cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57907/mirri/fqat0q/lv12ck
title: MIRRI0073490.json

description: Strain json file
DOI: 10.57907/mirri/fqzovl/ce6j9e
title: MIRRI0073970.json

description: Strain json file
DOI: 10.57907/mirri/frjgcm
title: MIRRI0073939

description: Organism type: Filamentous Fungi ; Taxon name: Teratosphaeria zuluensis ; Collection: CBS 117256 ; Country: Argentina
DOI: 10.57907/mirri/gmqolu/9ysm8o
title: MIRRI0073961.json

description: Strain json file
DOI: 10.57907/mirri/gx2o6f
title: MIRRI0073936

description: Organism type: Filamentous Fungi ; Taxon name: Amesia atrobrunnea ; Collection: CBS 117253 ; Country: Spain
DOI: 10.57907/mirri/i7nzwr
title: MIRRI0073819

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria carthami ; Collection: CBS 117091 ; Country: United States of America
DOI: 10.57907/mirri/kcoqyo
title: MIRRI0074070

description: Organism type: Filamentous Fungi ; Taxon name: Pseudallescheria boydii ; Collection: CBS 117424 ; Country: France
DOI: 10.57907/mirri/kr6fxa
title: MIRRI0073776

description: Organism type: Filamentous Fungi ; Taxon name: Stegonsporium acerophilum ; Collection: CBS 117035 ; Country: United States of America
DOI: 10.57907/mirri/m6npyq
title: MIRRI0073971

description: Organism type: Filamentous Fungi ; Taxon name: Grosmannia crassivaginata ; Collection: CBS 117304 ; Country: Czech Republic
DOI: 10.57907/mirri/mth38x
title: MIRRI0073958

description: Organism type: Filamentous Fungi ; Taxon name: Scopulariopsis brevicaulis ; Collection: CBS 117277 ; Country: Netherlands
DOI: 10.57907/mirri/njiw4g
title: MIRRI0073931

description: Organism type: Filamentous Fungi ; Taxon name: Rhizoctonia solani ; Collection: CBS 117247 ; Country: Spain
DOI: 10.57907/mirri/oh58gu/p5ncxf
title: MIRRI0073470.json

description: Strain json file
DOI: 10.57907/mirri/ovliuf/hu04cg
title: MIRRI0073930.json

description: Strain json file
DOI: 10.57907/mirri/pqeifq/folxvc
title: MIRRI0073921.json

description: Strain json file
DOI: 10.57907/mirri/qavoq7/jiurnh
title: MIRRI0073942.json

description: Strain json file
DOI: 10.57907/mirri/sk9dcz
title: MIRRI0073758

description: Organism type: Filamentous Fungi ; Taxon name: Spencermartinsia viticola ; Collection: CBS 117009 ; Country: Spain
DOI: 10.57907/mirri/smrvbh
title: MIRRI0073915

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria cucumerina ; Collection: CBS 117226 ; Country: Australia
DOI: 10.57907/mirri/snav5f
title: MIRRI0073941

description: Organism type: Filamentous Fungi ; Taxon name: Teratosphaeria ovata ; Collection: CBS 117258 ; Country: Argentina
DOI: 10.57907/mirri/svgfkl
title: MIRRI0073859

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria alternata ; Collection: CBS 117143 ; Country: Italy
DOI: 10.57907/mirri/w7w4d2
title: MIRRI0074086

description: Organism type: Filamentous Fungi ; Taxon name: Sporothrix schenckii ; Collection: CBS 117440 ; Country: South Africa
DOI: 10.57907/mirri/wezatf/a8ecpz
title: MIRRI0073935.json

description: Strain json file
DOI: 10.57907/mirri/wsh8rx/4bs0nv
title: MIRRI0073525.json

description: Strain json file
DOI: 10.57907/mirri/x5kbbk/zyo26y
title: MIRRI0073767.json

