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Latest preprint reviews

1. Chromosome-level genome assemblies of five Sinocyclocheilus species

   This article has 6 authors:

   1. Chao Bian
   2. Ruihan Li
   3. Yuqian Ouyang
   4. Junxing Yang
   5. Xidong Mu
   6. Qiong Shi

   This article has been curated by 1 group:

   • Curated by GigaByte

     **Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

2. Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

   This article has 19 authors:

   1. Hewei Liang
   2. Yuanqiang Zou
   3. Mengmeng Wang
   4. Tongyuan Hu
   5. Haoyu Wang
   6. Wenxin He
   7. Yanmei Ju
   8. Ruijin Guo
   9. Junyi Chen
   10. Fei Guo
   11. Tao Zeng
   12. Yuliang Dong
   13. Yuning Zhang
   14. Bo Wang
   15. Chuanyu Liu
   16. Xin Jin
   17. Wenwei Zhang
   18. Xun Xu
   19. Liang Xiao

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

3. Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia

   This article has 4 authors:

   1. Trinity Conn
   2. Jill Ashey
   3. Ross Cunning
   4. Hollie M. Putnam

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Acropora pulchra is a species small polyped stony corals in the family Acroporidae from the the Indo-Pacific. This Data Release is the first study in stony corals to present the DNA methylome in tandem with a high-quality genome assembled utilizing PacBio long-read HiFi sequencing. Sequencing an A. pulchra specimen from Mo’orea, French Polynesia. From this single molecule sequencing data DNA methylation data was also called and quantified, and additional short-read Illumina RNASeq data was used for gene annotation. This producing an assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp, and 40,518 protein-coding genes called. Peer review requested some improved benchmarking, and it is impressive to see from the results that the genome assembly represents the most complete and contiguous stony coral genome assembly to date. As an important indicator species and this data will hopefully serve as a resource to the coral and wider scientific community. Further quantification of the genome-wide methylation is needed aid the study epigenetics of non-model organisms, and specifically future analyses on methylation in coral.

     *This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

4. CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics

   This article has 1 author:

   1. Niema Moshiri

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     As volumes of viral and bacterial sequence data grow exponentially, the field of computational phylogenetics now demands resources to manage the burgeoning scale of this input data. This study introduces CompactTree, a C++ library designed for ultra-large phylogenetic trees with millions of tips. To address these scalability issues while maintaining ease of incorporation into external code bases, CompactTree is a header-only library with enhanced performance utilizing minimal dependencies, optimized node representation, and memory-efficient tree structure schemes. Resulting in significantly reduced memory footprints and improved processing times. Peer review requested some more detail on the functionality and some real-world examples, demonstrating the current utility of the tool. Although primarily supporting the (text-based) Newick format, the increased and extensibility scalability holds promise for multiple biological and epidemiological applications supporting more complex formats such as Nexus and NeXML. The tool is open source (GPLv3 licensed) and available in GitHub: https://niema.net/CompactTree

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

5. Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species

   This article has 8 authors:

   1. Ma. Carmel F. Javier
   2. Albert C. Noblezada
   3. Persie Mark Q. Sienes
   4. Robert S. Guino-o
   5. Nadia Palomar-Abesamis
   6. Maria Celia D. Malay
   7. Carmelo S. del Castillo
   8. Victor Marco Emmanuel N. Ferriols

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     The Visayan spotted deer (Rusa alfredi), is a small, endangered, primarily nocturnal species of deer found in the rainforests of the Visayan Islands in the Philippines. The present study reports the first draft genome assembly for the species, addressing a critical gap in genomic data for this IUCN-redlisted cervid. Using Illumina sequencing, the resulting genome assembly spans 2.52 Gb in size with a BUSCO completeness score of 95.5% and encompasses 24,531 annotated genes. Phylogenetic analysis suggests a close evolutionary relationship between R. alfredi and Cervus species suggesting that the genus Rusa is sister to Cervus. Peer-review teased out more benchmarking results and the annotation files, demonstrating this genomic resource is useful and usable for advancing population genetics and evolutionary studies, thereby informing conservation strategies and enhancing breeding programs for the critically threatened species. Providing whole genome sequences for other native species of Rusa could further provide genomic resources for detecting hybrids, which will also help the management and monitoring of these species, especially for the reintroduction of captive populations in the wild.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

6. The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

   This article has 6 authors:

