{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T08:47:13Z","timestamp":1783414033000,"version":"3.54.6"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.17258.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,12,3]],"date-time":"2021-12-03T00:00:00Z","timestamp":1638489600000}}],"reference-count":37,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2021,12,3]],"date-time":"2021-12-03T00:00:00Z","timestamp":1638489600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001215","name":"La Trobe University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001215","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1087697"],"award-info":[{"award-number":["OPP1087697"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010905","name":"Illumina","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010905","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","award":["MR\/T020733\/1"],"award-info":[{"award-number":["MR\/T020733\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p>\n                    We present a genome assembly and annotation of an individual female\n                    <ns4:italic>Cercopithifilaria johnstoni<\/ns4:italic>\n                    , a parasitic filarial nematode that is transmitted by hard ticks (Ixodidae) to infect a broad range of native Australian murid and marsupial hosts. The genome sequence is 76.9 Mbp in length, and although in draft form (N50 = 99 kbp, N50[n] = 232), is largely complete based on universally conserved orthologs (BUSCOs; genome = 94.9%, protein = 96.5%) and relative to other related filarial species. These data represent the first genomic resources for the genus\n                    <ns4:italic>Cercopithifilaria<\/ns4:italic>\n                    , a group of parasites with a broad host range, and form the basis for comparative analysis with the human-infective parasite,\n                    <ns4:italic>Onchocerca volvulus<\/ns4:italic>\n                    , both of which are responsible for similar eye and skin pathologies in their respective hosts.\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.17258.2","type":"journal-article","created":{"date-parts":[[2021,12,3]],"date-time":"2021-12-03T10:40:13Z","timestamp":1638528013000},"page":"259","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["The genome sequence of the Australian filarial nematode, Cercopithifilaria johnstoni"],"prefix":"10.12688","volume":"6","author":[{"given":"Kirsty","family":"McCann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Warwick","family":"Grant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen R.","family":"Doyle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2021,12,3]]},"reference":[{"key":"ref-33","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/s13071-017-2126-4","article-title":"Significant heterogeneity in Wolbachia copy number within and between populations of Onchocerca volvulus.","volume":"10","author":"S Armoo","year":"2017","journal-title":"Parasit Vectors."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"313-9","DOI":"10.1016\/j.ympev.2012.08.023","article-title":"MITOS: improved de novo metazoan mitochondrial genome annotation.","volume":"69","author":"M Bernt","year":"2013","journal-title":"Mol Phylogenet Evol."},{"key":"ref-1","doi-asserted-by":"publisher","first-page":"2114-2120","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data.","volume":"30","author":"A Bolger","year":"2014","journal-title":"Bioinformatics."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.","volume":"3","author":"T Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform."},{"key":"ref-34","doi-asserted-by":"publisher","first-page":"16207","DOI":"10.1038\/nmicrobiol.2016.207","article-title":"Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont.","volume":"2","author":"Y Choi","year":"2016","journal-title":"Nat Microbiol."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"16216","DOI":"10.1038\/nmicrobiol.2016.216","article-title":"The genome of Onchocerca volvulus, agent of river blindness.","volume":"2","author":"J Cotton","year":"2016","journal-title":"Nat Microbiol."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.","volume":"5","author":"A Darling","year":"2010","journal-title":"PLoS One."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"495-500","DOI":"10.1038\/ng.2585","article-title":"Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.","volume":"45","author":"C Desjardins","year":"2013","journal-title":"Nat Genet."},{"key":"ref-6","article-title":"stephenrdoyle\/cercopithifilaria_johnstoni: (v1.1).","author":"S Doyle","year":"2021","journal-title":"Zenodo."},{"key":"ref-35","doi-asserted-by":"publisher","first-page":"e20843","DOI":"10.1371\/journal.pone.0020843","article-title":"New Insights into the Evolution of Wolbachia Infections in Filarial Nematodes Inferred from a Large Range of Screened Species.","volume":"6","author":"E Ferri","year":"2011","journal-title":"PLoS One."