description: Strain json file
DOI: 10.57907/mirri/xg9p6e
title: MIRRI0073768

description: Organism type: Filamentous Fungi ; Taxon name: Stegonsporium acerophilum ; Collection: CBS 117025 ; Country: United States of America
DOI: 10.57907/mirri/xg9p6e/obihtl
title: MIRRI0073768.json

description: Strain json file
DOI: 10.57907/mirri/xqo2jo
title: MIRRI0074026

description: Organism type: Filamentous Fungi ; Taxon name: Diaporthe ambigua ; Collection: CBS 117372 ; Country: South Africa
DOI: 10.57907/mirri/zxiac1
title: MIRRI0073956

description: Organism type: Filamentous Fungi ; Taxon name: Penicillium citrinum ; Collection: CBS 117275 ; Country: Ghana
DOI: 10.57907/mirri/zxiac1/h9wqlr
title: MIRRI0073956.json

description: Strain json file
DOI: 10.3535/5j1-bm2-2jh
title: Tofieldia calyculata (L.) Wahlenb.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/mmj-sd7-rpr
title: Ammi majus L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/1ahpmc
title: MIRRI0073790

description: Organism type: Filamentous Fungi ; Taxon name: Ophiostoma piceaperdum ; Collection: CBS 117052 ; Country: Austria
DOI: 10.57907/mirri/3i24xs/bzsumq
title: MIRRI0074001.json

description: Strain json file
DOI: 10.57907/mirri/6aihiu/lvgzcb
title: MIRRI0073903.json

description: Strain json file
DOI: 10.57907/mirri/7x7e3b/h3tshi
title: MIRRI0074102.json

description: Strain json file
DOI: 10.57907/mirri/akonsa
title: MIRRI0074064

description: Organism type: Filamentous Fungi ; Taxon name: Pseudallescheria boydii ; Collection: CBS 117418 ; Country: France
DOI: 10.57907/mirri/ctfib8
title: MIRRI0074090

description: Organism type: Filamentous Fungi ; Taxon name: Cophinforma mamane ; Collection: CBS 117447 ; Country: Venezuela
DOI: 10.57907/mirri/dmpa8k
title: MIRRI0074087

description: Organism type: Filamentous Fungi ; Taxon name: Cophinforma mamane ; Collection: CBS 117444 ; Country: Venezuela
DOI: 10.57907/mirri/ehcq6x/zau9r3
title: MIRRI0073770.json

description: Strain json file
DOI: 10.57907/mirri/fbry3q/uljnnb
title: MIRRI0073895.json

description: Strain json file
DOI: 10.57907/mirri/guixsd
title: MIRRI0073927

description: Organism type: Filamentous Fungi ; Taxon name: Rhizoctonia solani ; Collection: CBS 117243 ; Country: Spain
DOI: 10.57907/mirri/i0tors
title: MIRRI0073940

description: Organism type: Filamentous Fungi ; Taxon name: Teratosphaeria zuluensis ; Collection: CBS 117257 ; Country: Argentina
DOI: 10.57907/mirri/korllh/yvtdkz
title: MIRRI0074100.json

description: Strain json file
DOI: 10.57907/mirri/kreo13
title: MIRRI0074088

description: Organism type: Filamentous Fungi ; Taxon name: Cophinforma mamane ; Collection: CBS 117445 ; Country: Venezuela
DOI: 10.57907/mirri/kukyxp/9w7zdu
title: MIRRI0073852.json

description: Strain json file
DOI: 10.57907/mirri/nfutgo
title: MIRRI0073796

description: Organism type: Filamentous Fungi ; Taxon name: Neosartorya fennelliae ; Collection: CBS 117060 ; Country: South Korea
DOI: 10.57907/mirri/os5wjd/gpqw9y
title: MIRRI0073933.json

description: Strain json file
DOI: 10.57907/mirri/ozp358
title: MIRRI0074095

description: Organism type: Filamentous Fungi ; Taxon name: Neofusicoccum arbuti ; Collection: CBS 117453 ; Country: Venezuela
DOI: 10.57907/mirri/p1wrcg/jga8uj
title: MIRRI0074152.json

