Ravi Tiwari

Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius, confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data. To dissect this classic cyto-nuclear conflict, we developed the ‘PhyloForensics’ framework, a novel diagnostic approach to systematically identify sources of phylogenetic instability. This framework revealed that signal heterogeneity (topological entropy variance) and information content (the proportion of informative sites) are the primary drivers of gene-tree conflict. Empirically validating this, we show that removing a small subset of “loudly conflicted” genes resolves deep-level incongruence, yielding a single, highly-supported topology previously obscured by noise. Finally, complementing this sequence-based resolution, we demonstrate that mitogenome architecture provides powerful phylogenetic signals, revealing predictable, mitogenome-wide evolutionary patterns, such as a significant negative correlation between branch length and both GC content and RNA editing sites. By integrating a validated conflict-resolution framework with architectural genomics, our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.

Members of the Haloferacaceae, a family of extremely halophilic archaea, exhibit unique physiological and genetic traits that make them promising candidates for biotechnological applications. These organisms thrive in hypersaline environments and tolerate a wide range of stresses, including high temperatures, UV radiation, and toxic metals. Their ability to grow on agro-industrial waste, coupled with their inherent resistance to contamination and the simplicity of downstream processing via osmotic shock, makes them ideal for sustainable bioproduction. Species such as Haloferax mediterranei have been explored for the biosynthesis of polyhydroxyalkanoates, carotenoids, halocins, and enzymes functional under extreme conditions. Species of Haloferacaceae can also bioremediate saline environments contaminated with hydrocarbons, heavy metals, and nitrogenous waste. Advances in genetic tools, including CRISPR interference, inducible promoters, and knock-in/knock-out systems, particularly in H. volcanii, have significantly expanded the engineering potential of these archaea. However, there remains a need for further innovation in genetic tools for this family. This review highlights the expanding potential of the Haloferacaceae for circular bioeconomy applications and identifies key technological gaps limiting their broader industrial adoption.

The Mendelian pea (Pisum sativa), a member of the Fabaceae family, is widely cultivated worldwide as an important food resource. While extensive genetic studies have been conducted on pea, a comprehensive pan-plastome assembly has not yet been achieved. The present study combined 103 newly assembled pea plastomes with 42 previously published plastomes to construct the first pea pan-plastome. The lengths of plastomes varied from 120,826 to 122,547 bp, with an average GC content of 34.8%. Protein-coding genes in the pan-plastome exhibited a strong bias towards A/T in the third codon position, with a notably high frequency of the amino acid arginine (RSCU value = 4.8) among plastome-encoded proteins. Additionally, the codon usage of petB, psbA, rpl16, rps14, and rps18 showed extreme influence from natural selection. Moreover, the genes ycf1, rpoC2, and matK were identified as hypervariable regions, suggesting their potential utility as DNA barcoding loci to distinguish maternal lineages for breeding and other agronomic purpose. The phylogenetic results indicated that cultivated peas had undergone at least two independent domestications, originating from the PA and PS groups. Compared to former research based on nuclear data, the PSeI-a group and PSeI-b group were newly found branched between the PA group and PF group.

The Haloferacaceae are a family of extremely halophilic archaea with many species producing enzymes and products beneficial for industrial biotechnology. They are, however, relatively under-characterised with regards to genetics and gene products. This study aims to use existing sequence data to highlight genetic diversity, create pangenomes for three genera, and provide secondary metabolite and pathway analysis. This will establish current knowledge and identify key gaps in research. We show that the Haloferacaceae have significant genetic diversity between genera, with numerous gene gain and loss events in key genera. It also found that the model genus, Haloferax, has relatively low identified secondary metabolites compared to other genera within the family. Additionally, this study has identified potential biotechnology targets for heterologous expression in model organisms.