Michi, A. N., Favetto, P. H., Kastelic, J. & Cobo, E. R. A review of sexually transmitted bovine trichomoniasis and campylobacteriosis affecting cattle reproductive health. Theriogenology 85, 781–791, https://doi.org/10.1016/j.theriogenology.2015.10.037 (2016).Article
PubMed
Google Scholar
Cobo, E. R., Corbeil, L. B. & BonDurant, R. H. Immunity to infections in the lower genital tract of bulls. Journal of Reproductive Immunology 89, 55–61, https://doi.org/10.1016/j.jri.2011.02.002 (2011).Article
CAS
PubMed
Google Scholar
Skirrow, S. Z. & Bondurant, R. H. Treatment of bovine trichomoniasis with ipronidazole. Aust Vet J 65, 156, https://doi.org/10.1111/j.1751-0813.1988.tb14446.x (1988).Article
CAS
PubMed
Google Scholar
BonDurant, R. H. Pathogenesis, Diagnosis, and Management of Trichomoniasis in Cattle. Veterinary Clinics of North America: Food Animal Practice 13, 345–361, https://doi.org/10.1016/S0749-0720(15)30346-7 (1997).Article
CAS
PubMed
Google Scholar
Martin, K. A., Henderson, J. & Brewer, M. T. Bovine Trichomonosis Cases in the United States 2015-2019. Front Vet Sci 8, 692199, https://doi.org/10.3389/fvets.2021.692199 (2021).Article
PubMed
PubMed Central
Google Scholar
Gifford, C. A. et al. Factors important for bull purchasing decisions and management in extensive rangeland production systems of New Mexico: a producer survey. Translational Animal Science 7, https://doi.org/10.1093/tas/txac167 (2022).Slapeta, J. et al. Comparative analysis of Tritrichomonas foetus (Riedmüller, 1928) cat genotype, T. foetus (Riedmüller, 1928) cattle genotype and Tritrichomonas suis (Davaine, 1875) at 10 DNA loci. Int J Parasitol 42, 1143–1149, https://doi.org/10.1016/j.ijpara.2012.10.004 (2012).Article
CAS
PubMed
Google Scholar
Yao, C. Diagnosis of Tritrichomonas foetus-infected bulls, an ultimate approach to eradicate bovine trichomoniasis in US cattle? Journal of medical microbiology 62, 1–9, https://doi.org/10.1099/jmm.0.047365-0 (2013).Article
CAS
PubMed
Google Scholar
Benchimol, M. et al. Draft Genome Sequence of Tritrichomonas foetus Strain K. Genome announcements 5, https://doi.org/10.1128/genomeA.00195-17 (2017).Senior, E. M. A reverse vaccinology approach to identifying vaccine candidate antigens for bovine Trichomoniasis. (The University of Liverpool (United Kingdom), 2020).Horner, D. S., Hirt, R. P., Kilvington, S., Lloyd, D. & Embley, T. M. Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proc Biol Sci 263, 1053–1059, https://doi.org/10.1098/rspb.1996.0155 (1996).Article
CAS
PubMed
Google Scholar
Wick, R. Porechop: Adapter trimmer for Oxford Nanopore reads. Github https://github.com/rrwick (2017).Wick, R. Filtlong: Quality filtering tool for long reads. GitHub https://github.com/rrwick (2017).Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890, https://doi.org/10.1093/bioinformatics/bty560 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nature biotechnology 37, 540–546, https://doi.org/10.1038/s41587-019-0072-8 (2019).Article
CAS
PubMed
Google Scholar
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nature Methods 17, 155–158, https://doi.org/10.1038/s41592-019-0669-3 (2020).Article
CAS
PubMed
Google Scholar
Vaser, R. & Šikić, M. Time- and memory-efficient genome assembly with Raven. Nature Computational Science 1, 332–336, https://doi.org/10.1038/s43588-021-00073-4 (2021).Article
PubMed
Google Scholar
Shafin, K. et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature biotechnology 38, 1044–1053, https://doi.org/10.1038/s41587-020-0503-6 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Solares, E. A. et al. Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing. G3 Genes|Genomes|Genetics 8, 3143–3154, https://doi.org/10.1534/g3.118.200162 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome research 27, 737–746, https://doi.org/10.1101/gr.214270.116 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100, https://doi.org/10.1093/bioinformatics/bty191 (2018).Article
