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

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

• Curated by GigaByte

  Competing Interest StatementThe authors have declared no competing interest.

  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

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

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

• Curated by GigaByte

  STATEMENT OF NEED Visualizations are powerful tools that have helped the field of genetics to better understand and communicate complex findings. By using visual aids like Manhattan and Volcano plots, genetic variants identified through genome-wide association studies can be more easily pinpointed. With the advancement of genome-wide association and sequencing studies, a mounting number of significant genetic variants, both common and rare, are being discovered. To better understand the relationship between these variants, combining these findings into single visualizations help to observe the relationship between effect size and allele frequency, providing a clearer picture of the genetic architecture of different traits and diseases. However, there is currently no consistent method for illustrating these results. In this paper, we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum, generate plots for over a hundred traits in the UK Biobank, and provide to the field a R package and R Shiny application to explore their own results.

  **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

Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

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

• 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

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

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

• 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

Mycobacterial Metabolic Model Development for Drug Target Identification

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

• 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

Genome assembly of the deep-sea coral Lophelia pertusa

1. Santiago Herrera
2. Erik E. Cordes

Reviewed by GigaByte

The first genome assembly of the amphibian nematode parasite ( Aplectana chamaeleonis )

1. Lei Han
2. Tianlu Liu
3. Fengping He
4. Zhijun Hou

Reviewed by GigaByte

PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects

1. Inês G. Gonçalves
2. David A. Hormuth
3. Sandhya Prabhakaran
4. Caleb M. Phillips
5. José Manuel García-Aznar

Reviewed by GigaByte

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

1. B Ramesh
2. CM Small
3. H Healey
4. B Johnson
5. E Barker
6. M Currey
7. S Bassham
8. M Myers
9. WA Cresko
10. AG Jones

Reviewed by GigaByte

Nanopore-Based Enrichment of Antimicrobial Resistance Genes – A Case-Based Study

1. Adrian Viehweger
2. Mike Marquet
3. Martin Hölzer
4. Nadine Dietze
5. Mathias W. Pletz
6. Christian Brandt

Reviewed by GigaByte