Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

The impact of global warming on the signature virulence gene, thermolabile hemolysin, of Vibrio parahaemolyticus

IMPORTANCE

In this study, Vibrio parahaemolyticus strains were collected from a large number of aquatic products globally and found that temperature has an impact on the virulence of these bacteria. As global temperatures rise, mutations in a gene marker called thermolabile hemolysin (tlh) also increase. This suggests that environmental isolates adapt to the warming environment and become more pathogenic. The findings can help in developing tools to analyze and monitor these bacteria as well as assess any link between climate change and vibrio-associated diseases, which could be used for forecasting outbreaks associated with them.

An ensemble learning approach to map the genetic connectivity of the parasitoid Stethynium empoasca (Hymenoptera: Mymaridae) and identify the key influencing environmental and landscape factors

The effect of landscape patterns and environmental factors on the population structure and genetic diversity of organisms is well-documented. However, this effect is still unclear in the case of Mymaridae parasitoids. Despite recent advances in machine learning methods for landscape genetics, ensemble learning still needs further investigation. Here, we evaluated the performance of different boosting algorithms and analyzed the effects of landscape and environmental factors on the genetic variations in the tea green leafhopper parasitoid Stethynium empoasca (Hymenoptera: Mymaridae). The S. empoasca populations showed a distinct pattern of isolation by distance. The minimum temperature of the coldest month, annual precipitation, the coverage of evergreen/deciduous needleleaf trees per 1 km2, and the minimum precipitation of the warmest quarter were identified as the dominant factors affecting the genetic divergence of S. empoasca populations. Notably, compared to previous machine learning studies, our model showed an unprecedented accuracy (r = 0.87) for the prediction of genetic differentiation. These findings not only demonstrated how the landscape shaped S. empoasca genetics but also provided an essential basis for developing conservation strategies for this biocontrol agent. In a broader sense, this study demonstrated the importance and efficiency of ensemble learning in landscape genetics.

Population expansion, divergence, and persistence in Western Fence Lizards (Sceloporus occidentalis) at the northern extreme of their distributional range

Population dynamics within species at the edge of their distributional range, including the formation of genetic structure during range expansion, are difficult to study when they have had limited time to evolve. Western Fence Lizards (Sceloporus occidentalis) have a patchy distribution at the northern edge of their range around the Puget Sound, Washington, where they almost exclusively occur on imperiled coastal habitats. The entire region was covered by Pleistocene glaciation as recently as 16,000 years ago, suggesting that populations must have colonized these habitats relatively recently. We tested for population differentiation across this landscape using genome-wide SNPs and morphological data. A time-calibrated species tree supports the hypothesis of a post-glacial establishment and subsequent population expansion into the region. Despite a strong signal for fine-scale population genetic structure across the Puget Sound with as many as 8-10 distinct subpopulations supported by the SNP data, there is minimal evidence for morphological differentiation at this same spatiotemporal scale. Historical demographic analyses suggest that populations expanded and diverged across the region as the Cordilleran Ice Sheet receded. Population isolation, lack of dispersal corridors, and strict habitat requirements are the key drivers of population divergence in this system. These same factors may prove detrimental to the future persistence of populations as they cope with increasing shoreline development associated with urbanization.

Cathepsin D knockdown regulates biological behaviors of granulosa cells and affects litter size traits in goats

