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  1. Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

    This article has 21 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Jerome H.L. Hui
    3. Ting Fung Chan
    4. Leo L. Chan
    5. Siu Gin Cheung
    6. Chi Chiu Cheang
    7. James K.H. Fang
    8. Juan D. Gaitan-Espitia
    9. Stanley C.K. Lau
    10. Yik Hei Sung
    11. Chris K.C. Wong
    12. Kevin Y.L. Yip
    13. Yingying Wei
    14. Wai Lok So
    15. Wenyan Nong
    16. Hydrogen S.F. Pun
    17. Wing Kwong Yau
    18. Colleen Y.L. Chiu
    19. Sammi S.S. Chan
    20. Kacy K.L. Man
    21. Ho Yin Yip
    This article has been curated by 1 group:
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      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presents the genome of the golden birdwing butterfly Troides aeacus (Lepidoptera, Papilionidae). A notable and popular species in Asia that faces habitat loss due to urbanization and human activities. The lack of genomic resources impedes conservation efforts based on genetic markers, as well as better understanding of its biology. Using PacBio HiFi long reads and Omni-C a 351Mb genome was assembled genome anchored to 30 pseudo-molecules. After reviewers requested more information on the genome quality it seems there was high sequence continuity with contig length N50 = 11.67 Mb and L50 = 14, and scaffold length N50 = 12.2 Mb and L50 = 13. Allowing a total of 24,946 protein-coding genes were predicted. This study presents the first chromosomal-level genome assembly of the golden birdwing T. aeacus, a potentially useful resource for further phylogenomic studies of birdwing butterfly species in terms of species diversification and conservation. This evaluation refers to version 1 of the preprint

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  2. Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

    This article has 25 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Project Coordinator and Co-Principal Investigators
    3. Jerome H.L. Hui
    4. Ting Fung Chan
    5. Leo L. Chan
    6. Siu Gin Cheung
    7. Chi Chiu Cheang
    8. James K.H. Fang
    9. Juan D. Gaitan-Espitia
    10. Stanley C.K. Lau
    11. Yik Hei Sung
    12. Chris K.C. Wong
    13. Kevin Y.L. Yip
    14. Yingying Wei
    15. DNA extraction, library preparation and sequencing
    16. Franco M.F. Au
    17. Wai Lok So
    18. Genome assembly and gene model prediction
    19. Wenyan Nong
    20. Gene family annotation
    21. Ming Fung Franco Au
    22. Samples collectors
    23. Tin Yan Hui
    24. Brian K.H. Leung
    25. Gray A. Williams
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      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality genome should hopefully be a valuable resource for gaining new insights into the environmental adaptations of L. japonica in residing the intertidal zones and for future investigations in the evolutionary biology in Polyplacophorans and other molluscs.

      This evaluation refers to version 1 of the preprint

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  3. Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

    This article has 22 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Project Coordinator and Co-Principal Investigators
    3. Jerome H.L. Hui
    4. Ting Fung Chan
    5. Leo L. Chan
    6. Siu Gin Cheung
    7. Chi Chiu Cheang
    8. James K.H. Fang
    9. Juan D. Gaitan-Espitia
    10. Stanley C.K. Lau
    11. Yik Hei Sung
    12. Chris K.C. Wong
    13. Kevin Y.L. Yip
    14. Yingying Wei
    15. DNA extraction, library preparation and sequencing
    16. Wai Lok So
    17. Genome assembly and gene model prediction
    18. Wenyan Nong
    19. Sample collector, animal culture and logistics
    20. Apple P.Y. Chui
    21. Thomas H.W. Fong
    22. Ho Yin Yip
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      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the long-spined sea urchin Diadema setosum (Leske, 1778). Using PacBio HiFi long-reads and Omni-C data the assembled genome size was 886 Mb, consistent to the size of other sea urchin genomes. The assembly anchored to 22 pseudo-molecules/chromosomes, and a total of 27,478 genes including 23,030 protein-coding genes were annotated. Peer review added more to the conclusion and future perspectives. The data hopefully providing a valuable resource and foundation for a better understanding of the ecology and evolution of sea urchins.