description: Strain json file
DOI: 10.57907/mirri/p4opjn/kg3gmj
title: MIRRI0073477.json

description: Strain json file
DOI: 10.57907/mirri/pfa0lj
title: MIRRI0073908

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria cichorii ; Collection: CBS 117218 ; Country: Greece
DOI: 10.57907/mirri/qornzu/5yj78a
title: MIRRI0073488.json

description: Strain json file
DOI: 10.57907/mirri/qxesja
title: MIRRI0073959

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus sydowii ; Collection: CBS 117278 ; Country: Ghana
DOI: 10.57907/mirri/t76vot
title: MIRRI0073911

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria argyroxiphii ; Collection: CBS 117222
DOI: 10.57907/mirri/vd0y3q
title: MIRRI0073980

description: Organism type: Filamentous Fungi ; Taxon name: Eurotium herbariorum ; Collection: CBS 117314 ; Country: Canada
DOI: 10.57907/mirri/wj4sn9
title: MIRRI0074014

description: Organism type: Filamentous Fungi ; Taxon name: Sporothrix protearum ; Collection: CBS 117358 ; Country: South Africa
DOI: 10.57907/mirri/wkuwtc/qw0ffp
title: MIRRI0073879.json

description: Strain json file
DOI: 10.57907/mirri/x5kbbk
title: MIRRI0073767

description: Organism type: Filamentous Fungi ; Taxon name: Stegonsporium galeatum ; Collection: CBS 117024 ; Country: Austria
DOI: 10.3535/3ep-bms-q17
title: Potentilla indica (Andrews) Th. Wolf

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/wwr-myc-qcp
title: Reseda phyteuma L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/dgxamm
title: MIRRI0073772

description: Organism type: Filamentous Fungi ; Taxon name: Stegonsporium pseudopyriforme ; Collection: CBS 117029 ; Country: Austria
DOI: 10.57907/mirri/fopp9w/ulvckm
title: MIRRI0073812.json

description: Strain json file
DOI: 10.57907/mirri/hapugc/yzpq17
title: MIRRI0073780.json

description: Strain json file
DOI: 10.57907/mirri/hb7r8x
title: MIRRI0073782

description: Organism type: Filamentous Fungi ; Taxon name: Graphium fimbriasporum ; Collection: CBS 117044 ; Country: Austria
DOI: 10.57907/mirri/lfd78x/g6wr2j
title: MIRRI0073886.json

description: Strain json file
DOI: 10.57907/mirri/nfutgo/wczhxq
title: MIRRI0073796.json

description: Strain json file
DOI: 10.57907/mirri/p9bqz8/5gg56e
title: MIRRI0073952.json

description: Strain json file
DOI: 10.57907/mirri/usoyky/v2f5f0
title: MIRRI0073801.json

description: Strain json file
DOI: 10.57907/mirri/v39ijt/u9hnyc
title: MIRRI0073771.json

description: Strain json file
DOI: 10.57907/mirri/xfxv3f/ffbf1d
title: MIRRI0073785.json

description: Strain json file
DOI: 10.57907/mirri/ymvcqn
title: MIRRI0073928

description: Organism type: Filamentous Fungi ; Taxon name: Rhizoctonia solani ; Collection: CBS 117244 ; Country: Spain
DOI: 10.3535/92t-twf-nlc
title: Nigella arvensis L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/ajt-d5n-l9y
title: Epilobium lamyi F. W. Schultz

