{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T13:08:25Z","timestamp":1784120905652,"version":"3.55.0"},"update-to":[{"DOI":"10.12688\/f1000research.177569.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000}}],"reference-count":32,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Colombian Coffee Growers Federation (FNC) \/ National Coffee Research Center","award":["PAT102006"],"award-info":[{"award-number":["PAT102006"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns5:p>\n                    <ns5:italic>Hemileia vastatrix<\/ns5:italic>\n                    is the fungal pathogen responsible for coffee leaf rust (CLR), the most economically important disease of\n                    <ns5:italic>Coffea arabica<\/ns5:italic>\n                    worldwide. Recently, the nuclear genome of this fungus was completely deciphered. However, the mitochondrial genome of\n                    <ns5:italic>H. vastatrix<\/ns5:italic>\n                    has remained undercharacterized. Here, we present the complete, circularized mitochondrial genome of\n                    <ns5:italic>H. vastatrix<\/ns5:italic>\n                    Race I (isolate HvRI), assembled using a hybrid approach combining PacBio HiFi long reads and BGIseq short reads. The genome is 173,525\u00a0bp in length with a GC content of 33.1% and encodes 41 functional genes, including 15 protein-coding genes, 2 rRNAs, and 24 tRNAs. The assembly reveals significant structural complexity, driven by intron expansion in the\n                    <ns5:italic>cox1<\/ns5:italic>\n                    and\n                    <ns5:italic>cob<\/ns5:italic>\n                    genes. Notably, the\n                    <ns5:italic>atp8<\/ns5:italic>\n                    gene contains a group II intron, rare for this locus, whose internal open reading frame displays evidence of pseudogenization via internal stop codons.. We also characterized a putative replication initiation zone (~1.2\u00a0kb) defined by a poly-G homopolymer and conserved regulatory motifs. The mitogenome of the HvRI isolate does not contain\n                    <ns5:italic>cob<\/ns5:italic>\n                    mutations that lead to amino acid substitutions G143A and F129L associated with the quinone outside inhibitor (QoI) fungicide resistance. This high-quality mitogenome is an important resource for comparative mitogenomics, population diversity studies, and the molecular surveillance of QoI fungicide resistance.\n                  <\/ns5:p>","DOI":"10.12688\/f1000research.177569.2","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T12:49:05Z","timestamp":1784119745000},"page":"759","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["The complete and annotated mitochondrial genome of Hemileia vastatrix Race I, causal agent of coffee leaf rust"],"prefix":"10.12688","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2145-9756","authenticated-orcid":false,"given":"Gustavo A.","family":"Mar\u00edn-Ram\u00edrez","sequence":"first","affiliation":[{"name":"Plant Pathology \/Laboratory of Genetics and Genomics of Plant-Pathogen Interaction Vi\u00e7osa State of Minas Gerais 36570-900 BIOAGRO"},{"name":"Plant Pathology Chinchin\u00e1 Caldas 170009 National Centre of Coffee Research"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos E.","family":"Maldonado","sequence":"additional","affiliation":[{"name":"Plant Pathology \/Laboratory of Genetics and Genomics of Plant-Pathogen Interaction Vi\u00e7osa State of Minas Gerais 36570-900 BIOAGRO"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatriz E.","family":"Padilla Hurtado","sequence":"additional","affiliation":[{"name":"Manizales Caldas 170003 Catholic University of Manizales"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio H.","family":"Brommonschenkel","sequence":"additional","affiliation":[{"name":"Plant Pathology \/Laboratory of Genetics and Genomics of Plant-Pathogen Interaction Vi\u00e7osa State of Minas Gerais 36570-900 BIOAGRO"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"303-321","DOI":"10.1007\/s12571-015-0446-9","article-title":"The coffee rust crises in Colombia and Central America (2008\u20132013): impacts, plausible causes and proposed solutions.","volume":"7","author":"J Avelino","year":"2015","journal-title":"Food Secur."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e00444-e00423","DOI":"10.1128\/MRA.00444-23","article-title":"Genome sequence of Hemileia vastatrix Berk. and Br. (Race I), the causal agent of coffee leaf rust, isolate from Risaralda, Colombia.","volume":"12","author":"C \u00c1ngel","year":"2023","journal-title":"Microbiol Resour Announc."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"335-343","DOI":"10.1038\/nature12985","article-title":"Mitochondrial form and function.","volume":"505","author":"J Friedman","year":"2014","journal-title":"Nature."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"21490","DOI":"10.12688\/f1000research.21490.1","article-title":"Recent advances in understanding mitochondrial genome diversity.","volume":"9","author":"R Zardoya","year":"2020","journal-title":"F1000Res."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"200","DOI":"10.12688\/f1000research.130615.1","article-title":"Genome-wide comparisons reveal broad variations in intraspecific SNP frequencies among species in Agaricomycetes, Basidiomycota.","volume":"12","author":"K Zhao","year":"2023","journal-title":"F1000Res."