      This evaluation refers to version 1 of the preprint

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  4. Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

    This article has 25 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Project Coordinator and Co-Principal Investigators
    3. Jerome H.L. Hui
    4. Ting Fung Chan
    5. Leo L. Chan
    6. Siu Gin Cheung
    7. Chi Chiu Cheang
    8. James K.H. Fang
    9. Juan Diego Gaitan-Espitia
    10. Stanley C.K. Lau
    11. Yik Hei Sung
    12. Chris K.C. Wong
    13. Kevin Y.L. Yip
    14. Yingying Wei
    15. DNA extraction, library preparation and sequencing
    16. Tze Kiu Chong
    17. Sean T.S. Law
    18. Genome assembly and gene model prediction
    19. Wenyan Nong
    20. Genome analysis and quality control
    21. Wenyan Nong
    22. Sample collector and logistics
    23. Tze Kiu Chong
    24. Sean T.S. Law
    25. Ho Yin Yip
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      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family Dacrymycetaceae and investigations on the biosynthesis of glycolipids with potential applications in the food industry.

      This evaluation refers to version 1 of the preprint

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  5. Genome assembly of the milky mangrove Excoecaria agallocha

    This article has 26 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Project Coordinator and Co-Principal Investigators
    3. Jerome H.L. Hui
    4. Ting Fung Chan
    5. Leo L. Chan
    6. Siu Gin Cheung
    7. Chi Chiu Cheang
    8. James K.H. Fang
    9. Juan Diego Gaitan-Espitia
    10. Stanley C.K. Lau
    11. Yik Hei Sung
    12. Chris K.C. Wong
    13. Kevin Y.L. Yip
    14. Yingying Wei
    15. DNA extraction, library preparation and sequencing
    16. Sean T.S. Law
    17. Wai Lok So
    18. Genome assembly and gene model prediction
    19. Wenyan Nong
    20. Genome analysis and quality control
    21. Wenyan Nong
    22. Sample collector and logistics
    23. David T.W. Lau
    24. Sean T.S. Law
    25. Shing Yip Lee
    26. Ho Yin Yip
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      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the milky mangrove Excoecaria agallocha, also known as blind-your-eye mangrove due to its toxic properties of its milky latex that can cause blindness when it comes into contact with the eyes. Living in the brackish water of tropical mangrove forests from India to Australia, they are an extremely important habitat for a diverse variety of aquatic species, including the mangrove jewel bug of which this tree is the sole food source for the larvae. Using PacBio HiFi long-reads and Omni-C technology a 1,332.45 Mb genome was assembled, with 1,402 scaffolds and a scaffold N50 of 58.95 Mb. After feedback the annotations were improved, predicting a very high number (73,740) protein coding genes. The data presented here provides a valuable resource for further investigation in the biosynthesis of phytochemical compounds in its milky latex with the potential of many medicinal and pharmacological properties. As well as increasing the understanding of biology and evolution in genome architecture in the Euphorbiaceae family and mangrove species adapted to high levels of salinity.

      This evaluation refers to version 1 of the preprint

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  6. Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific

    This article has 5 authors:
    1. Remy Gatins
    2. Carlos F. Arias
    3. Carlos Sánchez
    4. Giacomo Bernardi
    5. Luis F. De LeĂłn
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      Editors Assessment:

      The King Angelfish (Holacanthus passer) is a great example of a Holacanthus angelfish that are some of the most iconic marine fishes of the Tropical Eastern Pacific. However, very limited genomic resources currently exist for the genus and these authors have assembled and annotated the nuclear genome of the species, and used it examine the demographic history of the fish. Using nanopore long reads to assemble a compact 583 Mb reference with a contig N50 of 5.7 Mb, and 97.5% BUSCOs score. Scruitinising the data, the BUSCO score was high compared to the initial N50’s, providing some useful lessons learned on how to get the most out of ONT data. The analysis suggests that the demographic history in H. passer was likely shaped by historical events associated with the closure of the Isthmus of Panama, rather than by the more recent last glacial maximum. This data provides a genomic resource to improve our understanding of the evolution of Holacanthus angelfishes, and facilitating research into local adaptation, speciation, and introgression of marine fishes. In addition, this genome can help improve the understanding of the evolutionary history and population dynamics of marine species in the Tropical Eastern Pacific.

