Retrocopies are processed copies of other genes that originate through reverse transcription and are randomly integrated into the genome. Once considered genomic "junk," emerging evidence shows they contribute to novel gene evolution and may aid adaptation to environmental and lifestyle changes. However, the role of retrocopies in the emergence of virulence in Plasmodium parasites remains largely unexplored. This study systematically characterizes retrocopies across 23 Plasmodium pathogenic genomes to elucidate their evolutionary origins, functional relevance, and potential contributions to the emergence of virulence. Using a stringent computational framework, we identified 724 high-confidence retrocopies exhibiting canonical signatures of retroposition. Retrocopies are frequently intact, under purifying selection, and often display detectable apparent transcription during intraerythrocytic stages, with a subset showing FPKM values from RNA-seq data comparable to or exceeding those of their parental genes, particularly in PPIase, PIR, and actin-related families linked to host interaction and immune evasion. Domain, GO, and KEGG enrichment analyses indicate that retrocopies are preferentially associated with processes such as cytoadhesion, chromatin remodeling, stress response, and cytoskeletal organization, and that retroposition has contributed to the expansion and diversification of pathogenic gene families in a lineage and host-specific manner. Ancestral state reconstruction indicates episodic gains and losses of retrocopies, with notable expansions in primate-infecting lineages. The findings show retrocopies in Plasmodium are widespread, evolutionarily dynamic, and functionally associated with key virulence-associated pathways rather than representing inert genomic byproducts. This study highlights retroposition as an underappreciated mechanism contributing to genomic plasticity in malaria parasites and provides a framework for future functional investigations.

Santalum album L. (Sandalwood) is a commercially and medicinally significant tree species native to India and is widely distributed across Asia and Australia. Valued for its high-quality heartwood and essential oil, sandalwood plays a vital role in the pharmaceutical, cosmetic, and cultural industries. India contributes to more than 85% of global production, but natural populations have sharply declined due to overexploitation, habitat loss, and disease pressures. Recent genomic advancements, including chromosome-level genome assembly, transcriptomics, and proteomics, have provided critical insights into oil biosynthesis, heartwood formation, and stress response mechanisms. Studies have identified key transcription factors, such as MYB and WRKY; gene families, such as TPS and SAUR; and enzymes involved in secondary metabolism and abiotic stress tolerance. Molecular markers such as SSRs and SNPs have enabled the assessment of genetic diversity and structure across native and introduced populations, informing conservation and breeding programs. Functional genomic studies have also highlighted the importance of genotype-specific expression profiles for enhancing oil yield and climate resilience. Despite these advancements, key research gaps persist, including limited application of genomic tools in breeding, lack of functional gene validation, lack of CRISPR-based gene editing, and scanty early biomarkers. However, integrated silvicultural-genomic strategies, structured germplasm conservation, and supportive policies are crucial for enhancing productivity, resilience, and sustainable sandalwood cultivation. Therefore, the future research should focus on genome-assisted selection, CRISPR-based gene editing, and the development of functional markers for trait prediction. This review emphasizes the importance of multidisciplinary research in securing the long-term ecological and economic viability of S. album, addressing both production gaps and conservation challenges in the face of global climate change.

Phyllanthus fluitans, a member of the Phyllanthaceae, is a unique free-floating aquatic species exhibiting considerable ornamental value. In this study, we assembled the mitochondrial genome of P. fluitans representing the first mitochondrial genome report of the Phyllanthaceae family. The mitogenome comprises two circular chromosomes spanning 230,785bp (chromosome 1) and 143,421bp (chromosome 2), collectively harboring 32 protein-coding genes (PCGs), 25 tRNA genes, four rRNA genes, and one pseudogene. Structural analyses identified 118 simple sequence repeats (SSRs), 18 tandem repeats, and 191 dispersed repeats distributed throughout the mitochondrial genome. RNA editing prediction revealed 394 putative editing sites, with notable enrichment in NADH dehydrogenase genes. Critical modifications included start codon conversion in atp6 (ACG → AUG) and stop codon alterations in ccmFc (CGA → UGA) and rpl16 (UAG → UAA). Comparative genomic analyses detected 50 chloroplast-derived DNA fragments, constituting 6.0% of the mitogenome, indicative of historical plastid-to-mitochondrion transfer events. Codon usage bias analysis demonstrated phenylalanine (Phe) as the most frequently encoded amino acid, with selection pressure identified as the predominant driver of codon usage patterns. Phylogenetic reconstruction employing 22 conserved PCGs resolved intra-ordinal relationships among eight Malpighiales families, revealing Phyllanthaceae sister to Salicaceae with robust nodal support. This study advances the utilization of mitochondrial genomes for elucidating phylogenetic relationships within Phyllanthus while providing essential genomic resources for future comparative mitogenomic investigations in Phyllanthaceae. The structural complexity revealed through repeat analyses and RNA editing patterns offers novel insights into plant mitochondrial genome evolution.