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"9433-9448","DOI":"10.1007\/s00253-018-9350-5","article-title":"Fungal mitochondrial genomes and genetic polymorphisms.","volume":"102","author":"S Sandor","year":"2018","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"765","DOI":"10.3389\/fmicb.2020.00765","article-title":"Exploring the relationship among divergence time and coding and non-coding elements in the shaping of fungal mitochondrial genomes.","volume":"11","author":"P Fonseca","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"978","DOI":"10.3389\/fmicb.2020.00978","article-title":"Fungal mitogenomes: relevant features to planning plant disease management.","volume":"11","author":"R Medina","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"9013","DOI":"10.3390\/ijms25169013","article-title":"Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.","volume":"25","author":"H Li","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"649-662","DOI":"10.1002\/ps.520","article-title":"The strobilurin fungicides.","volume":"58","author":"D Bartlett","year":"2002","journal-title":"Pest Manag. Sci."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"2935-2952","DOI":"10.1002\/1873-3468.13868","article-title":"The cytochrome bc1 complex as an antipathogenic target.","volume":"594","author":"N Fisher","year":"2020","journal-title":"FEBS Lett."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"859-867","DOI":"10.1002\/ps.565","article-title":"Mechanisms influencing the evolution of resistance to Qo inhibitor fungicides.","volume":"58","author":"U Gisi","year":"2002","journal-title":"Pest Manag. Sci."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"465-472","DOI":"10.1002\/ps.1236","article-title":"Cytochrome b gene structure and consequences for resistance to Qo inhibitor fungicides in plant pathogens.","volume":"62","author":"V Grasso","year":"2006","journal-title":"Pest Manag. Sci."},{"key":"ref14","article-title":"A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy.","author":"P obias","year":"2006","journal-title":"bioRxiv."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"8-15","DOI":"10.1007\/BF02772108","article-title":"Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components.","volume":"15","author":"S Porebski","year":"1997","journal-title":"Plant Mol. Biol. Report."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"btag331","DOI":"10.1093\/bioinformatics\/btag331","article-title":"Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing.","volume":"42","author":"S Beier","year":"2026","journal-title":"Bioinformatics."},{"key":"ref17","article-title":"Unlocking the full potential of Oxford Nanopore reads with NOVOLoci.","author":"N Dierckxsens","year":"2025","journal-title":"bioRxiv."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1222186","DOI":"10.3389\/fpls.2023.1222186","article-title":"Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction.","volume":"14","author":"B Lang","year":"2023","journal-title":"Front. Plant Sci."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1754-1760","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform.","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.","volume":"9","author":"B Walker","year":"2014","journal-title":"PLoS One."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"3094-3100","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences.","volume":"34","author":"H Li","year":"2018","journal-title":"Bioinformatics."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"4572-4574","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy.","volume":"37","author":"H Li","year":"2021","journal-title":"Bioinformatics."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools.","volume":"10","author":"P Danecek","year":"2021","journal-title":"GigaScience."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/s13059-024-03252-4","article-title":"NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.","volume":"25","author":"J Hu","year":"2024","journal-title":"Genome Biol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes.","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"772-780","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1166-1167","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: a unified bioinformatics toolkit.","volume":"28","author":"K Okonechnikov","year":"2012","journal-title":"Bioinformatics."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"209-216","DOI":"10.1016\/j.ympev.2016.09.024","article-title":"Accurate annotation of protein-coding genes in mitochondrial genomes.","volume":"106","author":"M Al Arab","year":"2017","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"10543-10552","DOI":"10.1093\/nar\/gkz833","article-title":"Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.","volume":"47","author":"A Donath","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications.","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"887-897","DOI":"10.3852\/09-198","article-title":"Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae.","volume":"102","author":"C Stone","year":"2010","journal-title":"Mycologia."