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/9ducoi/fprmwg
title: MIRRI0073481.json

description: Strain json file
DOI: 10.57907/mirri/cwaiji
title: MIRRI0073778

description: Organism type: Filamentous Fungi ; Taxon name: Stegonsporium protopyriforme ; Collection: CBS 117040 ; Country: Austria
DOI: 10.57907/mirri/edjgrz/b2rsz0
title: MIRRI0074145.json

description: Strain json file
DOI: 10.57907/mirri/fmpv1o/8bcrik
title: MIRRI0074099.json

description: Strain json file
DOI: 10.57907/mirri/ko76mu
title: MIRRI0073997

description: Organism type: Filamentous Fungi ; Taxon name: Aspergillus restrictus ; Collection: CBS 117331 ; Country: Germany
DOI: 10.57907/mirri/ozp358/opocxg
title: MIRRI0074095.json

description: Strain json file
DOI: 10.57907/mirri/qavoq7
title: MIRRI0073942

description: Organism type: Filamentous Fungi ; Taxon name: Teratosphaeria zuluensis ; Collection: CBS 117259 ; Country: Argentina
DOI: 10.57907/mirri/rskpkm
title: MIRRI0073789

description: Organism type: Filamentous Fungi ; Taxon name: Ophiostoma piceaperdum ; Collection: CBS 117051 ; Country: Austria
DOI: 10.57907/mirri/xxsu8m
title: MIRRI0073836

description: Organism type: Filamentous Fungi ; Taxon name: Phaeoacremonium iranianum ; Collection: CBS 117114 ; Country: Azerbaijan
DOI: 10.3535/jh1-3rv-kr2
title: Carex umbrosa Host

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/2pmvxm
title: MIRRI0073876

description: Organism type: Filamentous Fungi ; Taxon name: Diaporthe ambigua ; Collection: CBS 117170 ; Country: South Africa
DOI: 10.57907/mirri/8thet4/qcsxfi
title: MIRRI0074103.json

description: Strain json file
DOI: 10.57907/mirri/dt5954
title: MIRRI0074166

description: Organism type: Filamentous Fungi ; Taxon name: Colletotrichum circinans ; Collection: CBS 117546 ; Country: Netherlands
DOI: 10.57907/mirri/hituwn
title: MIRRI0073805

description: Organism type: Filamentous Fungi ; Taxon name: Neosartorya laciniosa ; Collection: CBS 117070 ; Country: South Korea
DOI: 10.57907/mirri/jsi004/iagjbe
title: MIRRI0073809.json

description: Strain json file
DOI: 10.57907/mirri/kkfv88
title: MIRRI0074178

description: Organism type: Filamentous Fungi ; Taxon name: Stenocarpella macrospora ; Collection: CBS 117560 ; Country: South Africa
DOI: 10.57907/mirri/kyof6u
title: MIRRI0073794

description: Organism type: Filamentous Fungi ; Taxon name: Ophiostoma piceaperdum ; Collection: CBS 117056 ; Country: Austria
DOI: 10.57907/mirri/nl61n8
title: MIRRI0074116

description: Organism type: Filamentous Fungi ; Taxon name: Cladosporium anthropophilum ; Collection: CBS 117483 ; Country: United States of America
DOI: 10.57907/mirri/ov8eqh
title: MIRRI0074153

description: Organism type: Filamentous Fungi ; Taxon name: Acremonium fusidioides ; Collection: CBS 117532
DOI: 10.57907/mirri/p0jrfk/8e0zat
title: MIRRI0074184.json

description: Strain json file
DOI: 10.57907/mirri/q7vxpa
title: MIRRI0074173

description: Organism type: Filamentous Fungi ; Taxon name: Ceratosphaeria lampadophora ; Collection: CBS 117555 ; Country: France
DOI: 10.57907/mirri/rau1kw
title: MIRRI0074122

description: Organism type: Filamentous Fungi ; Taxon name: Exophiala lacus ; Collection: CBS 117497 ; Country: Netherlands
DOI: 10.57907/mirri/vkwjac/iqfql5
title: MIRRI0073919.json

description: Strain json file
DOI: 10.3535/2qs-1ks-qck
title: Bromus japonicus Houtt.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/cd9-rgl-8wx
title: Cerastium brachypetalum Desp. ex Pers.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.57907/mirri/0ohdxp
title: MIRRI0073824