The presence of Azotobacter bacteria in the soil plays an important role in increasing its fertility and enhancing plant health. Azotobacter diversity depends on several environmental factors, particularly soil texture, pH, and nutrient content. The current study investigated the diversity of Azotobacter in various soil samples collected from 10 different governorates along the river Nile valley and its delta, Northern Mediterranean shore, Sinai, and Upper Egypt regions. The sampling sites spanned different environmental and ecological conditions of the Egyptian land either cultivated (agricultural land) or uncultivated (desert land). Fifty Azotobacter isolates were isolated and characterized based on cell morphology, culture properties, physiological, biochemical, and molecular characteristics. In addition, the alginate production capacity of the isolates was investigated. The results indicated that Egyptian soils are rich in Azotobacter diversity. The isolates were Gram-negative short rods, appearing either as single cells or in diploid structures. The isolates showed high variability in alginate production where two isolates (BH3 and AST4) were the highest alginate producers (3.12 and 4.22g alginate L- 1), respectively. 16S-rDNA sequencing and 16S-rDNA RFLP analyses indicated that despite the presence of Azotobacter salinestris and Azotobacter vinelandii in the Egyptian soil, Azotobacter chroococcum was the predominant species. In addition, sequence analysis of the gene coding for the transcription factor AlgU confirmed the results of 16S-rRNA gene sequence analysis. RAPD-REP and BOX-PCR were used to study the polymorphism among the isolates. High levels of microbial diversity were found using these DNA primers as 6-9 fingerprinting profiles were retrieved.

Due to the increase in demand for food production worldwide, the cultivation of improved varieties is used as a strategy in order to maximize production. The improved Maradol papaya variety was introduced to the Yucatan Peninsula (YP), Mexico, the Mesoamerican diversity area of papaya, in the 1990s. The domesticated and wild papaya belong to the same species (Carica papaya L.), which promotes gene flow from crops to their wild relatives, threatening the genetic diversity of wild papaya populations in the region. In this study, we used a population genomic approach to evaluate the impact of domesticated-to-wild gene flow on the genetic structure and diversity of wild papaya in the YP. We used 2054 SNP markers for 227 wild individuals from 15 collection sites and 127 domesticated individuals from 13 Maradol papaya plantations. We found, (a) the presence of individuals that may be the result of a hybridization process between wild and domesticated papaya; (b) a higher genetic diversity in the wild group (HE = 0.18) in comparison to the domesticated group (HE = 0.09); and (c) low migration rates from domesticated to wild plants (m = 0.005). The domesticated-to-wild gene flow in C. papaya can have a negative effect on the genetic diversity and adaptive potential of wild populations from this region. The conservation of crop wild relatives should be a priority since they are part of various ecological processes and are considered natural reservoirs of genetic diversity for crops.

Eucalyptol is one of the major insecticidal active ingredients in a variety of plant essential oils, and has good killing and avoidance effects on Tribolium castaneum. The presence of detoxifying enzymes glutathione S-transferase (GST) in T. castaneum makes it resistant to a variety of insecticides. However, whether GST is involved in regulating the sensitivity of eucalyptol by T. castaneum is not well understood. In our previous study, a glutathione S-transferase, TcGSTu1, was significantly up-regulated in RNA sequencing data when T. castaneum was exposed to eucalyptol. Therefore, in this study, the role of TcGSTu1 in the regulating the sensitivity of T. castaneum to eucalyptol was studied. The enzyme activities of GST and the transcription levels of TcGSTu1 were significantly increased following stimulation with eucalyptol. When using RNA interference technology knockdown TcGSTu1 heightens the sensitivity of T. castaneum to eucalyptol, demonstrating a link between TcGSTu1 and eucalyptol detoxification metabolism. Furthermore, TcGSTu1 is expressed in all developmental stages of T. castaneum, with higher expression levels observed particularly in the late egg stage. There was significant expression of TcGSTu1 in various tissues of different organisms, including larval head, fat body, and adult head. This observation indicated a possible connection between high TcGSTu1 expression and eucalyptol detoxification. The present findings suggest that TcGSTu1 may be involved in regulating the sensitivity and response of T. castaneum to treatment with eucalyptol, providing new research insight into pest control.

DnaJs/Hsp40s/JPDs are obligate co-chaperones of heat shock proteins (Hsp70), performing crucial biological functions within organisms. A comparative genome analysis of four genomes (Vitis vinifera, Eucalyptus grandis, Lagerstroemia indica, and Punica granatum) revealed that the DnaJ gene family in L. indica has undergone expansion, although not to the extent observed in P. granatum. Inter-genome collinearity analysis of four plants indicates that members belonging to Class A and B are more conserved during evolution. In L. indica, the expanded members primarily belong to Class-C. Tissue expression patterns and the biochemical characterization of LiDnaJs further suggested that DnaJs may be involved in numerous biological processes in L. indica. Transcriptome and qPCR analyses of salt stressed leaves identified at least ten LiDnaJs that responded to salt stress. In summary, we have elucidated the expansion mechanism of the LiDnaJs, which is attributed to a recent whole-genome triplication. This research laid the foundation for functional analysis of LiDnaJs and provides gene resources for breeding salt-tolerant varieties of L. indica.