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"1964","DOI":"10.1038\/s41467-020-15654-6","article-title":"Sex chromosome evolution in parasitic nematodes of humans.","volume":"11","author":"J Foster","year":"2020","journal-title":"Nat Commun."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1186\/s13059-016-0951-y","article-title":"OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.","volume":"17","author":"S Gao","year":"2016","journal-title":"Genome Biol."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"1-5","DOI":"10.1093\/gigascience\/giy018","article-title":"Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.","volume":"7","author":"S Geib","year":"2018","journal-title":"GigaScience."},{"key":"ref-36","doi-asserted-by":"publisher","first-page":"5117","DOI":"10.1038\/ncomms6117","article-title":"Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic.","volume":"5","author":"M Gerth","year":"2014","journal-title":"Nat. Commun."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"2-10","DOI":"10.1016\/j.molbiopara.2016.11.005","article-title":"WormBase ParaSite \u2212 a comprehensive resource for helminth genomics.","volume":"215","author":"K Howe","year":"2017","journal-title":"Mol Biochem Parasitol."},{"key":"ref-30","doi-asserted-by":"publisher","first-page":"772-80","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":"ref-11","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":"ref-12","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.12688\/f1000research.12232.1","article-title":"BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations].","volume":"6","author":"D Laetsch","year":"2017","journal-title":"F1000Res."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"mgen000487","DOI":"10.1099\/mgen.0.000487","article-title":"Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.","volume":"6","author":"E Lefoulon","year":"2020","journal-title":"Microb Genom."},{"key":"ref-14","doi-asserted-by":"crossref","DOI":"10.5962\/p.272105","article-title":"Two new species of Dipetalonema (Nematoda: Filarioidea) from Australian marsupials.","author":"M Mackerras","year":"1954"},{"key":"ref-15","article-title":"MESQUITE: a modular system for evolutionary analysis.","author":"W Maddison","year":"2019"},{"key":"ref-37","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1186\/1471-2164-13-145","article-title":"Comparing the mitochondrial genomes of Wolbachia-dependent and independent filarial nematode species.","volume":"13","author":"S McNulty","year":"2012","journal-title":"BMC Genomics."},{"key":"ref-31","doi-asserted-by":"publisher","first-page":"1530-1534","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.","volume":"37","author":"B Minh","year":"2020","journal-title":"Mol Biol Evol."},{"key":"ref-16","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1186\/s13104-018-3686-x","article-title":"EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive.","volume":"11","author":"M Norling","year":"2018","journal-title":"BMC Res Notes."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler.","volume":"70","author":"A Prjibelski","year":"2020","journal-title":"Curr Protoc Bioinformatics."},{"key":"ref-18","doi-asserted-by":"publisher","first-page":"e113-e113","DOI":"10.1093\/nar\/gkw294","article-title":"Redundans: an assembly pipeline for highly heterozygous genomes.","volume":"44","author":"L Pryszcz","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref-19","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.","volume":"11","author":"T Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun."},{"key":"ref-20","doi-asserted-by":"publisher","first-page":"1892-1895","DOI":"10.1126\/science.1068732","article-title":"The role of endosymbiotic Wolbachia bacteria in the pathogenesis of river blindness.","volume":"295","author":"A Saint Andr\u00e9","year":"2002","journal-title":"Science."},{"key":"ref-21","doi-asserted-by":"publisher","first-page":"227-245","DOI":"10.1007\/978-1-4939-9173-0_14","article-title":"BUSCO: Assessing Genome Assembly and Annotation Completeness.","volume":"1962","author":"M Seppey","year":"2019","journal-title":"Methods Mol Biol."},{"key":"ref-22","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/1471-2105-6-31","article-title":"Automated generation of heuristics for biological sequence comparison.","volume":"6","author":"G Slater","year":"2005","journal-title":"BMC Bioinformatics."},{"key":"ref-23","doi-asserted-by":"publisher","first-page":"1087-1092","DOI":"10.1016\/0020-7519(88)90079-3","article-title":"Aspects of the life history of Cercopithifilaria johnstoni (Nematoda:Filarioidea).","volume":"18","author":"D Spratt","year":"1988","journal-title":"Int J Parasitol."