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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.23471.r91231, Arjen Van 't Hof, Biology Centre of the Czech Academy of Sciences, Institute of Entomology, \u010cesk\u00e9 Bud\u011bjovice, 25 Aug 2024, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#referee-response-91231","order":0,"name":"referee-response-91231","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tree of Life Team Sanger<\/b>; \n<i>Posted: 28 Sep 2025<\/i>; Thank you for your careful review of this data note. We have submitted a new version of the article and our responses to your comments are given below.  The assembly is based on a single male according to the manuscript, but the SAMEA112226468 BioSample details show: sex NOT COLLECTED (https:\/\/www.ebi.ac.uk\/ena\/browser\/view\/SAMEA112226468). Confusingly, the sequenced male has two different BioSample codes, SAMEA112226468 and SAMEA112232922 with only the first listed in Table 1.  \n<i>Response: This is a standard aspect of the structure of data at the European Nucleotide Archive BioSamples Database. One of the BioSample accessions (SAMEA112226468) identifies the individual or specimen, while the other (SAMEA112232922) identifies the part of the specimen that was used. This is useful if the specimen is dissected into multiple parts, as it can identify different parts used for different sequencing technologies. In this case, the whole organism was used. <\/i> &nbsp;  The identification of the Z chromosome is not explained well and based on a string of assumptions. What is missing here is an explanation that there is a large body of evidence that chromosomal gene content is conserved in Lepidoptera and can therefore be used to identify homologous chromosomes based on shared synteny. Some references supporting this would also be welcome. I do not object to the \u2018assumption-based\u2019 shared synteny Z-chromosome assignment as long as an \u2018evidence-based\u2019 Z chromosome is used for comparison. One might expect that the assembly used for shared synteny-based Z chromosome assignment was based on a female with a Z chromosome identified by having half the sequence read coverage of autosomes.  &nbsp; \n<i>Response: We identify Z-linked scaffolds by locating BUSCO genes known to be Z-linked across specimens, including heterogametic (ZW) individuals where the Z is unambiguous. In version 2 of the data note we have also applied Merian painting, which shows conserved Z synteny: ancestral Z-linked orthologues co-locate on this chromosome. We have provided a brief explanation and a reference for this paper in the text.<\/i> &nbsp;  It is impossible to understand the following sentence without background knowledge. \u201cChromosome Z was assigned based on synteny with Perizoma affinitatum (GCA_961405105.1) and Camptogramma bilineatum (GCA_958496255.1).\u201d  \n<i>Response: We have rephrased this slightly in Version 2.<\/i> \n<i>&nbsp;<\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v2#referee-comment-6274","order":1,"name":"referee-comment-6274","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.23471.r91233, Ananna Ghosh, Scientific officer, Insect Biotechnology Division, Atomic Energy Research Establishment, Dhaka, Dhaka Division, 29 Aug 2024, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#referee-response-91233","order":2,"name":"referee-response-91233","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.27603.r135459, Pritha Dey, National Centre for Biological Sciences-TIFR, Bengaluru, 28 Oct 2025, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v2#referee-response-135459","order":3,"name":"referee-response-135459","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https:\/\/doi.org\/10.35802\/206194>https:\/\/doi.org\/10.35802\/206194<\/a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https:\/\/doi.org\/10.35802\/218328>https:\/\/doi.org\/10.35802\/218328 <\/a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"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"}]},{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:13:04Z","timestamp":1772169184856,"version":"3.50.1"},"reference-count":33,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T00:00:00Z","timestamp":1715731200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218328"],"award-info":[{"award-number":["218328"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"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"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    We present a genome assembly from an individual male\n                    <ns3:italic>Pasiphila rectangulata<\/ns3:italic>\n                    (the Green Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 582.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. 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with reservations, Approved","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.23471.r91231, Arjen Van 't Hof, Biology Centre of the Czech Academy of Sciences, Institute of Entomology, \u010cesk\u00e9 Bud\u011bjovice, 25 Aug 2024, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#referee-response-91231","order":0,"name":"referee-response-91231","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tree of Life Team Sanger<\/b>; \n<i>Posted: 28 Sep 2025<\/i>; Thank you for your careful review of this data note. We have submitted a new version of the article and our responses to your comments are given below.  The assembly is based on a single male according to the manuscript, but the SAMEA112226468 BioSample details show: sex NOT COLLECTED (https:\/\/www.ebi.ac.uk\/ena\/browser\/view\/SAMEA112226468). Confusingly, the sequenced male has two different BioSample codes, SAMEA112226468 and SAMEA112232922 with only the first listed in Table 1.  \n<i>Response: This is a standard aspect of the structure of data at the European Nucleotide Archive BioSamples Database. One of the BioSample accessions (SAMEA112226468) identifies the individual or specimen, while the other (SAMEA112232922) identifies the part of the specimen that was used. This is useful if the specimen is dissected into multiple parts, as it can identify different parts used for different sequencing technologies. In this case, the whole organism was used. <\/i> &nbsp;  The identification of the Z chromosome is not explained well and based on a string of assumptions. What is missing here is an explanation that there is a large body of evidence that chromosomal gene content is conserved in Lepidoptera and can therefore be used to identify homologous chromosomes based on shared synteny. Some references supporting this would also be welcome. I do not object to the \u2018assumption-based\u2019 shared synteny Z-chromosome assignment as long as an \u2018evidence-based\u2019 Z chromosome is used for comparison. One might expect that the assembly used for shared synteny-based Z chromosome assignment was based on a female with a Z chromosome identified by having half the sequence read coverage of autosomes.  &nbsp; \n<i>Response: We identify Z-linked scaffolds by locating BUSCO genes known to be Z-linked across specimens, including heterogametic (ZW) individuals where the Z is unambiguous. In version 2 of the data note we have also applied Merian painting, which shows conserved Z synteny: ancestral Z-linked orthologues co-locate on this chromosome. We have provided a brief explanation and a reference for this paper in the text.<\/i> &nbsp;  It is impossible to understand the following sentence without background knowledge. \u201cChromosome Z was assigned based on synteny with Perizoma affinitatum (GCA_961405105.1) and Camptogramma bilineatum (GCA_958496255.1).\u201d  \n<i>Response: We have rephrased this slightly in Version 2.<\/i> \n<i>&nbsp;<\/i>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#referee-comment-6274","order":1,"name":"referee-comment-6274","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.23471.r91233, Ananna Ghosh, Scientific officer, Insect Biotechnology Division, Atomic Energy Research Establishment, Dhaka, Dhaka Division, 29 Aug 2024, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/9-256\/v1#referee-response-91233","order":2,"name":"referee-response-91233","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https:\/\/doi.org\/10.35802\/206194>https:\/\/doi.org\/10.35802\/206194<\/a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https:\/\/doi.org\/10.35802\/218328>https:\/\/doi.org\/10.35802\/218328 <\/a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"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"}]}],"items-per-page":5,"query":{"start-index":0,"search-terms":null}}}