Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Understanding the genetic basis of climatic adaptation is essential for predicting species’ responses to climate change. However, intraspecific variation of these responses arising from local adaptation remains ambiguous for most species. Here, we analyze genomic data from diamondback moth (Plutella xylostella) collected from 75 sites spanning six continents to reveal that climate-associated adaptive variation exhibits a roughly latitudinal pattern. By developing an eco-genetic index that combines genetic variation and physiological responses, we predict that most P. xylostella populations have high tolerance to projected future climates. Using genome editing, a key gene, PxCad, emerged from our analysis as functionally temperature responsive. Our results demonstrate that P. xylostella is largely capable of tolerating future climates in most of the world and will remain a global pest beyond 2050. This work improves our understanding of adaptive variation along environmental gradients, and advances pest forecasting by highlighting the genetic basis for local climate adaptation.

Transcriptome Profiling of Cellular Response to Kanamycin B in E.coli

Background: Aminoglycosides are not only antibiotics but also have wider and diverse non-antibiotic cellular functions. No genome-wide study focusing on the changes of gene expression by aminoglycosides in E.coli has been reported. Here, we report transcriptome-profiling analysis of E.coli with or without Kanamycin B to elucidate the understanding of non-antibiotic cellular functions. Results: The differentially expressed genes (DEGs) at two given concentrations of Kanamycin B were identified. The results indicated that Kanamycin B does not affect the expression of the majority of the genes. Functional classification of the DEGs revealed that they were mainly related to microbial metabolism including two-component systems, biofilm formation, oxidative phosphorylation and nitrogen metabolism in diverse environments. Conclusions: Kanamycin B treatment causes diverse changes in the transcriptional profile of E. coli JM109, that are not directly associated with the antibiotic activity of Kanamycin B.

Genome-wide identification, evolution, and transcript profiling of Aldehyde dehydrogenase superfamily in potato during development stages and stress conditions

The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scavenging of toxic aldehyde molecules by converting them into their corresponding non-toxic carboxylic acids. A genome-wide study in potato identified a total of 22 ALDH genes grouped into ten families that are presented unevenly throughout all the 12 chromosomes. Based on the evolutionary analysis of ALDH proteins from different plant species, ALDH2 and ALDH3 were found to be the most abundant families in the plant, while ALDH18 was found to be the most distantly related one. Gene expression analysis revealed that the expression of StALDH genes is highly tissue-specific and divergent in various abiotic, biotic, and hormonal treatments. Structural modelling and functional analysis of selected StALDH members revealed conservancy in their secondary structures and cofactor binding sites. Taken together, our findings provide comprehensive information on the ALDH gene family in potato that will help in developing a framework for further functional studies.

Genome-Wide Study of the ABI3 Gene Family and Identification of Putative miRNA Targeting ABI3 Gene in Oryza Sativa ssp. Indica

Rice is one of the important cereal crops mainly cultivated in Asia and its productivity is severely affected by drought stress. In response to drought stress, several genes are reported to be up-regulated or down-regulated in plants. Gene expression is negatively regulated by non-coding endogenous microRNAs post-transcriptionally either by mRNA degrading or translational silencing. In the past, single or multiple stress-responsive genes were over-expressed in order to generate drought-tolerant transgenic rice but with very little success. Recently, the development of transgenic plants by over-expressing transcription factors have received much attention because of their ability to regulate several genes. Abscisic Acid Insensitive 3 (ABI3) is a transcription factor, which is known to play a crucial role in mediating plant stress tolerance. Using the Ensembl plants database, we identified 83 putative OsABI3 genes in Oryza sativa Indica. Through in silico approach, five potential miRNAs i.e., ath-miR5021, csi-miR3948, osa-miRf11773-akr, osa-miRf12029-akr and ptc-miRf10053-akr that target OsABI3 genes were identified. Further, the expression of the selected ABI3 genes were analyzed in rice seedlings exposed to 15% PEG, using the RT-qPCR. In comparison to control, OsABI3 genes showed relatively enhanced expression when exposed to drought stress treatment. This indicates that OsABI3 genes may play important role in development and drought stress in rice seedlings.

Chromatin architectural proteins regulate flowering time by precluding gene looping

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

Genome wide study of tardive dyskinesia in schizophrenia

Tardive dyskinesia (TD) is a severe condition characterized by repetitive involuntary movement of orofacial regions and extremities. Patients treated with antipsychotics typically present with TD symptomatology. Here, we conducted the largest GWAS of TD to date, by meta-analyzing samples of East-Asian, European, and African American ancestry, followed by analyses of biological pathways and polygenic risk with related phenotypes. We identified a novel locus and three suggestive loci, implicating immune-related pathways. Through integrating trans-ethnic fine mapping, we identified putative credible causal variants for three of the loci. Post-hoc analysis revealed that SNPs harbored in TNFRSF1B and CALCOCO1 independently conferred three-fold increase in TD risk, beyond clinical risk factors like Age of onset and Duration of illness to schizophrenia. Further work is necessary to replicate loci that are reported in the study and evaluate the polygenic architecture underlying TD.