Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling.

The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.

Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii).

Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.

Three Novel C-Repeat Binding Factor Genes of Dimocarpus longan Regulate Cold Stress Response in Arabidopsis.

Longan (Dimocarpus longan) is a typical southern subtropical fruit tree species that is sensitive to cold stress. C-repeat binding factors (CBFs), as transcription factors, are crucial components involved in the molecular regulation of the plant response to cold stress. However, the role of CBF homologs in the cold response regulation of longan remains largely unknown. Here, three novel CBF genes, DlCBF1, DlCBF2, and DlCBF3, were cloned from longan. DlCBF1 and DlCBF2 contain an AP2 domain and PKKPAGR and DSAWR CBF signature motifs, while DlCBF3 has mutations within these conserved signature motifs. DlCBF1/2/3 were mainly localized in the nucleus and specifically bound to CRT/DRE cis-elements, resulting in strong transcriptional activation. DlCBF1/2 exhibited tissue expression specificity, and their expression was induced by low temperature, while DlCBF3 had no tissue specificity and barely responded to low temperature. DlCBF1, DlCBF2, and DlCBF3 overexpression in Arabidopsis-enhanced cold tolerance by increasing proline accumulation and reducing reactive oxygen species (ROS) content, accompanied by upregulated expression of cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47, and AtKIN1) in the CBF cold stress response signaling pathway. In conclusion, the biological functions of DlCBF1/2/3 were somewhat conserved, but slow expression of DlCBF1/2 and low expression of DlCBF3 may partly cause the cold sensitivity of longan. Collectively, these results indicated that differences exist in the expression and function of CBF orthologs in the cold-sensitive plant species longan, and these findings may help to improve the understanding of the cold response regulation mechanism and provide important theoretical support for cold-tolerant breeding of longan.

DlICE1, a stress-responsive gene from Dimocarpus longan, enhances cold tolerance in transgenic Arabidopsis.

ICE1 (inducer of CBF expression 1) encodes a typical MYC-like basic helix-loop- helix (bHLH) transcription factor that acts as a pivotal component in the cold signalling pathway. In this study, DlICE1, a novel ICE1-like gene, was isolated from the southern subtropical fruit tree longan (Dimocarpus longan Lour.). DlICE1 encodes a nuclear protein with a highly conserved bHLH domain. DlICE1 expression was slightly upregulated under cold stress. Overexpression of DlICE1 in Arabidopsis conferred enhanced cold tolerance via increased proline content, decreased ion leakage, and reduced malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. Expression of the ICE1-CBF cold signalling pathway genes, including AtCBF1/2/3 and cold-responsive genes (AtRD29A, AtCOR15A, AtCOR47 and AtKIN1), was also significantly higher in DlICE1-overexpressing lines than in wild-type (WT) plants under cold stress. In conclusion, these findings indicate that DlICE1 is a member of the bHLH gene family and positively regulates cold tolerance in D. longan.