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"29-30","DOI":"10.1080\/23802359.2019.1674744","article-title":"The complete mitochondrial genomes of Puccinia striiformis f. sp. tritici and Puccinia recondita f. sp. tritici.","volume":"5","author":"C Li","year":"2020","journal-title":"Mitochondrial DNA B."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/15-759\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-759\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-759\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T12:49:07Z","timestamp":1784119747000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/15-759\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,15]]},"references-count":32,"URL":"https:\/\/doi.org\/10.12688\/f1000research.177569.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/f1000research.177569.1","asserted-by":"subject"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,15]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/15-759\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.195807.r489837, Theo Llewellyn, Comparative Fungal Biology, Jodrell Laboratory Royal Botanic Gardens Kew Richmond, England, 10 Jun 2026, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/15-759\/v1#referee-response-489837","order":0,"name":"referee-response-489837","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Gustavo Marin<\/b>; \n<i>Posted: 08 Jul 2026<\/i>; Dear Prof. \n<b>Theo Llewellyn<\/b>,  We would like to sincerely thank you for the careful evaluation of our manuscript and for the constructive comments and suggestions. We greatly appreciate the time and effort invested in reviewing our work. Your feedback has helped us improve the clarity, precision, and methodological transparency of the manuscript. Below, we provide a point-by-point response to the comments.  \n<b>Comment 1<\/b> \u201cthe opposite is often observed in fungi\u201d this sentence requires a citation. It also feels overly generalised as mitochondrial evolutionary rates vary across the kingdom. Whilst this may be true for some asexual Basidiomycota, I think \u2018often observed in fungi\u2019 does not accurately represent this.  \n<b>Response<\/b>: We agree that our original wording was too broad and could be interpreted as overgeneralizing mitochondrial evolutionary patterns across fungi. In response, we revised the sentence to be more precise and cautious, and we added appropriate citations supporting the observation that, in some fungal lineages, nuclear genomes may exhibit higher polymorphism than mitochondrial genomes, while acknowledging that these patterns are not universal across the kingdom.&nbsp; \n<i>We replaced the original statement with a more nuanced phrasing that avoids generalization and reflects the heterogeneity of mitochondrial evolutionary rates in fungi.<\/i>   \n<b>Comment 2<\/b> Methods: which quality-filtering thresholds and tools were applied to reads that were then mapped back to contigs with pilon? I could not find this in the text  \n<b>Response:<\/b> We have revised the Methods section to explicitly describe the preprocessing and polishing workflow. Specifically, the raw BGIseq reads were adapter-trimmed and converted to Phred+33 format using Trimmomatic v0.40. After the initial assembly with NOVOPlasty v4.3.5, the reads were further quality-trimmed prior to polishing using Trimmomatic with the following parameters: leading and trailing base quality &lt; 20, a 4-bp sliding window requiring an average quality score of at least 30, and a minimum read length of 100 bp. The filtered reads were then aligned to the draft assembly with BWA-MEM v0.7.17 and the assembly was polished with Pilon v1.24.&nbsp;\n<i>To improve clarity, we also suggest incorporating the following text into the manuscript.<\/i>  We again thank the reviewer for the constructive feedback, which has significantly improved the manuscript. We hope that the revisions adequately address the concerns raised and enhance the quality and reproducibility of our study.  Sincerely, &nbsp;  On behalf of all authors.","URL":"https:\/\/f1000research.com\/articles\/15-759\/v2#referee-comment-16610","order":1,"name":"referee-comment-16610","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Gustavo Marin<\/b>; \n<i>Posted: 09 Jul 2026<\/i>; Dear&nbsp; \n<b>Reviewers<\/b>,  Paragraph 2: 'the opposite is often observed in fungi' this sentence requires a citation. It also feels overly generalised as mitochondrial evolutionary rates vary across the kingdom. Whilst this may be true for some asexual Basidiomycota, I think 'often observed in fungi' does not accurately represent this.  