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Open research questions in Genomics and Phylogenetic Studies

758 gap statements mined from Genomics and Phylogenetic Studies papers in our 7.9M-paper local library, which holds 4,007 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.

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What the literature leaves open

  • The lack of a complete chloroplast genome sequence for A. gigas. Limited understanding of the phylogenetic placement of A. gigas within the genus Amorphophallus. The need for a comprehensive analysis of the A. gigas chloroplast genome.

    The complete chloroplast genome sequence and phylogenetic analysis of Amorphophallus gigas · 2026 · DOI

  • The need for high-quality sequencing data. The challenge of annotating the genome accurately.

    The complete chloroplast genome sequence of Elatostema involucratum · 2026 · DOI

  • The limited availability of comprehensive mitogenomic data for owls hinders our understanding of their genomic organization and phylogenetic relationships. The genomic organization and structural features of the genus Strix are not well understood, making it difficult to study their evolution and adaptation.

    Mitogenomic characterization and phylogenetic placement of the mottled wood-owl strix ocellata with gene rearrangement patterns in strigiformes · 2026 · DOI

  • Limited access to decentralized diagnostic tools. Gaps in accessible and decentralized diagnostics for infectious diseases. Technical constraints, including high raw read error rates and the need for host depletion or target enrichment, which add to cost, complexity, and risk of sample loss.

    Nanopore sequencing in infectious disease diagnostics and surveillance · 2026 · DOI

  • There is a lack of understanding of codon usage bias in mangrove species. The evolutionary forces shaping the genetic architecture of mangrove species are not well understood. There is a need for comprehensive analyses of chloroplast genomes from mangrove species.

    Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights · 2026 · DOI

  • The lack of description of the novel species of bacteria, Sphingobium agrisoli sp. nov. The need for genomic and phenotypic characterization of the species.

    Correction to: A Novel Species Description of Sphingobium agrisoli sp. nov. · 2026 · DOI

  • Lack of high-quality genome assemblies for Coreius heterodon and Coreius guichenoti. Limited understanding of the genomic features and gene content of these species. Need for advanced sequencing technologies to generate high-quality genome assemblies.

    Telomere-to-telomere gapless genome assemblies of Coreius heterodon and Coreius guichenoti · 2026 · DOI

  • BioProject is confounded with tissue, developmental stage, treatment, time point, and sequencing platform. The need to balance the removal of technical noise and the preservation of biological differences encoded by the project variable.

    EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens · 2026 · DOI

  • Current maximum growth rate prediction models require complete gene sequences from assembled contigs. The complexity of soil metagenomes often precludes high quality assembly. There is a need for techniques to analyze the functional capabilities of soil microbes that do not require cultivation.

    Assembly-free short-read metagenomic maximum growth rate prediction · 2026 · DOI

  • Limited mitochondrial genomes have been reported for the family Potamanthidae. The lack of complete mitochondrial genome sequences for Potamanthidae species hinders the understanding of their evolutionary relationships.

    Two Complete Mitochondrial Genomes of Potamanthidae (Ephemeroptera): Genome Features and Phylogenetic Implications · 2025 · DOI

  • There is limited understanding of the taxonomic diversity of the genus Niveibacterium. There is limited understanding of the environmental adaptations and functional roles of the genus Niveibacterium.

    Taxonomic and Genomic Characterization of Niveibacterium terrae sp. nov., a New Species from Riparian Soil in the Seomjin River, Republic of Korea · 2025 · DOI

  • The lack of understanding of the organelle genomes of mycoheterotrophic orchids. The need for characterization of the mitogenome and plastomes of Epipogium roseum. The gap in knowledge of the evolutionary relationships among mycoheterotrophic orchids.

    Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids · 2024 · DOI

  • Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood.

    Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep‐Sea Molluscs · 2026 · DOI

  • Decreasing the complexity of the simulated metagenome by increasing the abundance of the dominant strain improved both MLST and serotype prediction performance, while long-read analyses indicated that increased read length was insufficient to overcome the challenges associated with mixed-strain communities.

    The impact of strain heterogeneity on genomic profiling accuracy in mixed-strain Escherichia coli metagenomes · 2026 · DOI

  • Reference-genome choice can introduce mapping bias when sequencing data are analysed against a heterospecific genome, but it remains unclear how strongly this bias affects species-level phylogenomic inference.