description: Organism type: Filamentous Fungi ; Taxon name: Alternaria dauci ; Collection: CBS 117097 ; Country: United States of America
DOI: 10.57907/mirri/1ahpmc/eazhwq
title: MIRRI0073790.json

description: Strain json file
DOI: 10.57907/mirri/1atce3/e1hwas
title: MIRRI0073968.json

description: Strain json file
DOI: 10.57907/mirri/3oooun/ftocvc
title: MIRRI0073849.json

description: Strain json file
DOI: 10.57907/mirri/3y3guf/o5wp0z
title: MIRRI0074230.json

description: Strain json file
DOI: 10.57907/mirri/6jrbkd/6jq4vg
title: MIRRI0073865.json

description: Strain json file
DOI: 10.5524/102669
title: Supporting data for "Network-based anomaly detection algorithm reveals proteins with major roles in human tissues"

description: Proteins act through physical interactions with other molecules to maintain organismal health. Protein-protein interaction (PPI) networks proved to be a powerful framework for obtaining insight into protein functions, cellular organization, response to signals, and disease states. In multicellular organisms, protein content varies between tissues, influencing tissue morphology and function. Weighted PPI networks, reflecting the likelihood of interactions in specific tissues, offer insights into tissue-specific processes and disease mechanisms. We hypothesized that detecting anomalous nodes in these networks could reveal proteins with key tissue-specific functions. <br>Here, we introduce Weighted Graph Anomalous Node Detection (WGAND), a novel machine-learning algorithm to identify anomalous nodes in weighted graphs. WGAND estimates expected edge weights and uses deviations to generate anomaly detection features, which are then used to score network nodes. We applied WGAND to weighted PPI networks of 17 human tissues. High-ranking anomalous nodes were enriched for proteins associated with tissue-specific diseases and tissue-specific biological processes, such as neuron signaling in the brain and spermatogenesis in the testis. WGAND outperformed other methods in terms of Area Under the ROC Curve (AUC) and Precision at K (P@K), highlighting its effectiveness in uncovering biologically meaningful anomalies. <br>Our findings demonstrate WGANDs potential as a powerful tool for detecting anomalous proteins with significant biological roles. By identifying proteins involved in critical tissue-specific processes and diseases, WGAND offers valuable insights for discovering novel biomarkers and therapeutic targets. Its versatile algorithm is suitable for any weighted graph and is broadly applicable across various fields.
DOI: 10.5524/102691
title: Supporting data for "A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications"

description: In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning (for example, ML algorithms for translating natural language questions to SPARQL), if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. <br>We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including almost 100 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.
DOI: 10.5524/102666
title: Genome assembly of the deep-sea octocoral <i>Paragorgia papillata</i>

description: <i>Paragorgia</i> corals, commonly referred to as bubblegum octocorals, are deep-sea sessile invertebrates belonging to the Paragorgiidae family. These organisms inhabit various ecosystems, including seamounts and canyons, where they play a crucial role in providing three-dimensional habitats that support a wide array of marine species, significantly more than those found in shallow-water gorgonians. Nevertheless, these corals and their habitats are increasingly threatened by anthropogenic activities, particularly harmful fishing methods. Recently, a new species of <i>Paragorgia</i> was discovered in the tropical Western Pacific at a depth of 858 meters on the Caroline Ridge. This species is distinguished by its white coloration, uniplanar morphology, and prominent autozooids, indicating a close relationship with <i>P. coralloides</i>, although some differences were noticed in calyx dimensions, cortex pigmentation, and the arrangement of medullar spindles. [from: Li Y. et al., 2021; Herrera S. et al., 2010] <br>We present a publicly available genome assembly of the octocoral <i>Paragorgia papillata</i>, with 111.9 Gb (~181 fold coverage) of sequence data. The complete assembly spans 618 Mb, with contig N50 of 2.7 Mb. The BUSCO analysis indicates a completeness of 91.61%.
DOI: 10.5524/102685
title: Supporting data for "Cross-modal contrastive learning decodes developmental regulatory features through chromatin potential analysis"

