolerance were discovered, but mechanisms underpinning resistance remain poorly understood. Previous studies on other species suggested that the elevated basal expression of innate immune genes may lead to increased resistance to infection. Here, we test whether such transcriptional patterns occur in Egyptian fruit bat tissues through single-cell and spatial transcriptomics of gut, lung, and blood cells, comparing gene expression between bat, mouse, and human. Despite numerous recent loss and expansion events of interferons in the bat genome, interferon expression and induction are remarkably similar to that of mouse. In contrast, central complement system genes are highly and uniquely expressed in key regions in bat lung and gut epithelium, unlike in human and mouse. Interestingly, the unique expression of these genes in the bat gut is strongest in the crypt, where developmental expression programs are highly conserved. The complement system genes also evolve rapidly in their coding sequences across the bat lineage. Finally, the bat complement system displays strong hemolytic activity. Together, these results indicate a distinctive transcriptional divergence of the complement system, which may be linked to bat resistance, and highlight the intricate evolutionary landscape of bat immunity.

Comparative analysis of chromosome-level genomes provides insights into chromosomal evolution in Chiroptera

Chiroptera (bats) presents a fascinating model due to its remarkable variation in chromosome numbers, which range from 14 to 62. This astonishing diversity makes bats an excellent subject for studying chromosome evolution. The black-bearded tomb bat (Taphozous melanopogon) occupies a pivotal phylogenetic position within Chiroptera, emphasizing its crucial role in the systematic examination of bat chromosome evolution. In this study, we present the first chromosome-level genome of T. melanopogon within the family Emballonuridae. Together with previously published genomes, we construct a strongly supported phylogenetic tree of bats, which supports that Emballonuridae forms a basal group within Yangochiroptera. Furthermore, we reconstruct ancestral karyotypes at key nodes along the bat phylogeny and conduct a synteny analysis among the genomes of 12 bat species. Our findings identified evolutionary breakpoint regions (EBRs) that are of particular interest. Notably, some bat genomes exhibit an enrichment of genes related to host defense against microbial pathogens within EBRs. Remarkably, one species possesses multiple copies of some β-defensin genes, while six other species have experienced the loss of some β-defensin genes due to EBRs. Furthermore, some olfactory receptor genes are located in EBRs of 12 species, 4 of which have a significant enrichment in sensory perception of smell. Together, our comparative genomic analysis underscores the potential link between chromosome rearrangements and the adaptation of bats to defend against microbial pathogens.

The changes in zoological publication rates and focal subdisciplines between 1960 and 2022

Since ancient times, zoology, as the branch of biology dealing with animals, has been a cornerstone of natural science and has developed substantially over the last century. We conducted a bibliometric analysis using structural topic modeling (STM) to determine changes in the representation of principal zoological subdisciplines in the literature between 1960 and 2022. We collated a corpus of 217 414 articles from 88 top-ranked zoology journals and identified three main fields: (i) ecology, (ii) evolution, and (iii) applied research. Within these, we identified 10 major subdisciplines. The number of studies published per year grew from 118 in 1960 to 6635 in 2022. Macroscale-related subdisciplines increased while classical and traditional subdisciplines decreased. Mammals (34.4%) and insects (18.1%) were the dominant taxa covered, followed by birds (15.2%) and fish (8.0%). Research on mammals, insects, and fish involved a broad range of subdisciplines, whereas studies of birds focused on ecological subdisciplines. Most publications were from the United States, followed by the United Kingdom, Germany, Canada, Australia, China, and Japan, with two developing countries, China and South Africa among the top 15 countries. There were different subdiscipline biases between countries, and the gross domestic product of each country correlated positively with its publication output (R2 = 0.681). We discuss our findings in the context of advances in technological innovations and computing power, as well as the emergence of ecology as a formal sister discipline, driven by changing environmental pressures and societal values. We caution that valuable publications from traditional zoological fields must not be completely supplanted by more contemporary topics and increasingly sophisticated analyses.

Transporters and phytohormones analysis reveals differential regulation of ryegrass (Lolium perenne L.) in response to cadmium and arsenic stresses

Cadmium (Cd) and arsenic (As) are two highly toxic heavy metals and metalloids that coexist in many situations posing severe threats to plants. Our investigation was conducted to explore the different regulatory mechanisms of ryegrass (Lolium perenne L.) responding to individual and combined Cd and As stresses in hydroponics. Results showed that the ryegrass well-growth phenotype was not affected by Cd stress of 10 mg·L-1. However, As of 10 mg·L-1 caused rapid water loss, proline surge, and chlorosis in shoots, suggesting that ryegrass was highly sensitive to As. Transcriptomic analysis revealed that the transcription factor LpIRO2 mediated the upregulation of ZIP1 and YSL6 that played an important role in Cd tolerance. We found that the presence of As caused the overexpression of LpSWT12, a process potentially regulated by bHLH14, to mitigate hyperosmolarity. Indoleacetic acid (IAA) and abscisic acid (ABA) contents and expression of their signaling-related genes were significantly affected by As stress rather than Cd. We predict a regulatory network to illustrate the interaction between transporters, transcription factors, and signaling transduction, and explain the antagonism of Cd and As toxicity. This present work provides a research basis for plant protection from Cd and As pollution.

Immunological features of bats: resistance and tolerance to emerging viruses

Bats are among the most diverse mammalian species, representing over 20% of mammalian diversity. The past two decades have witnessed a disproportionate spillover of viruses from bats to humans compared with other mammalian hosts, attributed to the viral richness within bats, their phylogenetic likeness to humans, and increased human contact with wildlife. Unique evolutionary adaptations in bat genomes, particularly in antiviral protection and immune tolerance genes, enable bats to serve as reservoirs for pandemic-inducing viruses. Here, we discuss current limitations and advances made in understanding the role of bats as drivers of pandemic zoonoses. We also discuss novel technologies that have revealed spatial, dynamic, and physiological factors driving virus and host coevolution.