Cathepsin D (CTSD), the major lysosomal aspartic protease that is widely expressed in different tissues, potentially regulates the biological behaviors of various cells. Follicular granulosa cells are responsive to the increase of ovulation number, hence indirectly influencing litter size. However, the mechanism underlying the effect of CTSD on the behaviors of goat granulosa cells has not been fully elucidated. This study used immunohistochemistry to analyze CTSD localization in goat ovarian tissues. Moreover, western blotting was applied to examine the differential expression of CTSD in the ovarian tissues of monotocous and polytocous goats. Subsequently, the effects of CTSD knockdown on cell proliferation, apoptosis, cell cycle, and the expression of candidate genes of the prolific traits, including bone morphogenetic protein receptor IB (BMPR-IB), follicle-stimulating hormone (FSHR), and inhibin α (INHA), were determined in granulosa cells. Results showed that CTSD was expressed in corpus luteum, follicle, and granulosa cells. Notably, CTSD expression in the monotocous group was significantly higher than that in the polytocous group. In addition, CTSD knockdown could improve granulosa cell proliferation, inhibit cell apoptosis, and significantly elevate the expression of proliferating cell nuclear antigen (PCNA) and B cell lymphoma 2 (Bcl-2), but it lowered the expression of Bcl-2-associated X (Bax) and caspase-3. Furthermore, CTSD knockdown significantly reduced the ratios of cells in the G0/G1 and G2/M phases but substantially increased the ratio of cells in the S phase. The expression levels of cyclin D2 and cyclin E were elevated followed by the obvious decline of cyclin A1 expression. However, the expression levels of BMPR-IB, FSHR, and INHA clearly increased as a result of CTSD knockdown. Hence, our findings demonstrate that CTSD is an important factor affecting the litter size trait in goats by regulating the granulosa cell proliferation, apoptosis, cell cycle, and the expression of candidate genes of the prolific trait.

False and true positives in arthropod thermal adaptation candidate gene lists

Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the respective genomes. This is consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the "omnigenic" concept of genetic architecture of complex traits.

Polymorphisms in BMPR-IB gene and their association with litter size trait in Chinese Hu sheep

Identification and utilization of sheep major fecundity genes offer opportunities for the increase in litter size, as well as the improvement of production efficiency in livestock industry. BMPR-IB gene belongs to the TGF-β superfamily, and is also considered as a regulator for sheep reproductive performance due to its involvement in the mammalian gametogenesis pathway. This study aimed to detect the variations of BMPR-IB gene in Hu sheep (N = 934) and to evaluate their effects on the litter size trait. qRT-PCR results showed that the mRNA expression level of BMPR-IB in kidney was the highest. And in the tissues of ovary and pituitary, the expression levels of prolific group were significantly higher than that of non-prolific group (p < 0.05). Through DNA sequencing and PCR-RFLP, three SNPs were identified in the genomic region of BMPR-IB gene; the individuals with CC in g.29362047T > C, AA in g.29427689G > A and GG in FecB had better fecundity characterization. Additionally, association analysis indicated that two diplotypes of Hap2/2 and Hap2/4 showed larger litter size. Overall, our results verified several useful markers which would contribute to further development of sheep breeding strategies.

Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes

BACKGROUND

Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation.

RESULTS

A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species.

CONCLUSIONS

The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.

Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics

Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.

Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation

Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or "hypothetical" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for "hypothetical proteins" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnia's genetic and phenotypic variability.

Transcriptome Analysis Reveals Candidate Genes for Cold Tolerance in Drosophila ananassae

Coping with daily and seasonal temperature fluctuations is a key adaptive process for species to colonize temperate regions all over the globe. Over the past 18,000 years, the tropical species Drosophila ananassae expanded its home range from tropical regions in Southeast Asia to more temperate regions. Phenotypic assays of chill coma recovery time (CCRT) together with previously published population genetic data suggest that only a small number of genes underlie improved cold hardiness in the cold-adapted populations. We used high-throughput RNA sequencing to analyze differential gene expression before and after exposure to a cold shock in cold-tolerant lines (those with fast chill coma recovery, CCR) and cold-sensitive lines (slow CCR) from a population originating from Bangkok, Thailand (the ancestral species range). We identified two candidate genes with a significant interaction between cold tolerance and cold shock treatment: GF14647 and GF15058. Further, our data suggest that selection for increased cold tolerance did not operate through the increased activity of heat shock proteins, but more likely through the stabilization of the actin cytoskeleton and a delayed onset of apoptosis.