      This evaluation refers to version 1 of the preprint

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  7. De novo transcriptome assembly and genome annotation of the fat-tailed dunnart ( Sminthopsis crassicaudata )

    This article has 6 authors:
    1. Neke Ibeh
    2. Charles Y. Feigin
    3. Stephen R. Frankenberg
    4. Davis J. McCarthy
    5. Andrew J. Pask
    6. Irene Gallego Romero
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      Editors Assessment: Marsupial species are invaluable for comparative studies due to their distinctive modes of reproduction and development, but there are a shortage of genomic resources to do these types of analyses. To help address that data gap multi-tissue transcriptomes and transcriptome assemblies have been sequenced and shared for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that due to is ease of breeding is emerging as a useful lab model. Using ONT nanopore and Pacbio long-reads and illumina short reads 2,093,982 transcripts were sequenced and assembled, and functional annotation of the assembled transcripts was also carried out. Some addition work was required to provide more details on the QC metrics and access to the data but this was resolved during review. This work ultimately producing dunnart genome assembly measuring 3.23 Gb in length and organized into 1,848 scaffolds, with a scaffold N50 value of 72.64 Mb. These openly available resources hopefully provide novel insights into the unique genomic architecture of this unusual species and provide valuable tools for future comparative mammalian studies.

      This evaluation refers to version 1 of the preprint

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  8. Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19 ): An open access disease specific drug discovery portal

    This article has 19 authors:
    1. Lipsa Priyadarsinee
    2. Esther Jamir
    3. Selvaraman Nagamani
    4. Hridoy Jyoti Mahanta
    5. Nandan Kumar
    6. Lijo John
    7. Himakshi Sarma
    8. Asheesh Kumar
    9. Anamika Singh Gaur
    10. Rosaleen Sahoo
    11. S. Vaikundamani
    12. N. Arul Murugan
    13. U. Deva Priyakumar
    14. G.P.S. Raghava
    15. Prasad V. Bharatam
    16. Ramakrishnan Parthasarathi
    17. V. Subramanian
    18. G. Madhavi Sastry
    19. G. Narahari Sastry
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      Editors Assessment:

      MPDSCOVID-19 has been developed as a one-stop solution for drug discovery research for COVID-19, running on the Molecular Property Diagnostic Suite (MPDS) platform. This is built upon the open-source Galaxy workflow system, integrating many modules and data specific to COVID-19. Data integrated includes SARS-CoV-2 targets, genes and their pathway information; information on repurposed drugs against various targets of SARS-CoV-2, mutational variants, polypharmacology for COVID-19, drug-drug interaction information, Protein-Protein Interaction (PPI), host protein information, epidemiology, and inhibitors databases. After improvements to the technical description of the platform, testing helped demonstrate the potential to drive open-source computational drug discovery with the platform.

      This evaluation refers to version 1 of the preprint

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  9. Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19 ): An open access disease specific drug discovery portal

    This article has 19 authors:
    1. Lipsa Priyadarsinee
    2. Esther Jamir
    3. Selvaraman Nagamani
    4. Hridoy Jyoti Mahanta
    5. Nandan Kumar
    6. Lijo John
    7. Himakshi Sarma
    8. Asheesh Kumar
    9. Anamika Singh Gaur
    10. Rosaleen Sahoo
    11. S. Vaikundamani
    12. N. Arul Murugan
    13. U. Deva Priyakumar
    14. G.P.S. Raghava
    15. Prasad V. Bharatam
    16. Ramakrishnan Parthasarathi
    17. V. Subramanian
    18. G. Madhavi Sastry
    19. G. Narahari Sastry
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      Editors Assessment:

      MPDSCOVID-19 has been developed as a one-stop solution for drug discovery research for COVID-19, running on the Molecular Property Diagnostic Suite (MPDS) platform. This is built upon the open-source Galaxy workflow system, integrating many modules and data specific to COVID-19. Data integrated includes SARS-CoV-2 targets, genes and their pathway information; information on repurposed drugs against various targets of SARS-CoV-2, mutational variants, polypharmacology for COVID-19, drug-drug interaction information, Protein-Protein Interaction (PPI), host protein information, epidemiology, and inhibitors databases. After improvements to the technical description of the platform, testing helped demonstrate the potential to drive open-source computational drug discovery with the platform.

