Latest preprint reviews

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:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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 León

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

    This article has been curated by 1 group:

    • Curated by GigaByte

      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

    Reviewed by GigaByte