CAS
PubMed
PubMed Central
Google Scholar
Wick, R. R. & Holt, K. E. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLOS Computational Biology 18, e1009802, https://doi.org/10.1371/journal.pcbi.1009802 (2022).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
García-Alcalde, F. et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28, 2678–2679, https://doi.org/10.1093/bioinformatics/bts503 (2012).Article
CAS
PubMed
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760, https://doi.org/10.1093/bioinformatics/btp324 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079, https://doi.org/10.1093/bioinformatics/btp352 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Broad Institute of MIT and Harvard. Picard: A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. https://broadinstitute.github.io/picard (2014).Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, https://doi.org/10.1093/bioinformatics/btac808 (2022).Zeng, X. et al. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. bioRxiv, 2023.2011. 2018.567668 (2023).Xu, W.-D., Lun, Z.-R. & Gajadhar, A. Chromosome numbers of Tritrichomonas foetus and Tritrichomonas suis. Vet Parasitol 78, 247–251, https://doi.org/10.1016/S0304-4017(98)00150-2 (1998).Article
CAS
PubMed
Google Scholar
Zubáčová, Z., Cimbůrek, Z. & Tachezy, J. Comparative analysis of trichomonad genome sizes and karyotypes. Molecular and Biochemical Parasitology 161, 49–54, https://doi.org/10.1016/j.molbiopara.2008.06.004 (2008).Article
CAS
PubMed
Google Scholar
Benchimol, M. et al. Tritrichomonas foetus strain K, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:MLAK00000000.1 (2016).Senior, E. Tritrichomonas foetusisolate Belfast, whole genome shotgun sequencing project, GenBank, https://identifiers.org/ncbi/insdc:CAJHQR000000000.1 (2021).Carlton, J. M. et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (New York, N.Y.) 315, 207–212, https://doi.org/10.1126/science.1132894 (2007).Article
ADS
PubMed
Google Scholar
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution 38, 4647–4654, https://doi.org/10.1093/molbev/msab199 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770, https://doi.org/10.1093/bioinformatics/btr011 (2011).Article
CAS
PubMed
PubMed Central
Google Scholar
Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204, https://doi.org/10.1093/bioinformatics/btx153 (2017).Article
CAS
PubMed
PubMed Central
Google Scholar
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 27, 573–580, https://doi.org/10.1093/nar/27.2.573 (1999).Article
CAS
PubMed
PubMed Central
Google Scholar
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences 117, 9451–9457, https://doi.org/10.1073/pnas.1921046117 (2020).Article
ADS
CAS
Google Scholar
Smith, A., Hubley, R. & Green, P. RepeatMasker Open-4.0. RepeatMasker Open-4.0 (2013).Du, L., Zhang, C., Liu, Q., Zhang, X. & Yue, B. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics 34, 681–683, https://doi.org/10.1093/bioinformatics/btx665 (2017).Article
CAS
Google Scholar
Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335–1337, https://doi.org/10.1093/bioinformatics/btp157 (2009).Article
CAS
PubMed
PubMed Central
Google Scholar
Kalvari, I. et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic acids research 49, D192–D200, https://doi.org/10.1093/nar/gkaa1047 (2020).Article
CAS
PubMed Central
Google Scholar
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767–769, https://doi.org/10.1093/bioinformatics/btv661 (2016).Article
CAS
PubMed
Google Scholar
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom Bioinform 3, lqaa108, https://doi.org/10.1093/nargab/lqaa108 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Hoff, K. J., Lomsadze, A., Borodovsky, M. & Stanke, M. Whole-Genome Annotation with BRAKER. Methods Mol Biol 1962, 65–95, https://doi.org/10.1007/978-1-4939-9173-0_5 (2019).Article
CAS
PubMed
PubMed Central
Google Scholar