Mitochondria are double-membrane organelles, present in high copy numbers per cell. They are essential for fungal metabolism and the site for oxidative phosphorylation.3 In sexual eukaryotes, mitochondrial inheritance is predominantly uniparental; however, in fungi, both uniparental and biparental inheritance modes have been reported.4 Another distinction across the tree of life is the mutation rate: while mitochondrial genomes evolve faster than nuclear genomes in animals, the opposite is often observed in fungi. Predominantly asexual species of the division Basidiomycota present SNP frequencies up to 7.69% in nuclear genomes but only up to 4.41% in their mitochondrial counterpar ts.5 This slower mutation rate makes mitochondrial DNA markers useful for resolving deep evolutionary relationships between species.6\u20138 Despite the slow mutation rate in Basidiomycota, high variability in genome size, gene order, and intron content has been found while maintaining a conserved core set of protein-coding genes, this genomic plasticity is valuable not only for phylogenetics of distant species but also for population genomics within a species.9  \n<b>Response<\/b>  We agree with the reviewer that our original statement was overly generalized, given the vast evolutionary diversity within the fungal kingdom. We have revised the text to clarify that slower mitochondrial evolution is not universal but has been documented in specific lineages, seamlessly leading into our cited example of Basidiomycota (Reference 5).  Reviewer comment:  Methods: which quality-filtering thresholds and tools were applied to reads that were then mapped back to contigs with pilon? I could not find this in the text  Original paragraph:  The mitochondrial genome was assembled using a hybrid approach integrating multiple tools. Initially, a de novo assembly was performed using NOVOPlasty v4.3.516 with BGIseq reads (SRA SRR22911637), using the cob gene sequence of Puccinia striiformis f. sp. tritici isolate CYR32 (GenBank MH891489.1) as a seed. The resulting contig was annotated with MFannot v2.017 using Genetic Code 4 (Mold, Protozoan, and Coelenterate Mitochondrial). The NADH dehydrogenase subunit 4 (nad4) gene from this preliminary assembly was then used as a seed for a second round of NOVOPlasty. Finally, the assembly was polished with Pilon v1.2418 by mapping quality-trimmed reads back to the draft assembly using BWA-MEM v0.7.17.19  Edited paragraph:  The mitochondrial genome was assembled using a hybrid approach. Initially, raw BGIseq reads (SRA SRR22911637) were adapter-trimmed using Trimmomatic v0.40 (Beier et al., 2026). A de novo assembly was then performed using NOVOPlasty v4.3.516, which utilizes internal read quality filtering, using the cob gene sequence of Puccinia striiformis f. sp. tritici isolate CYR32 (GenBank MH891489.1) as a seed. The resulting contig was annotated with MFannot v2.017 using Genetic Code 4 (Mold, Protozoan, and Coelenterate Mitochondrial). The NADH dehydrogenase subunit 4 (nad4) gene from this preliminary assembly was subsequently used as a seed for a second round of NOVOPlasty. Finally, prior to error correction, the raw reads underwent quality trimming with Trimmomatic (leading\/trailing Q &lt; 20; 4-bp sliding window average Q \u2265 30; minimum length 100 bp). These high-quality reads were mapped to the draft assembly using BWA-MEM v0.7.17, and the assembly was polished with Pilon v1.24.  Beier, S., Bolger, A.M., Bolger, M.E., Schwacke, R. and Usadel, B., 2026. Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing. Bioinformatics, 42(6), p.btag331.  Reviewer Comment:  &quot;Methods: which quality-filtering thresholds and tools were applied to reads that were then mapped back to contigs with pilon? I could not find this in the text&quot;  \n<b>Response:<\/b>  We thank the reviewer for pointing this out. This comment made us realize that the initial data preprocessing was not clearly explained. We have updated the Methods section to clarify how the paired-end data was handled in two stages. First, we removed adapters using Trimmomatic v0.40, allowing NOVOplasty to use its own internal read filtering for the assembly. Second, we clarified that a strict quality filtering step (leading\/trailing Q &lt; 20; 4-bp sliding window average Q \u2265 30; minimum length 100 bp) was applied using Trimmomatic prior to mapping the reads for Pilon polishing.","URL":"https:\/\/f1000research.com\/articles\/15-759\/v2#referee-comment-16624","order":2,"name":"referee-comment-16624","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.195807.r494852, Martin Coetzee, University of Pretoria, Pretoria, 07 Jul 2026, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/15-759\/v1#referee-response-494852","order":3,"name":"referee-response-494852","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Gustavo Marin<\/b>; \n<i>Posted: 08 Jul 2026<\/i>; Dear Prof.&nbsp;\n<b>Martin Coetzee<\/b>,  We sincerely thank the reviewer for the positive evaluation of our manuscript and for recognizing the value of the mitochondrial genome presented here for future research on \n<i>Hemileia vastatrix<\/i>. We are also grateful for the reviewer\u2019s agreement that there are no major concerns regarding the methods or results.  As suggested, we have carefully addressed all remaining comments raised by \n<b>Reviewer <\/b>(Theo Llewellyn) in the revised manuscript, including clarification of the wording regarding fungal mitochondrial evolutionary rates and the addition of the quality-filtering and polishing details in the Methods section. These revisions have improved the precision, reproducibility, and overall clarity of the manuscript  Sincerely, &nbsp;  On behalf of all authors","URL":"https:\/\/f1000research.com\/articles\/15-759\/v2#referee-comment-16612","order":4,"name":"referee-comment-16612","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Colombian Coffee Growers Federation (FNC) \/ National Coffee Research Center (CENICAFE) under the project ID: PAT102006. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}