      This evaluation refers to version 1 of the preprint

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  10. An improved chromosome-level genome assembly of perennial ryegrass ( Lolium perenne L.)

    This article has 7 authors:
    1. Yutang Chen
    2. Roland Kölliker
    3. Martin Mascher
    4. Dario Copetti
    5. Axel Himmelbach
    6. Nils Stein
    7. Bruno Studer
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      Editors Assessment:

      This Data Release paper presents an updated genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss (Kyuss v2.0). To correct for structural the authors de novo assembled the genome again with ONT long-reads and generated 50-fold coverage high-throughput chromosome conformation capture (Hi-C) data to assist pseudo-chromosome construction. After being asked for some more improvements to gene and repeat annotation the authors now demonstrate the new assembly is more contiguous, more complete, and more accurate than Kyuss v1.0 and shows the correct pseudo-chromosome structure. This more accurate data have great potential for downstream genomic applications, such as read mapping, variant calling, genome-wide association studies, comparative genomics, and evolutionary biology. These future analyses being able to benefit forage and turf grass research and breeding.

      This evaluation refers to version 1 of the preprint

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  11. Citizen science data on urban forageable plants: a case study in Brazil

    This article has 21 authors:
    1. Filipi Miranda Soares
    2. LuĂ­s Ferreira Pires
    3. Maria Carolina Garcia
    4. Lidio Coradin
    5. Natalia Pirani Ghilardi-Lopes
    6. Rubens Rangel Silva
    7. Aline Martins de Carvalho
    8. Anand Gavai
    9. Yamine Bouzembrak
    10. Benildes Coura Moreira dos Santos Maculan
    11. Sheina Koffler
    12. Uiara Bandineli Montedo
    13. Debora Pignatari Drucker
    14. Raquel Santiago
    15. Maria Clara Peres de Carvalho
    16. Ana Carolina da Silva Lima
    17. Hillary Dandara Elias Gabriel
    18. Stephanie Gabriele Mendonça de França
    19. Karoline Reis de Almeida
    20. Bárbara Junqueira dos Santos
    21. Antonio Mauro Saraiva
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      Editors Assessment:

      This is a Data Release paper describing data sets derived from the Pomar Urbano project cataloging edible fruit-bearing plants in Brazil. Including data sourced from the citizen science iNaturalist app, tracking the distribution and monitoring of these plants within urban landscapes (Brazilian state capitals). The data was audited and peer reviewed and put into better context, and there is a companion commentary in GigaScience journal better explaining the rationale for the study. Demonstrating this data providing a platform for understanding the diversity of fruit-bearing plants in select Brazilian cities and contributing to many open research questions in the existing literature on urban foraging and ecosystem services in urban environments.

      This evaluation refers to version 1 of the preprint

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  12. SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

    This article has 17 authors:
    1. Chun Gong
    2. Shengkang Li
    3. Leying Wang
    4. Fuxiang Zhao
    5. Shuangsang Fang
    6. Dong Yuan
    7. Zijian Zhao
    8. Qiqi He
    9. Mei Li
    10. Weiqing Liu
    11. Zhaoxun Li
    12. Hongqing Xie
    13. Sha Liao
    14. Ao Chen
    15. Yong Zhang
    16. Yuxiang Li
    17. Xun Xu
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      Editors Assessment:

      One limiting factor in the adoption of spatial omics research are workflow systems for data preprocessing, and to address these authors developed the SAW tool to process Stereo-seq data. The analysis steps of spatial transcriptomics involve obtaining gene expression information from space and cells. Existing tools face issues with large data sets, such as intensive spatial localization, RNA alignment, and excessive memory usage. These issues affect the process's applicability and efficiency. To address this, this paper presents a high-performance open-source workflow called SAW for Stereo-Seq. This includes mRNA position reconstruction, genome alignment, matrix generation, clustering, and result file generation for personalized analysis. During review the authors have added examples of MID correction in the article to make the process easier to understand. And In the future, more accurate algorithms or deep learning models may further improve the accuracy of this pipeline.

