The Asian buffalo leech, Hirudinaria manillensis, has long been prized in traditional medicine across Southeast Asia, but its real value to modern science lies in a chemical arsenal that evolution spent millions of years perfecting. When a leech bites its host, it must keep blood flowing freely for the duration of its meal, which means it has to block clotting, calm platelet activation, and dissolve fibrin all at once. That combination of pharmacological tricks has made blood-feeding leeches a persistent source of interest for biomedical researchers hunting for new antithrombotic drugs. Now, a team led by Tahir Farooq, Muhammad Naeem, Nawaz Haider Bashir, Zichao Liu, Yuanhai Chen and Huanhuan Chen has published an integrated whole-genome and transcriptome analysis of H. manillensis in BMC Genomics, offering the most detailed sample-level view yet of the genes behind this leech’s blood-thinning repertoire.
The study, published on 2 October 2026, tackles a problem that has limited previous work in the field. Although H. manillensis has recently emerged as a key genomic reference among medicinal leeches, researchers had not systematically combined whole-genome read mapping with RNA sequencing data at the level of individual samples. The new workflow does exactly that, layering together genome alignment, transcriptome alignment and counting, DNA barcoding to confirm species identity, phylogenetic placement, reference-guided cataloging of known antithrombotic genes, transcript-supported discovery of new candidates, and targeted sequence comparison of selected loci. By integrating these strands of evidence, the authors could distinguish genes that are genuinely present and expressed from those that merely appear in a reference annotation, a distinction that matters enormously when the goal is to prioritize candidates for drug development.
A crucial early step was making sure the samples really were what the researchers thought they were. Species misidentification is a surprisingly common hazard in leech research, where closely related species can look nearly identical. The team used the mitochondrial cytochrome c oxidase subunit I gene, the standard DNA barcode for animals, to verify all four samples. BLAST searches against reference databases returned a top hit of MN882684 with 99.842 percent identity across 1,266 base pairs for every sample, and phylogenetic analysis placed each one squarely within the H. manillensis reference clade. That confirmation matters because any downstream claim about antithrombotic gene content would be undermined if the animals had been mislabeled, and it gives future users of the dataset confidence that the gene catalog truly describes this species.
The sequencing data itself was of high quality. Whole-genome mapping rates ranged from 72.17 percent to 92.75 percent across the four samples, with mean sequencing depths between 108.0-fold and 134.4-fold, deep enough to support confident read mapping and variant calling. The RNA-seq alignment rates ranged from 67.62 percent to 70.49 percent, providing a solid transcriptomic backbone for expression analysis. With these datasets in hand, the researchers turned to the central question: how many antithrombotic genes does the Asian buffalo leech carry, and which of them are actually switched on?
The reference-guided analysis recovered 72 known antithrombotic genes, matching the published annotation framework for the species and confirming that the pipeline was reproducing established results. The more exciting outcome came from the transcript-supported discovery stage, which added 38 new candidate transcripts. Of these, 30 represent novel isoforms of already-known gene loci, flagged by the annotation tool gffcompare with class code “j”, meaning they are splice variants or alternative transcripts of characterized genes. The remaining 8 are overlap-type candidates with class codes “o” and “x”, indicating transcripts that overlap known loci in ways that suggest either alternative structures or potentially distinct genes sharing genomic space. Notably, after filtering, no high-confidence class code “u” candidates, which would represent entirely unknown intergenic transcripts, survived, suggesting that the antithrombotic repertoire of this leech is largely built from elaborations of known gene families rather than from wholly novel loci hiding between annotated genes.
Among the gene families, one stood out for its sheer size. The H. manillensis elastase inhibitor family, abbreviated HMEI, was the largest supported family in the catalog, followed by hirustasin-related genes. Elastase inhibitors are of particular interest because elastase plays roles in inflammation and tissue remodeling as well as in clot-related processes, so a leech family that has expanded this class of inhibitors may be modulating more than just coagulation. Hirustasin, meanwhile, is a known serine protease inhibitor first characterized from the medicinal leech, and its relatives in H. manillensis reinforce the picture of a leech that deploys multiple independent inhibitory strategies against its host’s hemostatic system. The expansion of these families points to strong evolutionary pressure on blood-feeding animals to maintain a diverse and redundant toolkit for keeping blood liquid.
Expression data revealed a strikingly uneven picture across the four samples. The most abundant antithrombotic transcript overall was lefaxin_Hman2, a member of a family of anticoagulant proteins, yet expression of other loci varied dramatically from animal to animal, with clear sample-specific patterns among the HMEI genes in particular. This heterogeneity suggests that individual leeches may deploy somewhat different pharmacological cocktails when they feed, whether due to feeding status, physiological condition, or individual genetic variation. For drug discovery, that variability is a double-edged sword: it complicates any attempt to harvest a uniform product from leeches, but it also means that different individuals may naturally emphasize different bioactive molecules, broadening the pool of candidates accessible from this species.