},{"key":"ref-24","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1186\/1471-2164-15-788","article-title":"Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.","volume":"15","author":"L Tallon","year":"2014","journal-title":"BMC Genomics."},{"key":"ref-25","doi-asserted-by":"publisher","first-page":"245-284","DOI":"10.1016\/S0065-308X(05)60004-8","article-title":"Wolbachia bacterial endosymbionts of filarial nematodes.","volume":"60","author":"M Taylor","year":"2005","journal-title":"Adv Parasitol."},{"key":"ref-26","doi-asserted-by":"publisher","first-page":"176-181","DOI":"10.1051\/parasite\/1993684176","article-title":"Onchocerca-like lesions induced by the filarioid nematode Cercopithifilaria johnstoni, in its natural hosts and in the laboratory rat.","volume":"68","author":"P Vuong","year":"1993","journal-title":"Ann Parasitol Hum Comp."},{"key":"ref-38","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments.","volume":"15","author":"D Wood","year":"2014","journal-title":"Genome Biol."},{"key":"ref-39","doi-asserted-by":"publisher","first-page":"28-36","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data.","volume":"8","author":"G Yu","year":"2017","journal-title":"Methods Ecol Evol."},{"key":"ref-28","doi-asserted-by":"publisher","first-page":"821-829","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: Algorithms for de novo short read assembly using de Bruijn graphs.","volume":"18","author":"D Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,13]],"date-time":"2023-11-13T10:38:27Z","timestamp":1699871907000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,3]]},"references-count":37,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.17258.2","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.19331.r47424","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19331.r47422","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,3]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.19074.r46394, James Wasmuth, Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada, 26 Oct 2021, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v1#referee-response-46394","order":0,"name":"referee-response-46394","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Stephen Doyle<\/b>; <i>Posted: 01 Dec 2021<\/i>; <b>Reviewer 1 \u2013 James Wasmuth<\/b> &nbsp; The authors have done an excellent job in describing the sequencing, assembly and annotation of the genome of a parasitic nematode, whose broad host range recommends it for understanding how host-parasite interactions evolve. While the sequencing is only short-read (300 bp), the depth of sequencing and careful assembly gives us confidence in the gene models. The level of detail in the methods should be considered the new standard of reporting. I enjoyed the data in table 2, which demonstrates the value of careful assembly. &nbsp; I have three requests in any future version: &nbsp; 1. It would be helpful to know the phylogenetic placement of C. johnstoni in the filarial nematodes from this paper. Perhaps Table 1 could include the phylogenetic relationships. &nbsp; <i><b>Response: We agree that this is would be useful to show. &nbsp; We have now included a phylogeny of filarial species based on whole mitochondrial genome alignment as Figure 3. &nbsp;<\/b><\/i> 2a. In the search for Wolbachia in C. johnstoni the authors found that 0.02% of reads mapped to Rickettsiales. What is the % of reads from the O. volvulus sequencing project that maps to Rickettsiales? This comparison is necessary as this report will be cited as evidence of Wolbachia loss. &nbsp; <i><b>Response: This is a really good question and one that we had not originally asked. &nbsp; To address this comment, we determined the proportion of reads classified as Wolbachia from 32 O. volvulus whole-genome sequencing datasets described in Choi et al. 2016 (https:\/\/doi.org\/10.1038\/nmicrobiol.2016.207). We also improved the sensitivity of analysis using a new custom kraken database with all known filarial Wolbachia genomes added to it, including the Wolbachia genome from O. volvulus. This was important, as an initial analysis of a single O. volvulus read set performed poorly with the original kraken database used.&nbsp; &nbsp; The new analysis revealed only a single C. johnstoni sequencing read classified as Wolbachia (rather than Rickettsiales as we reported originally), whereas, on average, 1.98% of O. volvulus reads classified as Wolbachia (range: 0.08-13.26%, average library size = 34 million reads). Considering the O. volvulus Wolbachia genome is ~1 Mb and the nuclear genome ~100 Mb, it suggests there are ~ 2 Wolbachia genomes for every nuclear genome, which is within the range we have observed previously estimated from mapped reads to the nuclear and Wolbachia genomes (see https:\/\/doi.org\/10.1186\/s13071-017-2126-4).