ArticlePlant communications2025
HiMT: An integrative toolkit for assembling organelle genomes using HiFi reads.
Article in Plant communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed.
- The Complete Mitogenome ofJournal of fungi (Basel, Switzerland) · 2026Article
- A Compact Multipartite Mitogenome ofInternational journal of molecular sciences · 2026Article
- Chromosome-scale Genome Assembly and Annotation of Anise Hyssop (Agastache foeniculum).Scientific data · 2026Article
- Assembly and Comparative Analysis of Five Complete Mitochondrial Genomes of theInternational journal of molecular sciences · 2026Article
- Article
- The complete chloroplast genome assembly ofMitochondrial DNA. Part B, Resources · 2026Article
- Newly assembled mitochondrial genomes ofFrontiers in plant science · 2026Article
- Comparative organellar genomics ofFrontiers in plant science · 2026Article
- Editorial: Evolutionary dynamics, functional variation and application of plant organellar genomes.Frontiers in plant science · 2026Article
- Complete mitochondrial sequencing reveals the horizontal transfer and gene rearrangement ofFrontiers in plant science · 2026Article
- Assembly and sequence analysis of the chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- Complete chloroplast genome and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2026Article
- The complete mitochondrial genome ofFrontiers in plant science · 2026Article
- The complete plastome sequence ofMitochondrial DNA. Part B, Resources · 2026Article
- Assembly and comparative analysis of the mitochondrial genome ofFrontiers in plant science · 2025Article
- From genome assembly to functional interpretation: an epistemological shift in understanding plant mitochondrial architecture.Frontiers in plant science · 2025Review
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Chloroplast and mitochondrial genomes, which coexist with the nuclear genome, are extensively used in gene function studies, evolutionary analyses, and targeted breeding. However, assembling these organelle genomes remains challenging due to frequent recombination events and abundant repetitive sequences. Although some assembly tools are available, many are difficult to install or require extensive parameter tuning and computational resources. To address these limitations, we present a high-fidelity, data-driven mitochondrial genome assembly toolkit (HiMT), a user-friendly, out-of-the-box software solution that enables one-click chloroplast and mitochondrial genome assembly using default parameters, particularly for plant species. HiMT automatically estimates read coverage depth and employs a fixed k-mer prefix strategy to minimize computational demands, making it suitable for use on standard laptops. Benchmark tests show that HiMT delivers complete assemblies with a high success rate, fast runtimes, and low hardware requirements. Additionally, HiMT features a graphical user interface (GUI) and generates interactive reports for assessing the quality of organelle genome assemblies. We anticipate that HiMT will facilitate high-quality plant mitochondrial genome research and significantly streamline organelle genome assembly workflows. To support the research community, HiMT is freely available to non-commercial users at https://github.com/tang-shuyuan/HiMT.
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Registered trials
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