    Reference mapping and whole-genome alignment yield comparable phylogenomic inferences · 2026 · DOI

  • Community-scale metabolic modelling further identified 777 StGBs encoding both complete nitrate and sulfate reduction pathways, 154 of which were not fully recovered by other binners, highlighting understudied microbial contributors to local element cycling.

    CompleteBin: A transformer-based framework unlocks microbial dark matter through improved short contig binning · 2026 · DOI

  • The chloroplast genome only reflects the maternally inherited evolutionary history, - Broader taxonomic sampling and multi-genomic data are needed to further validate phylogenetic…

    The complete chloroplast genome sequence of Elatostema involucratum · 2026 · DOI

  • Incomplete deposited mitogenome assembly of the American Black-and-white Owl, - Limited availability of comprehensive mitogenomic data…

    Mitogenomic characterization and phylogenetic placement of the mottled wood-owl strix ocellata with gene rearrangement patterns in strigiformes · 2026 · DOI

  • Improvements in patient outcomes are emerging and need further research, - Technical challenges in low-biomass settings and metagenomic samples need to be addressed, - Regulatory, bioinformatic, and equity-related gaps need to be…

    Nanopore sequencing in infectious disease diagnostics and surveillance · 2026 · DOI

  • Further studies on the genetic basis of the decline of C. guichenoti and C.

    Telomere-to-telomere gapless genome assemblies of Coreius heterodon and Coreius guichenoti · 2026 · DOI

  • Further study of the biosynthetic basis of prenylflavonoid production in Epimedium, - Investigation of the functions of candidate protein-protein interactions, - Analysis of the co-expression network in different biological…

    EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens · 2026 · DOI

  • Investigating the underlying causes of the observed differences between duckweed species, - Evaluating the potential applications of duckweeds in biomass production and phytoremediation, - Examining the transcriptomic and physiological profiles of additional duckweed…

    Comparative Transcriptomic and Physiological Profiling Reveals Species-Associated Differences Across Five Duckweed Species · 2026 · DOI

  • Further phylogenetic and taxonomic research on Potamanthidae is needed, - Investigation of the evolutionary relationships within Ephemeroptera, - Study of the mitogenomes of other mayfly…

    Two Complete Mitochondrial Genomes of Potamanthidae (Ephemeroptera): Genome Features and Phylogenetic Implications · 2025 · DOI

  • Further study of the taxonomic diversity and environmental adaptations of Niveibacterium species, - Investigation of the potential interactions between Niveibacterium species and cyanobacteria, - Exploration of the biotechnological applications of Niveibacterium…

    Taxonomic and Genomic Characterization of Niveibacterium terrae sp. nov., a New Species from Riparian Soil in the Seomjin River, Republic of Korea · 2025 · DOI

  • Additionally, we applied VEHoP to reconstruct the phylogeny of the enigmatic deep-sea gastropod order Neomphalida, resolving a well-supported phylogenetic backbone for this poorly understood group.

    Reliable Inference of Phylogenomic Relationship via Assembly‐Based Strategy Accommodating Raw Reads and Proteins · 2026 · DOI

Most-cited papers in Genomics and Phylogenetic Studies

Most recent work

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Open questions raised by papers listed on this page include: (1) The lack of a complete chloroplast genome sequence for A. gigas (“The complete chloroplast genome sequence and phylogenetic analysis of…”, 2026); (2) The genomic organization and structural features of the genus Strix are not well understood, making it difficult to study their evolution and adaptation (“Mitogenomic characterization and phylogenetic placement of the mottled wood-owl…”, 2026); (3) There is a lack of understanding of codon usage bias in mangrove species (“Comprehensive analysis of chloroplast genomes from 15 mangrove species…”, 2026); (4) The lack of description of the novel species of bacteria, Sphingobium agrisoli sp. nov (“Correction to: A Novel Species Description of Sphingobium agrisoli sp. nov”, 2026); (5) Lack of high-quality genome assemblies for Coreius heterodon and Coreius guichenoti (“Telomere-to-telomere gapless genome assemblies of Coreius heterodon and Coreius…”, 2026). 758 gap statements have been mined from Genomics and Phylogenetic Studies papers in our 7.9M-paper local library, which holds 4,007 papers on the topic; the gaps come from whichever of those papers state one. They are mostly the research gaps the authors state and the papers' abstracts, plus future-work, limitations and challenges passages. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one, so you can read the original claim in context.

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