Latest preprint reviews

1. 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

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

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

   This article has 2 authors:

   1. Danielle C. Wrenn
   2. Devin M. Drown

   This article has been curated by 1 group:

   • Curated by GigaByte

     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

   Reviewed by GigaByte

3. 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

4. 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

5. 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

6. A Database of Restriction Maps to Expand the Utility of Bacterial Artificial Chromosomes

   This article has 6 authors:

   1. Eamon Winden
   2. Alejandro Vasquez-Echeverri
   3. Susana Calle-Casteneda
   4. Yumin Lian
   5. Juan Pablo Hernández-Ortiz
   6. David C. Schwartz

   This article has been curated by 1 group:

   • Curated by GigaByte

     **Editors Assessment: **

     While Bacterial Artificial Chromosomes libraries were once a key resource for building the human genome project over time they have been rendered relatively obsolete by long-read technologies. In the era of CRISPR-Cas systems pairing this data with one of the many guide-RNA libraries to find targets for manipulation with CRISPR tools is bringing back BACs advantages for genomics. With this in mind the authors have developed a BAC restriction map database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of available restriction enzymes. Alongside a set of Python functions to reconstruct the database and more easily access it (which were debugged and had improved documentation added during review). The presented data should be valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

     *This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

7. Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

   This article has 4 authors:

   1. Lucia Corte
   2. Lathan Liou
   3. Paul F. O’Reilly
   4. Judit García-González

   This article has been curated by 1 group:

   • Curated by GigaByte

     **Editors Assessment: **

     This work presents a new standardized graphical approach for visualizing genetic associations across a wide range of allele frequencies. These proposed TrumpetPlots have a distinctive trumpet shape, hence the proposed name. With the majority of variants having low frequency and small effects, while a small number of variants have higher frequency and larger effects, this view can help to provide new and valuable insights into the genetic basis of traits and diseases, and also help prioritize efforts to discover new risk variants. The tool is provided as a novel R package and R Shiny application and to demonstrate its use the article illustrates the distribution of variant effect sizes across the allele frequency range for over 100 continuous traits available in the UK Biobank. After some problems in testing the package is now available and easy to deploy via CRAN.

     *This assessment refers to version 1 of this preprint. *

   Reviewed by GigaByte

8. Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

   This article has 5 authors:

   1. Sagar Patel
   2. Zachary N. Harris
   3. Jason P. Londo
   4. Allison Miller
   5. Anne Fennell

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editor’s Assessment

     Hybrid genomes are tricky to assemble, and few genomic resources are available for hybrid grapevines such as ‘Chambourcin’, a French-American interspecific hybrid grape grown in the eastern and midwestern United States. Here is an attempt to assemble Chambourcin’ using a combination of PacBio HiFi long-reads, Bionano optical maps, and Illumina short-read sequencing technologies. Producing an assembly with 26 scaffolds, an N50 length 23.3 Mb and an estimated BUSCO completeness of 97.9% that can be used for genome comparisons, functional genomic analyses, and genome-assisted breeding research. Error correction and pilon polishing was a challenge with this hybrid assembly, but after trying a few different approaches in the review process have improved it, and as they have documented what they did and are clear about the final metrics, users can assess the quality themselves.

     This assessment refers to version 2 of this preprint.

   Reviewed by GigaByte

9. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

   This article has 9 authors:

   1. André Gomes-dos-Santos
   2. Manuel Lopes-Lima
   3. André M. Machado
   4. Thomas Forest
   5. Guillaume Achaz
   6. Amílcar Teixeira
   7. Vincent Prié
   8. L. Filipe C. Castro
   9. Elsa Froufe

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editor’s Assessment

     Like other mollusc species, the freshwater pearl mussel (Margaritifera margaritifera) has a challenging genome to assemble owing to the large size of their genomes, heterozygosity, and repetitive sequence. The first published M. margaritifera genome was highly fragmented, but here an improved reference genome assembly was generated using PacBio CLR long reads to reduce fragmentation levels, missing and truncated genes, and chimerically assembled regions. The number of gene models predicted is a bit higher compared than other molluscan genomes, but after clarification and double checking these seem in line with some Mollusca and Bivalvia with similar and higher numbers of gene predictions. This new genome represents a new resource to start exploring the many biological, ecological, and evolutionary features of this threatened and commercially important group of organisms.

     This assessment refers to version 1 of this preprint.

   Reviewed by GigaByte

10. Mycobacterial Metabolic Model Development for Drug Target Identification

    This article has 3 authors:

    1. Bridget P. Bannerman
    2. Alex Oarga
    3. Jorge Júlvez

    This article has been curated by 1 group:

    • Curated by GigaByte

      Editor’s Assessment

      This work has generated metabolic models for the human pathogens Mycobacterium leprae and Mycobacteroides abscessus, alongside a new computational tool that can be used to identify potential drug targets. The standardised genomic scale metabolic models have been developed using the systems biology community standards for quality control and evaluation of models. After providing more detail on reproducibility, comparative performance of the models, and reuse, these resources are now published and are available for reuse by the global scientific community via the GigaDB, Biomodels, and PatMeDB repositories.

      This assessment refers to version 1 of this preprint.

    Reviewed by GigaByte