1. The GC-content at the 5’ends of human protein-coding genes is undergoing mutational decay

    This article has 6 authors:
    1. Yi Qiu
    2. Yoon Mo Kang
    3. Christopher Korfmann
    4. Fanny Pouyet
    5. Andrew Eckford
    6. Alexander F. Palazzo

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  2. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  3. Genome sequences of four Ixodes species expands understanding of tick evolution

    This article has 32 authors:
    1. Alexandra Cerqueira de Araujo
    2. Benjamin Noël
    3. Anthony Bretaudeau
    4. Karine Labadie
    5. Matéo Boudet
    6. Nachida Tadrent
    7. Benjamin Istace
    8. Salima Kritli
    9. Corinne Cruaud
    10. Robert Olaso
    11. Jean-François Deleuze
    12. Maarten Voordouw
    13. Caroline Hervet
    14. Olivier Plantard
    15. Aya Zamoto-Niikura
    16. Thomas Chertemps
    17. Martine Maïbèche
    18. Frédérique Hilliou
    19. Gaëlle Le Goff
    20. Jindrich Chmelar
    21. Vilém Mazák
    22. Mohammed Amine Jmel
    23. Michalis Kotsyfakis
    24. José María Medina
    25. Michael Hackenberg
    26. Ladislav Šimo
    27. Fotini A. Koutroumpa
    28. Patrick Wincker
    29. Petr Kopacek
    30. Jan Perner
    31. Jean-Marc Aury
    32. Claude Rispe

    Reviewed by Arcadia Science

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

    This article has 19 authors:
    1. Hong Kong Biodiversity Genomics Consortium
    2. Jerome H. L. Hui
    3. Ting Fung Chan
    4. Leo Lai Chan
    5. Siu Gin Cheung
    6. Chi Chiu Cheang
    7. James Kar-Hei Fang
    8. Juan Diego Gaitan-Espitia
    9. Stanley Chun Kwan Lau
    10. Yik Hei Sung
    11. Chris Kong Chu Wong
    12. Kevin Yuk-Lap Yip
    13. Yingying Wei
    14. Ming Fung Franco Au
    15. Wai Lok So
    16. Wenyan Nong
    17. Tin Yan Hui
    18. Brian Kai Hin Leung
    19. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  5. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  6. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  7. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  8. 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  9. Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

    This article has 30 authors:
    1. Sungwon Jeon
    2. Hansol Choi
    3. Yeonsu Jeon
    4. Whan-Hyuk Choi
    5. Hyunjoo Choi
    6. Kyungwhan An
    7. Hyojung Ryu
    8. Jihun Bhak
    9. Hyeonjae Lee
    10. Yoonsung Kwon
    11. Sukyeon Ha
    12. Yeo Jin Kim
    13. Asta Blazyte
    14. Changjae Kim
    15. Yeonkyung Kim
    16. Younghui Kang
    17. Yeong Ju Woo
    18. Chanyoung Lee
    19. Jeongwoo Seo
    20. Changhan Yoon
    21. Dan Bolser
    22. Orsolya Biro
    23. Eun-Seok Shin
    24. Byung Chul Kim
    25. Seon-Young Kim
    26. Ji-Hwan Park
    27. Jongbum Jeon
    28. Dooyoung Jung
    29. Semin Lee
    30. Jong Bhak

    Reviewed by GigaScience

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  10. Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function

    This article has 3 authors:
    1. Magdalena Topolska
    2. Antoni Beltran
    3. Ben Lehner

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
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