&nbsp; &nbsp; These new results are now included in the manuscript.<\/b><\/i> 2b. For the other Wolbachia searches, it is unclear to me if the authors used the assembled contigs before or after blobtools decontamination. If after, it is not surprising that there is so little evidence of matches. &nbsp; <i><b>Response: Well observed. We originally analysed matches between Wolbachia and the assembled genomes pre- and post-decontamination, but in the end, only reported the analysis of the final genome assembly. &nbsp; To address this comment, we now report the analysis performed on the Spades assembly prior to blobtools processing; encouragingly, we find only 1.4% of Wolbachia matches in the Spades-only assembly, which is consistent with the 1.38% we originally reported using the decontaminated genome. &nbsp; Collectively, these results strengthen our argument that C. johnstoni does not harbour Wolbachia.<\/b><\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2#referee-comment-4824","order":1,"name":"referee-comment-4824","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19074.r46393, Jane Hodgkinson, Veterinary Parasitology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK, 27 Oct 2021, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v1#referee-response-46393","order":2,"name":"referee-response-46393","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Stephen Doyle<\/b>; <i>Posted: 01 Dec 2021<\/i>; <i><b>Response: We are grateful for the positive appraisal of our work.<\/b><\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2#referee-comment-4825","order":3,"name":"referee-comment-4825","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19074.r46395, Neil Young, Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Vic, Australia, 02 Nov 2021, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v1#referee-response-46395","order":4,"name":"referee-response-46395","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Stephen Doyle<\/b>; <i>Posted: 01 Dec 2021<\/i>; <b>Reviewer 3 \u2013 Neil Young<\/b> &nbsp; The article by McKann <i> et al.<\/i> reports an annotated draft genome of Cercopithifilaria johnstoni, a filarial nematode parasitising Australian mammals. Despite the fragmented nature of the assembly, the genome is of significant value to the research community because of its taxonomic position, its adaptive evolution to parasitise marsupials and its potential use as a laboratory model system for onchocerchiasis. Combined fundamental and applied applications make it a valuable nematode genomic resource. &nbsp; I was surprised to see genome completeness scores over 94% with an assembly using only short-read sequence data. Could this relate to short introns with less repetitive elements? &nbsp; <b><i>Response: We were also pleasantly surprised by the relatively high genome completeness statistics for an Illumina-only assembly. We attribute it in part to the low diversity of sequencing a freshly-collected individual parasite at high coverage with relatively long Illumina reads (3x300 bp). The genome at 76 Mb is on the smaller side compared to other nematodes, and while its overall repetitive content was not noticeably different from other filarial nematodes, it must compact its genome content into a smaller space suggesting it is \u201cless complex\u201d to some degree. &nbsp; Regarding the intron lengths - we do find that C. johnstoni introns are shorter than O. volvulus introns (See table below on intron length stats). To what extent this is due to assembly contiguity (i.e., a technical effect - the O. volvulus genome is assembled into chromosomal-scale scaffolds and so provides a more robust framework for longer gene models), or true biological differences, is difficult to determine without having a more contiguous C. johnstoni assembly.&nbsp;<\/i><\/b> &nbsp; | Species | count | mean_length | stdev&nbsp; &nbsp;| median_length | q1&nbsp; &nbsp; | q3&nbsp; | |------------|----------|------------------|-----------|----------------------|-------|------| |&nbsp; OV&nbsp; &nbsp; &nbsp; &nbsp;| 93854 | 435.9&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | 2311.6 | 257&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | 155 | 409 | |&nbsp; CJ&nbsp; &nbsp; &nbsp; &nbsp; | 97658 | 299.0&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | 298.73 | 229&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;| 143 | 350 | &nbsp; As this parasite is a useful model for onchocerciasis, it would be good to show the completeness of gene models specific to parasite-host interactions in Onchocerca and related species. &nbsp; <i><b>Response: We provide an estimate of the overall geneset completeness, as indicated by the BUSCO scores for the genome and proteome in Table 1. Arguably, these data show that the genome and proteome are highly representative based on conserved orthologs \u201cexpected\u201d to be present, and relative to closely related species. We agree that to further establish C. johnstoni as a model for onchocerciasis, a better understanding of the genes involved in host-parasite interactions is needed; these data are in fact the focus of a separate follow up publication. As a Wellcome Open Research Data Note aims to focus specifically on the data themselves and \u201cnot\u2026 analyses or conclusions\u201d, we initially (and now again, subsequently after peer review) decided against presenting these downstream analyses of the genome resources.