      *This evaluation refers to version 1 of the preprint

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  13. Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images

    This article has 14 authors:
    1. Bohan Zhang
    2. Mei Li
    3. Qiang Kang
    4. Zhonghan Deng
    5. Hua Qin
    6. Kui Su
    7. Xiuwen Feng
    8. Lichuan Chen
    9. Huanlin Liu
    10. Shuangsang Fang
    11. Yong Zhang
    12. Yuxiang Li
    13. Susanne Brix
    14. Xun Xu
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      Editors Assessment:

      This paper describes a new spatial transcriptomics method that that utilizes cell nuclei staining images and statistical methods to generate high-confidence single-cell spatial gene expression profiles for Stereo-seq data. STCellbin is an update of StereoCell, now using a more advanced cell segmentation technique, so more accurate cell boundaries can be obtained, allowing more reliable single-cell spatial gene expression profiles to be obtained. After peer review more comparisons were added and more description given on what was upgraded in this version to convince the reviewers. Demonstrating it is a more reliable method, particularly for analyzing high-resolution and large-field-of-view spatial transcriptomic data. And extending the capability to automatically process Stereo-seq cell membrane/wall staining images for identifying cell boundaries.

      This evaluation refers to version 2 of the preprint

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  14. BatchEval Pipeline: Batch Effect Evaluation Workflow for Multiple Datasets Joint Analysis

    This article has 6 authors:
    1. Chao Zhang
    2. Qiang Kang
    3. Mei Li
    4. Hongqing Xie
    5. Shuangsang Fang
    6. Xun Xu
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      Editors Assessment:

      For better data quality assessment of large spatial transcriptomics datasets this new BatchEval software has been developed as a batch effect evaluation tool. This generates a comprehensive report with assessment findings, including basic information of integrated datasets, a batch effect score, and recommended methods for removing batch effects. The report also includes evaluation details for the raw dataset and results from batch effect removal methods. Through peer review and clarification of a number of points it now looks convincing that this tool helps researchers identify and remove batch effects, ensuring reliable and meaningful insights from integrated datasets. Potentially making the tool valuable for researchers who need to analyze large datasets of this type, as it provides an easy and reliable way to assess data quality and ensures that downstream analyses are robust and reliable.

      This evaluation refers to version 1 of the preprint

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  15. Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

    This article has 20 authors:
    1. Magnus Wolf
    2. Bruno Lopes da Silva Ferrette
    3. Raphael T. F. Coimbra
    4. Menno de Jong
    5. Marcel Nebenfuehr
    6. David Prochotta
    7. Yannis Schöneberg
    8. Konstantin Zapf
    9. Jessica Rosenbaum
    10. Hannah A. Mc Intyre
    11. Julia Maier
    12. Clara C.S. de Souza
    13. Lucas M. Gehlhaar
    14. Melina J. Werner
    15. Henrik Oechler
    16. Marie Wittekind
    17. Moritz Sonnewald
    18. Maria A. Nilsson
    19. Axel Janke
    20. Sven Winter
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      Editors Assessment:

      The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.

      **This evaluation refers to version 1 of the preprint

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  16. Species composition and distribution of the Anopheles gambiae complex circulating in Kinshasa

    This article has 11 authors:
    1. Josue Zanga
    2. Emery Metelo
    3. Nono Mvuama
    4. Victoire Nsabatien
    5. Vanessa Mvudi
    6. Degani Banzulu
    7. Osée Mansiangi
    8. Maxwel Bamba
    9. Narcisse Basosila
    10. Rodrigue Agossa
    11. Roger Wumba
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      Editors Assessment: Understanding the distribution of Anopheles mosquito species is essential for planning and implementing malaria control programmes, a task undertaken in this study that assesses the composition and distribution of the Anopheles in different districts of Kinshasa in the Democratic Republic of Congo. Mosquitoes were collected using CDC light traps, and then identified by morphological and molecular means. In total 3,839 Anopheles were collected, and data was digitised, validated and shared via the GBIF database under a CC0 waiver. The project monitoring the monthly dynamics of four species of Anopheles, showing a fluctuation in their respective frequencies during the study period. Review improved the metadata by adding more accurate date information, and this data can provide important information for further basic and advanced studies on the ecology and phenology of these vectors in West Africa.