Brůna, T., Lomsadze, A. & Borodovsky, M. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom Bioinform 2, lqaa026, https://doi.org/10.1093/nargab/lqaa026 (2020).Article
CAS
PubMed
PubMed Central
Google Scholar
Gabriel, L., Hoff, K. J., Brůna, T., Borodovsky, M. & Stanke, M. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566, https://doi.org/10.1186/s12859-021-04482-0 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Stanke, M., Schöffmann, O., Morgenstern, B. & Waack, S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62, https://doi.org/10.1186/1471-2105-7-62 (2006).Article
CAS
PubMed
PubMed Central
Google Scholar
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644, https://doi.org/10.1093/bioinformatics/btn013 (2008).Article
CAS
PubMed
Google Scholar
Iwata, H. & Gotoh, O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic acids research 40, e161, https://doi.org/10.1093/nar/gks708 (2012).Article
CAS
PubMed
PubMed Central
Google Scholar
Gotoh, O. A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic acids research 36, 2630–2638, https://doi.org/10.1093/nar/gkn105 (2008).Article
CAS
PubMed
PubMed Central
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12, 59–60, https://doi.org/10.1038/nmeth.3176 (2015).Article
CAS
PubMed
Google Scholar
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic acids research 33, 6494–6506, https://doi.org/10.1093/nar/gki937 (2005).Article
CAS
PubMed
PubMed Central
Google Scholar
Kuznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic acids research 51, D445–d451, https://doi.org/10.1093/nar/gkac998 (2023).Article
CAS
PubMed
Google Scholar
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic acids research 28, 45–48, https://doi.org/10.1093/nar/28.1.45 (2000).Article
CAS
PubMed
PubMed Central
Google Scholar
Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nature genetics 25, 25–29, https://doi.org/10.1038/75556 (2000).Article
CAS
PubMed
PubMed Central
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic acids research 47, D309–d314, https://doi.org/10.1093/nar/gky1085 (2019).Article
CAS
PubMed
Google Scholar
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28, 27–30, https://doi.org/10.1093/nar/28.1.27 (2000).Article
CAS
PubMed
PubMed Central
Google Scholar
Götz, S. et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic acids research 36, 3420–3435, https://doi.org/10.1093/nar/gkn176 (2008).Article
CAS
PubMed
PubMed Central
Google Scholar
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240, https://doi.org/10.1093/bioinformatics/btu031 (2014).Article
CAS
PubMed
PubMed Central
Google Scholar
Paysan-Lafosse, T. et al. InterPro in 2022. Nucleic acids research 51, D418–D427, https://doi.org/10.1093/nar/gkac993 (2022).Article
CAS
PubMed Central
Google Scholar
Jassal, B. et al. The reactome pathway knowledgebase. Nucleic acids research 48, D498–d503, https://doi.org/10.1093/nar/gkz1031 (2020).Article
CAS
PubMed
Google Scholar
Mölder, F. et al. Sustainable data analysis with Snakemake [version 2; peer review: 2 approved]. F1000Research 10, https://doi.org/10.12688/f1000research.29032.2 (2021).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP514276 (2024).Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075, https://doi.org/10.1093/bioinformatics/btt086 (2013).Article
CAS
PubMed
PubMed Central
Google Scholar
Huang, N. & Li, H. compleasm: a faster and more accurate reimplementation of BUSCO. Bioinformatics 39, https://doi.org/10.1093/bioinformatics/btad595 (2023).Nevers, Y. et al. Quality assessment of gene repertoire annotations with OMArk. Nature biotechnology https://doi.org/10.1038/s41587-024-02147-w (2024).Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477, https://doi.org/10.1089/cmb.2012.0021 (2012).Article
MathSciNet
CAS
PubMed
PubMed Central
Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359, https://doi.org/10.7717/peerj.7359 (2019).Article
PubMed
PubMed Central
Google Scholar