Mammalian fertilization exhibits species specificity, and the proteins mediating sperm-egg interactions evolve rapidly between species. In this study, we demonstrate that the evolution of seven genes involved in mammalian fertilization is promoted by positive Darwinian selection by using likelihood ratio tests (LRTs). Several of these proteins are sperm proteins that have been implicated in binding the mammalian egg coat zona pellucida glycoproteins, which were shown previously to be subjected to positive selection. Taken together, these represent the major candidates involved in mammalian fertilization, indicating positive selection is pervasive amongst mammalian reproductive proteins. A new LRT is implemented to determine if the d(N)/d(S) ratio is significantly greater than one. This is a more refined test of positive selection than the previous LRTs which only identified if there was a class of sites with a d(N)/d(S) ratio >1 but did not test if that ratio was significantly greater than one.

Some plants like Arabidopsis thaliana increase in freezing tolerance when exposed to low nonfreezing temperatures, a process known as cold acclimation. Other plants including tomato, Solanum lycopersicum, are chilling sensitive and incur injury during prolonged low temperature exposure. A key initial event that occurs upon low temperature exposure is the induction of genes encoding the CBF transcription factors. In Arabidopsis three CBF genes, present in a tandemly-linked cluster, are induced by low temperatures. Tomato also harbors three tandemly-linked CBF genes, Sl-CBF3-CBF1-CBF2, but only one of these, Sl-CBF1, is low-temperature responsive. Here we report that Solanum species that are closely-allied to cultivated tomato essentially share this structural organization, but the locus is in a dynamic state of flux. Additional paralogs and in-frame deletions between adjacent genes occur, and the genomic regions flanking the CBF genes are dissimilar across Solanum species. Nevertheless, the CBF1 upstream region remains intact and highly conserved. This feature differed for CBF2 and CBF3, whose upstream regions were far less conserved. CBF1 was also the only low-temperature responsive gene in the cluster and its expression was greatly affected by a circadian clock. The tuber-bearing S. tuberosum and S. commersonii also harbored a fourth gene, CBF4, which was also low temperature responsive. CBF4 was physically linked to CBF5 in S. tuberosum, but CBF5 was absent from S. commersonii. Phylogenic analyses suggest that CBF5-CBF4 resulted from the duplication of the CBF3-CBF1-CBF2 cluster. DNA sequence motifs shared between the Solanum CBF1 and CBF4 upstream regions were identified, portions of which were also present in the Arabidopsis CBF1-3 upstream regions. These results suggest that much greater functional constraints are placed upon the Solanum CBF1 upstream regions over the other CBF upstream regions and that CBF4 has retained the capacity for low temperature responsiveness following the duplication event that gave rise to CBF4.

Powdery mildew is a fungal disease that represents a ubiquitous threat to crop plants. Transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in Tibetan hulless barley in response to powdery mildew. There were 3418 genes and 405 metabolites differentially expressed between the complete resistance cultivar G7 and the sensitive cultivar Z13. Weighted gene coexpression network analysis was carried out, and the differentially expressed genes were enriched in five and four major network modules in G7 and Z13, respectively. Further analyses showed that phytohormones, photosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways were altered during Qingke-Blumeria graminis (DC.) f.sp. hordei (Bgh) interaction. Comparative analyses showed a correspondence between gene expression and metabolite profiles, and the activated defenses resulted in changes of metabolites involved in plant defense response, such as phytohormones, lipids, flavone and flavonoids, phenolamides, and phenylpropanoids. This study enabled the identification of Bgh responsive genes and provided new insights into the dynamic physiological changes that occur in Qingke during response to powdery mildew. These findings greatly improve our understanding of the mechanisms of induced defense response in Qingke and will provide new clues for the development of resistant Tibetan hulless barley varieties.

No abstract