      *This evaluation refers to version 1 of the preprint

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  17. Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities

    This article has 2 authors:
    1. Danielle C. Wrenn
    2. Devin M. Drown
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      Editors Assessment: Antimicrobial resistance (AMR) is a global public health threat, and environmental microbial communities can act as reservoirs for resistance genes. There is a need for genomic surveillance could provide insights into how these reservoirs change and impact public health. With that goal in mind this study tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. On average adaptive sampling resulting in a target composition 4x higher than without adaptive sampling, and increased target yield in most replicates. The methods and scripts for this approach were reviewed and curated together, although the scope of this study was limited in terms of communities tested and AMR genes targeted. And the authors improved their analysis by conducting an additional analysis of a diverse microbial community. Demonstrating the method is reusable and its results are promising for developing a flexible, portable, and cost-effective AMR surveillance tool.

      *This evaluation refers to version 1 of the preprint

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  18. Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo

    This article has 18 authors:
    1. Victoire Nsabatien
    2. Josue Zanga
    3. Fiacre Agossa
    4. Nono Mvuama
    5. Maxwell Bamba
    6. Osée Mansiangi
    7. Leon Mbashi
    8. Vanessa Mvudi
    9. Glodie Diza
    10. Dorcas Kantin
    11. Narcisse Basosila
    12. Hyacinthe Lukoki
    13. Arsene Bokulu
    14. Christelle Bosulu
    15. Erick Bukaka
    16. Jonas Nagahuedi
    17. Jean Claude Palata
    18. Emery Metelo
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment: Aedes mosquito spread Arbovirus epidemics (e.g. Chikungunya, dengue, West Nile, Yellow Fever, and Zika), are a growing threat in Africa but a lack of vector data limits our ability to understand their propagation dynamics. This work describes the geographical distribution of Ae. aegypti and Ae. albopictus in Kinshasa, Democratic Republic of Congo between 2020 and 2022. Sharing 6,943 observations under a CC0 waiver as a Darwin Core archive in the University of Kinshasa GBIF database. Review improved the metadata by adding more accurate date information, and this data can provide important information for further basic and advanced studies on the ecology and phenology of these vectors in West Africa.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

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  19. A reference assembly for the legume cover crop hairy vetch (Vicia villosa)

    This article has 11 authors:
    1. Tyson Fuller
    2. Derek M. Bickhart
    3. Lisa M. Koch
    4. Lisa Kissing Kucek
    5. Shahjahan Ali
    6. Haley Mangelson
    7. Maria J. Monteros
    8. Timothy Hernandez
    9. Timothy P. L. Smith
    10. Heathcliffe Riday
    11. Michael L. Sullivan
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      The hairy vetch Vicia villosa is an annual legume widely used as a cover crop due to its ability to withstand harsh winters. Here a new a 2.03GB reference-quality genome is presented, assembled from PacBio HiFi long-sequence reads and Hi-C scaffolding. After adding some more methodological details and long-terminal repeat (LTR) assembly index (LAI) analysis the assembly quality and metrics look quite convincing as a chromosome-scale assembly. This resource hopefully providing the foundation for a genetic improvement program for this important cover crop and forage species.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

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  20. Genome assembly of the bearded iris Iris pallida Lam

    This article has 10 authors:
    1. Robert E. Bruccoleri
    2. Edward J. Oakeley
    3. Ann Marie E Faust
    4. Marc Altorfer
    5. Sophie Dessus-Babus
    6. David Burckhardt
    7. Mevion Oertli
    8. Ulrike Naumann
    9. Frank Petersen
    10. Joanne Wong
    This article has been curated by 1 group:
    • Curated by GigaByte

      **Editors Assessment: **

      Irises on top of being a popular and beautiful ornamental plant, have wider commercial interest due to the many interesting secondary metabolites present in their rhizomes that have value to the fragrance and pharmaceutical industries. Many of these have large and difficult to assemble genomes, and to fill that gap the Dalmatian Iris (Iris pallida Lam.) is sequenced here. Using PacBio long-read sequencing and bionano optical mapping to produce a giant 10Gbp assembly with a scaffold N50 of 14.34 Mbp. The authors didn’t manage to handle the haplotigs separately or to study the ploidy, but as all of the data is available for reuse others can explore these questions further. This reference genome should also allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity