Bibliometric review finds genome editing missing from Ficus research landscape

A new review combining a systematic bibliometric analysis with a synthesis of plant biotechnology literature reports that genome editing has yet to take hold in the genus Ficus, despite a quarter-century of expanding genomic research on figs. Searching the PubMed database for publications from 2000 to 2025, the authors first identified 3,465 publications addressing diverse aspects of Ficus research. When the search was narrowed with a predefined set of terms covering genomes, genome editing, transformation, and protoplasts, only 392 publications remained, corresponding to approximately 11.3 percent of the broader baseline. Notably, terms directly associated with editing technologies, such as CRISPR, Cas9, and gene knockout, were absent from the thematic maps built from article titles, keywords, and abstracts, indicating that functional gene manipulation strategies have not progressed alongside sequencing efforts.

The thematic evolution analysis, based on bigrams extracted from titles, keywords, and abstracts, traced how the field has shifted over three periods. Between 2000 and 2010, Ficus studies centered on traditional biological themes, with terms such as Ficus carica, gene flow, fig wasp, and sp. nov. reflecting a strong emphasis on taxonomic discovery, reproductive biology, and the complex fig wasp pollination system. From 2011 to 2020, research diversified into applied and interdisciplinary themes, including silver nanoparticles, leaf extract, and plant chemistry, signaling growing interest in phytochemical properties. In the most recent period, 2021 to 2025, the focus moved toward molecular and genomic research, with new topics such as chloroplast genome, genome analysis, and biological activities reflecting the influence of next-generation sequencing and functional genomics. Publication output peaked in 2022, after which the visible trend was restricted, which the authors attribute to a lag in indexing after acceptance.

Structural network analysis reinforced the picture of a field anchored in evolutionary biology. In the co-occurrence network of the top 50 keyword nodes, the term phylogeny achieved the highest betweenness centrality at 311.129, meaning it sat on more than 311 shortest paths connecting otherwise separate research domains and acted as the primary bridge linking evolutionary relationships, sequence analysis, and molecular comparisons. Three major clusters emerged: a red cluster dominated by phylogeny and genomics, a green cluster covering genetic diversity, pollination, and microsatellite studies, and a blue cluster representing chemical, spectroscopic, and analytical work. The clear spatial separation between the phytochemical and genomic clusters suggested weak integration between metabolite profiling and functional gene validation. Editing-related keywords such as CRISPR, gene knockout, transformation systems, or regeneration protocols did not form a distinct cluster anywhere in the network.

This translational bottleneck stands in contrast to the rapid expansion of genomic resources for Ficus species documented in the review. Recent milestones include the telomere-to-telomere reference genome of Ficus hispida, in which researchers annotated six centromeres and 28 telomeres and refined the previously reported two-megabase male-specific region into a 7.2-megabase region containing 51 newly predicted genes, and a chromosome-level assembly of Ficus benjamina spanning 362.73 megabases across 13 pseudochromosomes with 28,840 protein-coding genes and 98.10 percent BUSCO completeness. A complete mitochondrial genome of Ficus hirta was reported as a single circular molecule of 486,226 base pairs containing 31 protein-coding genes. Chloroplast genomes across multiple Ficus species are each approximately 160 kilobase pairs in length with a GC content of 35.88 to 36.02 percent and 114 unique genes. The review also cites work identifying approximately 36,000 gene clusters across 15 Ficus species, more than 7,500 genes shared among species, more than 500 single-copy orthologs, and over 570 genes unique to Ficus carica, along with RNA sequencing that helped identify 938 novel protein-coding genes in F. carica.

The authors argue that these gapless, high-contiguity assemblies are crucial foundational tools for editing, providing unambiguous single-guide RNA off-target screening templates, resolved promoter motifs for tissue-specific vector expression, and precise gene-family maps. However, they note that gene family characterization studies remain largely descriptive, with limited downstream functional validation, and that orthology-based editing frameworks commonly employed in model plants have not yet been systematically adapted for Ficus. The disconnect between genomic resource availability and editing research is identified through the present bibliometric analysis as a critical translational bottleneck.

Looking forward, the review outlines potential editing targets in figs, while stressing that these candidates are primarily inferred from functional studies in model plant species and should be considered potential rather than validated targets for Ficus carica. The review does not include gene-level orthology, copy number, paralog, or synteny analyses to establish whether candidate genes are single-copy or members of multi-copy gene families in F. carica. Among the proposed directions are knockout or modification of susceptibility genes, which pathogens co-opt to grow and survive on the plant, to achieve resistance to fungal, bacterial, or viral pathogens; modification of ACC synthase and ACC oxidase, the enzymes governing ethylene biosynthesis, to improve texture, shelf life, or sugar profile; alteration of FcFT flowering gene expression using TALENs or CRISPR mechanisms to improve flowering time and reduce risks of a prolonged juvenile phase; modification of NAC transcription factors, heat stress transcription factors, and heat shock proteins for abiotic stress tolerance; and CRISPR-based base editing and prime editing to knock out homologs and reduce gene redundancy in naturally polyploid figs.

Major biological and technical barriers stand between these proposals and practice. Recalcitrance, the inability of plants to respond to in vitro techniques, is described as a fundamental physiological barrier frequently expressed as the rate-limiting step for applying editing in non-model horticultural species, arising from low cell division competence, hormone sensitivity, genotype dependence, and ineffective gene expression in target cells. A distinctive biochemical barrier comes from laticifers, which in many Ficus species trigger latex production upon wounding; the exudate is oxidized by polyphenol oxidase, turning brown and converting into quinones that are highly toxic to plant cells, forming localized toxicity around tissue-cultured explants that can block gene transfer entirely. Even when transformation succeeds, protocols are often limited to specific cultivars or tissue types, and scalable editing requires genotype-independent recipes optimized across explant source, sterilization, growth regulator combinations, antioxidants, and Agrobacterium infection parameters.

Genome complexity adds further difficulty. Figs are highly heterozygous perennials, and edits introduced into somatic cells may produce chimeric plants in which only some cell layers carry the change, reducing the chance that edits transfer into meristems that form new plants. High heterozygosity also complicates guide RNA design and edit validation during sequencing. Long juvenile periods and large plant size slow the assessment of edited phenotypes under field conditions. Market and social acceptance presents an additional constraint: regulatory frameworks differ by country, and while farmers show relative acceptance toward genome modification to enhance quality, consumer acceptance trends downward, with concerns centered on dietary implications and traditional approaches such as grafting or cross-breeding viewed as more acceptable than introducing foreign DNA.

The review proposes strategies to overcome these barriers, framed as complementary and progressive options rather than equally feasible alternatives, with regeneration and transformation optimization as the initial priority. Transient overexpression of developmental regulators such as Wuschel and Baby boom, or GRF-GIF chimeras, can switch somatic cells to behave like meristematic cells and has substantially increased regenerative responses in recalcitrant systems, though WUS/BBM approaches require careful control of expression because of potential pleiotropic abnormalities, and GRF-GIF chimeras require validation in woody species. Viral vectors, including Tobacco mosaic virus, Tobacco rattle virus, Bean yellow dwarf virus, Barley stripe mosaic virus, and Potato virus X, could enable in planta editing that bypasses tissue culture, but host compatibility and systemic movement in Ficus require experimental assessment given that laticifers embedded in the phloem may hinder viral movement. DNA-free editing through CRISPR-Cas ribonucleoprotein delivery may reduce unintended integration events and somaclonal variation, though RNP delivery has not been demonstrated in woody plants such as Ficus and depends on efficient protoplast isolation, delivery, and regeneration.

On the tissue culture side, the review notes that many studies have successfully optimized surface sterilization and protocols for different fig varieties, providing references for regenerating edited plantlets. Pre-treatment additives including polyvinylpyrrolidone, citric acid, L-cysteine, and silver nitrate can help absorb phenolics and reduce browning from latex exudates, while editing strategies targeting polyphenol oxidase or phenylalanine ammonia lyase homologs, and modulation of reactive oxygen species scavenging genes such as superoxide dismutase or catalase, may further improve explant survival. Integrating transcriptomic, metabolomic, and proteomic datasets could facilitate identification of target genes regulating economically important traits, with genes involved in phenolic and flavonoid biosynthesis such as chalcone synthase representing promising editing targets for enhancing antioxidant properties in Ficus fruits and leaves. The authors conclude that for this less-researched horticultural and medicinally important genus, the fundamental barrier is not only the availability of editing tools but the biological and technical systems that allow edited cells to be regenerated into whole, fertile plants or commercially useful planting material, and that coordinated investment in tissue culture optimization, transient delivery methods, validated target selection, and proactive regulatory and stakeholder engagement is essential for converting editing from a laboratory proof-of-concept into a practical improvement tool for Ficus.

Subject of Research: Genome editing research trends and barriers in the genus Ficus

Article Title: From genomic landscape to precision editing in Ficus : A critical review

Article References: Parab, A. R., Ayyagari, R., Subramaniam, S., & Jaleel, A. (2026). From genomic landscape to precision editing in Ficus: A critical review. Current Research in Biotechnology, Article 100432. https://doi.org/10.1016/j.crbiot.2026.100432

Image Credits: AI Generated

DOI: 10.1016/j.crbiot.2026.100432

Keywords: Ficus, fig, genome editing, CRISPR, bibliometric analysis, tissue culture, transformation recalcitrance, functional genomics, plant biotechnology, phylogeny, genomic, landscape