<\/b><\/i> &nbsp; The mt genome was also assembled and annotated but there was no description of the mt genome herein. A mt phylogenomic tree might provide the reader with more context of the taxonomic position of this parasite. &nbsp; <i><b>Response: The reviewer is correct \u2013 we did not specifically describe the mitochondrial genome. However, we agree that a phylogeny using the mitochondrial genome would illustrate where C. johnstoni is placed relative to other filarial species. &nbsp; To address this comment, we now include this phylogeny in Figure 3.<\/b><\/i> Did the lack of RNAseq data affect gene model predictions? If not, then the findings herein would be strong support for relying only on amino acid sequence homology for training ab initio gene predictors. It would simplify efforts to complete the genome annotations for some taxa. &nbsp; <i><b>Response: This is a difficult question to respond to specifically, given we didn\u2019t generate RNA-seq data for C. johnstoni. However, the BUSCO predictions were respectable given we did use amino acid homology from a broad range of metazoan species. &nbsp; To explore this idea as a purely academic exercise, we reannotated the genomes of a closely related but less-well annotated species (Acanthocheilonema viteae) and a species with a high-quality genome \/ good annotation (Onchocerca volvulus). The predicted proteins inferred from these new annotations were assessed using BUSCO. We note that both A. viteae and O. volvulus are not (yet) included in the OrthoDB database from which the metazoan proteins used to generate the hints were derived; thus, the de novo annotations described below are not biased by pre-existing species-specific protein models. &nbsp; A. viteae -&nbsp; Genes: &nbsp; &nbsp;o &nbsp; original: 10,397 &nbsp; &nbsp;o &nbsp; de novo: 12,056 -&nbsp; BUSCOS: &nbsp; &nbsp;o &nbsp; original: C: 88.3 [S:86.5, D:1.8], F:8.8, M:2.9 &nbsp; &nbsp;o &nbsp; de novo: C: 92.4 [S:82.6, D:9.8], F:5.6, M:2.0 -&nbsp; Conclusion: New models are more complete, less fragmented, fewer missing, however, there is a higher duplication rate, which may relate to new alternative transcripts present. &nbsp; O. volvulus -&nbsp; Genes &nbsp; &nbsp; o &nbsp; original: 12,109 &nbsp; &nbsp; o &nbsp; de novo: 12473 -&nbsp; BUSCOs: &nbsp; &nbsp; o &nbsp; original: C:99.2 [S:98.3, D:0.9], F:0.8, M:0.0 &nbsp; &nbsp; o &nbsp; de novo: C:98.8 [S:88.9, D:9.9], F:1.0, M:0.2 -&nbsp; Conclusion: Minor differences overall - slightly fewer complete models, slightly more fragmented, and slightly more missing. Higher duplication rates. However, O. volvulus is outstanding already, and the de novo annotation is still very good overall. &nbsp; These results suggest, based on a relatively simple metric of the proportion of conserved orthologous genes, that using a large collection of diverse metazoan proteins as hints for Braker2 can improve existing annotations and does a respectable job when compared with a well-curated genome annotation. Therefore, it is likely that this represents a valid approach for annotation of genomes from species where collecting additional species-species evidence, ie, RNA-seq, is difficult. This needs further testing, which is outside the scope of this work. &nbsp; This validation exercise of the approach used to annotate the C. johnstoni genome as we describe provides further support for the high BUSCO scores we report and completeness of the C. johnstoni genome and annotation.<\/b><\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-259\/v2#referee-comment-4826","order":5,"name":"referee-comment-4826","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This research was supported by a Bill and Melinda Gates Grand Challenges Exploration Grant (WG) [OPP1087697], internal research funding from La Trobe University (WG), and an Illumina MiSeq Grant (SRD). SRD is supported by a UKRI Future Leaders Fellowship [MR\/T020733\/1] and the Wellcome Trust through core funding to the Wellcome Sanger Institute [206194]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":6,"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"}]}}