Sher-e-Bangla Agricultural University

BACKGROUND:Humped featherback or clown-knife fish, Chitala chitala is an endangered and globally near threatened species. Mitochondrial genome or mitogenome and its bioinformatic analysis play important roles for the effective conservation of threatened fish species. METHODS AND RESULTS:Next generation sequencing decoded the complete circular mitochondrial genome of Chitala chitala which is endowed with typical organizational features of 13 protein coding genes (PCGs), 22 tRNA genes, two genes for ribosomal RNA subunits, and two non-coding regions. The mitochondrial genome of C. chitala displayed 92.87% homology with that of spotted knifefish, C. ornata (AP008923.1), followed by 91.4% homology with Indonesian featherback, C. lopis (AP008922.1). The phylogenetic analysis revealed that the mitogenome of C. chitala shares a close relationship with six other notopterids, which diverged in the Eocene period as a result of Gondwanan fragmentation and vicariant evolution of ancestral Osteoglossiform lineages. By applying bioinformatic tools, we elucidated several potential termination-associated sequence motifs, a tandem repeat array, and a short motif of conserved sequence block in the control region of C. chitala mitogenome. Consensus repeat motif and origin of light strand replication displayed predicted and potential secondary hairpin structures. The AT-GC skewness analysis exhibited a prominent negative GC-skew (-0.338) across all PCGs, revealing an "overrepresentation" of cytosine bases. The PCGs of C. chitala had the highest codon adaptation indices ranging from 0.707 to 0.816 compared to its congeners. Investigation of relative synonymous codon usage patterns revealed that a substantial set of codons in the C. chitala mitogenome were "overrepresented" and "underrepresented" indicating clear existence of codon usage bias. Comparative mutation rate analysis demonstrated that nearly all PCGs, excluding COX2, ND5, and CYTB of C. chitala mitogenome acquired non-synonymous to synonymous substitution rates (dN/dS) less than 0.1 proving the existence of intense purifying selection. CONCLUSION:We reported the first complete, verified, reference mitogenome of C. chitala and revealed distinct codon usage bias and strong purifying selection.

The integration of hyperspectral imaging (HSI) with machine learning enables non-destructive prediction and visualization of food quality. However, multicollinearity and redundant features in spectral data can reduce model accuracy and increase computational time, emphasizing the need for key wavelength selection. In response, this study presents an inventive method combining a genetic algorithm (GA) with explainable artificial intelligence (XAI) to select key wavelengths for predicting apple dry matter content (DMC). A partial least squares regression (PLSR) model using the selected features outperformed recursive feature elimination (RFE) and competitive adaptive reweighted sampling (CARS), achieving a coefficient of determination (R2) of 0.46 and a root mean squared error (RMSE) of 0.70%. The approach was further applied to hyperspectral images to visualize pixelwise DMC distribution, providing spatial insights into fruit composition. Results demonstrate that integrating XAI with evolutionary feature selection offers a noninvasive, transparent, and efficient strategy for assessing and visualizing fruit quality.

Auxin, a plant growth regulator responsive to environmental stresses like drought, plays a crucial role in signaling, gene regulation, and plant sustainability. Drought sensitivity is linked to auxin-mediated cellular interactions, and gaining insights at genomic, cellular, and physiological levels can enhance plant resilience. This review discusses drought stress impacts and auxin sensitivity in cellular and nuclear modules. The biosynthetic and catabolic routes of auxin influence influx and metabolic reprogramming at both cellular and subcellular levels. Auxin interaction with other hormones affects rhizosphere sensitivity and systematic plant signaling. Subcellular drought tolerance is maintained by metabolizing reactive oxygen species, ensuring redox homeostasis. The review also covers transcriptomes regulated by auxin-responsive factors and miRNAs that modulate selective transcripts under drought. It emphasizes epigenetic regulation, including methylation, histone modification, and chromatin remodeling. Specific nucleotide residues and their auxin-induced modifications may help recall stress memory to better combat drought. For sustainable development under drought, strategies involving specific rhizobacteria and nanomaterials are discussed. New perspectives on genome stability, particularly with CRISPR/Cas9 for editing auxin-sensitive genes, aim to improve drought tolerance in crop varieties and selectable traits. Conclusively, the present review highlights auxin’s imperative role in plant reprogramming under osmotic stress, making it a key candidate for eco-friendly crop production to ensure food security.

Environmental toxicity from metal/metalloid pollution threatens the sustainability of crop species by impeding growth and yield. The acquisition of toxic elements (TEs) is manifested in tissues mostly through water relations and oxidative stress. Tolerant species can thrive through chelation, sequestration, and induction of antioxidative genes. The cellular-level regulations are controlled by non-coding small RNAs, microRNAs (miRNAs), which induce gene silencing and cause metal toxicity. With the advent of next-generation sequencing (NGS), miRNAs play a role in interpreting TE sensitivity via signaling pathways for stress tolerance. Recently, NGS technologies have identified more miRNAs with various roles in TEs. The regulation targets post-transcriptional modification following translational inhibition of specific genes. With another regulatory web, miRNAs are associated with genes concerned with transcription factors (TFs), membrane transporters, chaperons, growth regulators, signaling residues, etc. The redox balance in sensitive tissues, linking metabolic cycles and biogenesis, is influenced by feedback regulation of oxidative stress. Epigenetic alterations, including DNA methylation, following post-translational modification of regulatory proteins, play roles in modulating tolerance to TEs. The identified miRNAs synchronize signaling pathways that regulate cellular turgidity, the integrity of wall proteins, ion trafficking or sequestration, redox equilibrium, and metal transporter-like functions. Moreover, miRNA target sequences encoding TFs imply the involvement of major metabolic flux in the regulation of biogenesis for tolerance to TEs. In this review, we highlighted TE-mediated miRNA regulation and their associated roles in oxidative stress, signaling pathways, and coordinated physiological responses to TEs in plants.

Cotton production in Bangladesh faces significant pest management challenges, with farmers relying heavily on chemical pesticides. This study investigated 247 cotton farmers' perceptions and practices regarding pesticide use and their willingness to pay for insect-resistant Bt cotton. Perceptions were assessed using a five-point Likert scale (Cronbach's alpha = 0.76), complemented by data on pesticide practices and Bt cotton adoption potential, collected in 2022. Results revealed substantial perception-practice gaps: while 96% recognized health risks from excessive pesticide use, only 77% used personal protective equipment. Critical knowledge deficits were evident, with only 68.4% understanding stage-specific application requirements and 53.4% aware that insect-resistant varieties reduce pesticide costs. Most farmers (55%) relied on peer consultation rather than extension services for pesticide application decisions. Concerning disposal practices prevailed, with 39.7% burying containers and 30% leaving them in fields. Despite chemical reliance, farmers demonstrated high adoption of nature-based practices, particularly pheromone traps (89.5%) and removal of affected parts (84.6%). Regarding Bt cotton, 86% expressed willingness to adopt at current prices, declining to 52.5% at 50% premium, revealing severe price sensitivity. Findings highlight critical gaps between risk awareness and safety practices. Realizing Bt cotton adoption potential requires intensive extension programming addressing knowledge deficits, improved waste management infrastructure, and financial support for resource-constrained smallholder farmers.