description: Emerging large-scale multimodal single-cell data jointly measures chromatin accessibility and transcription in the same cell, thus reconciling matched data paves integrated route for comprehensive regulatory analysis. <br> Here, we introduce Attune, a cross-modal contrastive learning framework to align paired gene expression and accessibility information. Systematic benchmarking shows Attune's superior performance for omics integration and gene expression prediction. We further introduce Transformer-based cross-modal attention over fine-tuned gene and peak embeddings to infer regulatory interaction and discover significant differential signals of cell subtypes. Applied to hair follicle maturation dataset, Attune reveals chromatin potential for bifunctional transcription factor Gli3 at the gene level. In addition, the paired representations determine transmitted states across neonatal and mature cell types of cortical neuron differentiation at the cell level. Taken together, Attune features a promising paradigm for regulatory inference across omics layers and allows for extending more complex omics analysis. <br>Attune offers a versatile framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data.
DOI: 10.5524/102658
title: Supporting data for "NanoMnT: An STR Analysis Tool for Oxford Nanopore Sequencing Data Driven by a Comprehensive Analysis of Error Profile in STR regions"

description: Oxford Nanopore sequencing (ONT) is a third-generation sequencing technology that enables cost-effective long-read sequencing with broad applications in biological research. However, its high sequencing error rate in low-complexity regions hampers its applications in short tandem repeat (STR) related research. <br>To address this, we generated a comprehensive STR error profile of ONT by analyzing publicly available Nanopore sequencing datasets. We show that the sequencing error rate is influenced not only by STR length but also by the repeat unit and the flanking sequences of STR regions. Interestingly, certain flanking sequences were associated with higher sequencing accuracy, suggesting that certain STR loci are more suitable for Nanopore sequencing compared to other loci. While base quality scores of substitution errors within the STR regions were lower than those of correctly sequenced bases, such patterns were not observed for indel errors. Furthermore, choosing the most recent basecaller version and using the super accuracy (SUP) model significantly improved STR sequencing accuracy. <br>Finally, we present NanoMnT, a lightweight Python tool that corrects STR sequencing errors in sequencing data and estimates STR allele sizes. NanoMnT leverages the characteristics of ONT when estimating STR allele size and exhibits superior results for 1bp- and 2bp-repeat STR compared to existing tools. By integrating our findings, we improved STR allele estimation accuracy for Ax10 repeats from 55% to 78%, and up to 85% when excluding loci with unfavorable flanking sequences. Using NanoMnT, we present the utility of our findings by identifying microsatellite instability (MSI) status in cancer sequencing data.
DOI: 10.5524/102659
title: Supporting data for "Phased High-Quality Genome of the Gymnosperm Himalayan Yew Assists in Paclitaxel Pathway Exploration"

description: <i>Taxus wallichiana</i> is an important species for paclitaxel production. Previous genome versions for <i>Taxus spp.</i> have been limited by extensive gaps, hindering the complete annotation and mining of paclitaxel (known as taxol commercially) synthesis pathway-related genes. <br>Here, we present the first phased high-quality reference genome of <i>Taxus wallichiana</i>, which significantly improves assembly quality and corrects large-scale assembly errors present in previous versions. The two haplotypes are 9.87 Gb and 9.98 Gb in length, respectively, and all 24 chromosomes were assembled with telomeres at both ends. Based on this high-quality genome (TWv1), we inferred that the candidate sex chromosome of <i>Taxus wallichiana</i> is chr12, and its sex determination system may follow a ZW model. Particularly, we identified and experimentally validated a batch of 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODDs), which may be key C4-C20 epoxidases in the paclitaxel synthesis pathway.<br>This study not only provides a valuable data resource for gene mining in the biosynthetic pathways of secondary metabolites such as paclitaxel but also offers the highest-quality reference genome of gymnosperms to date for the identification of sex chromosomes, facilitating comparative genomic studies among gymnosperms.