Genetic variation added another layer of insight. The researchers assessed the variant burden across the antithrombotic genes and found it was highest for hyaluronidase_Hman2 and progranulin_Hman, two loci involved in tissue penetration and inflammation-related processes respectively. Intriguingly, the most highly expressed genes were not always the most variable, decoupling expression level from sequence diversity in a way that hints at different evolutionary constraints acting on different parts of the arsenal. Genes that interact directly with host immune and clotting proteins may be under pressure to diversify, while core anticoagulants may be conserved because their function cannot be tinkered with without cost. Selected-gene alignments confirmed localized substitutions and indel-rich regions in informative loci, providing concrete sequence differences that future functional studies can test.
The practical significance of the work lies in its framework as much as its findings. By combining species confirmation, deep genome mapping, transcriptome evidence, and rigorous annotation-based filtering, the study provides a reproducible pipeline for prioritizing antithrombotic candidates not just in H. manillensis but potentially in other blood-feeding species. The 38 transcript-supported candidates, particularly the 30 novel isoforms of known loci, represent a concrete shortlist for laboratory follow-up: expressing these variants recombinantly and testing their activity against thrombin, factor Xa, elastase, and platelet pathways would be the logical next step. The authors are affiliated with the Yunnan International Joint Laboratory with South and Southeast Asia for the Integrated Development of Animal-Derived Anti-Thrombosis Chinese Medicine at Qujing Normal University, and the work was funded under grant number 202503AP140025, reflecting a broader national effort to translate leech-derived molecules into modern antithrombotic therapies.
For a field that began with the discovery of hirudin in medicinal leech saliva more than a century ago, this study marks a shift from serendipity to systematic genomics. Cardiovascular disease remains the leading cause of death worldwide, and existing anticoagulants carry well-known risks of bleeding complications, so the demand for molecules with refined, targeted activity continues to grow. The Asian buffalo leech, now genomically characterized at the sample level with a verified catalog of 72 known genes and 38 new transcript-supported candidates, offers researchers a richer starting point than ever before. What remains is the functional work: confirming what these newly identified isoforms actually do, and whether any of them can be developed into the next generation of clot-preventing drugs. The leech, it turns out, still has plenty to teach modern medicine.
Subject of Research: Whole-genome and transcriptome profiling of antithrombotic genes in the Asian buffalo leech Hirudinaria manillensis
Article Title: Integrated whole-genome and transcriptome profiling of antithrombotic genes in Asian buffalo leech (Hirudinaria manillensis)
Article References: Farooq, T., Naeem, M., Bashir, N. H., Liu, Z., Chen, Y., & Chen, H. (2026). Integrated whole-genome and transcriptome profiling of antithrombotic genes in Asian buffalo leech (Hirudinaria manillensis). BMC Genomics. https://doi.org/10.1186/s12864-026-13354-x
Image Credits: AI Generated
DOI: 10.1186/s12864-026-13354-x
Keywords: Hirudinaria manillensis, antithrombotic genes, leech genomics, whole-genome sequencing, RNA-seq, COI barcoding, hirudin, medicinal leech, transcriptomics, drug discovery, anticoagulants, BMC Genomics
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Juliet Wilcox. (October 2, 2026). Leech Genome Study Maps the Full Arsenal of Antithrombotic Genes in the Asian Buffalo Leech. Scienmag. https://scienmag.com/leech-genome-study-maps-the-full-arsenal-of-antithrombotic-genes-in-the-asian-buffalo-leech/
Juliet Wilcox. “Leech Genome Study Maps the Full Arsenal of Antithrombotic Genes in the Asian Buffalo Leech.” Scienmag, 2 October 2026, https://scienmag.com/leech-genome-study-maps-the-full-arsenal-of-antithrombotic-genes-in-the-asian-buffalo-leech/. Accessed 2 October 2026.
Juliet Wilcox. “Leech Genome Study Maps the Full Arsenal of Antithrombotic Genes in the Asian Buffalo Leech.” Scienmag. October 2, 2026. https://scienmag.com/leech-genome-study-maps-the-full-arsenal-of-antithrombotic-genes-in-the-asian-buffalo-leech/
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Tags: anticoagulantsantithrombotic gene mappingantithrombotic genesbiomedical applications of leech genomeblood clotting inhibition genesblood-feeding mechanismsBMC GenomicsCOI barcodingdrug discoverygenome and transcriptome integrationhirudinHirudinaria manillensisHirudinaria manillensis genetic studyLeech genome analysisleech genomicsleech venom and saliva gene functionsleech-derived anticoagulant compoundsmedicinal leechmedicinal leech pharmacologyRNA-seqtraditional medicine to modern drug discoveryTranscriptomicswhole genome sequencingwhole-genome sequencing of leeches