   1. Eleanore J. Ritter
   2. Noé Cochetel
   3. Andrea Minio
   4. Peter Cousins
   5. Dario Cantu
   6. Chad Niederhuth

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Teinturier grapes produce berries with pigmented skin and flesh, and are used in red wine blends, as they provide a deeper colour. This paper presents the genomes of two popular teinturier varieties (Dakapo and Rubired); sequenced, assembled, and annotated to provide additional resources for their use in breeding. Combining Nanopore and Illumina sequencing for Dakapo, scaffolding to the existing grapevine assembly to generate a final assembly of 508.5 Mbp and 36,940 gene annotations. For Rubired PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long and 56,681 genes annotated. Peer review has helped validate their high quality, these genomes hopefully enabling more insight into the genetics of grapevine berry colour and their other traits like frost and mildew-resistance.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

7. SqueezeCall: nanopore basecalling using a Squeezeformer network

   This article has 1 author:

   1. Zhongxu Zhu

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     The accuracy of basecalling of nanopore sequencing still needs to be improved. With recent advances in deep learning this paper introduces SqueezeCall, a novel end-to-end tool for accurate basecalling. This uses Squeezeformer-achitecture which integrates local context extraction through convolutional layers and long-range dependency modeling via global context acquisition. Testing and peer review demonstrated that SqueezeCall outperformed traditional RNN and Transformer-based basecallers across multiple datasets, indicating its potential to refine genomic assembly and facilitate direct detection of modified bases in future genomic analytics. Future work is ongoing that will focus on training on highly curated datasets, including known modifications, to further increase research value. SqueezeCall is MIT licensed and available from GitHub here: https://github.com/labcbb/SqueezeCall

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

8. A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine

   This article has 11 authors:

   1. Deruilin Liu
   2. Demin Xu
   3. Liuxin Shi
   4. Jiayuan Zhang
   5. Kewei Bi
   6. Bei Luo
   7. Chen Liu
   8. Yuxiang Li
   9. Guangyi Fan
   10. Wen Wang
   11. Zhi Ping

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     DNA has huge potential as a data storage medium because of its incredibly high storage density and stability. This work addresses the potential of modified bases, specifically 5-methylcytosine (5mC), in enhancing DNA data storage systems. This paper introduces a transcoding scheme named R+, which incorporates this modified 5mC base to increase information density beyond the standard limits. By encoding various file types into DNA sequences of between 1.3 to 1.6 kb in size, this method achieves an average recovery rate of 98.97% (with reference), validating the effectiveness of the method. On top of a wet-lab protocol (hosted in protocols.io) for the experimental validation of the transcoding scheme, it also includes open source code for in-silico simulation tests. Peer review scruitinising the protocols and validation are reusable and provide convincing results. As nanopore sequencing has enabled reading of these modified bases, it is timely making them applicable as extra letters in the molecular alphabet for DNA data storage

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

9. Polyploid genome assembly of Cardamine chenopodiifolia

   This article has 8 authors:

   1. Aurélia Emonet
   2. Mohamed Awad
   3. Nikita Tikhomirov
   4. Maria Vasilarou
   5. Miguel Pérez-Antón
   6. Xiangchao Gan
   7. Polina Yu. Novikova
   8. Angela Hay

   This article has been curated by 1 group:

   • Curated by GigaByte

     This evaluation refers to version 1 of the preprint

     This work presents the genome of Cardamine chenopodiifolia, an amphicarpic plant (developing two fruit types, one above and another below ground) in the mustard (Brassicaceae) family. Cardamines also known as bittercresses and toothworts. As an octoploid species it has been challenging to create a genome reference for this species, and in this case the authors finally managed to achieve this using PacBio HiFi long-reads and Omni-C technology to assemble a fully phased, chromosome-level genome. Obtaining a 597Mb genome assembled into 32 phased chromosomes (plus mitochondrial and plastid genomes), and only having one gap in the centromeric region of chromosome 9. Peer review asked for additional QC and benchmarking, helping demonstrate the genome quality was very high, with only one gap and a N50 of 18.80Mb. The data presented here potentially helping to develop this species as an emerging model organism in the Brassicaceae for studying the development and evolution of amphicarpy by allopolyploidy.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

10. The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

    This article has 5 authors:

    1. Emma Gairin
    2. Saori Miura
    3. Hiroki Takamiyagi
    4. Marcela Herrera
    5. Vincent Laudet

    This article has been curated by 1 group:

    • Curated by GigaByte

      Editors Assessment:

      Among hot topics in coral reef research, the difference between anemonefish and other damselfish is currently a popular area of research. In this study the authors provide a new high-quality non-anemonefish genome, which will be of high relevance to further the depth of such analyses. In this case of the sapphire damselfish Chrysiptera cyanea, a widely distributed damselfish in the Indo-Pacific area, often studied to elucidate the roles of various environmental controls on their reproduction, and investigate related hormonal processes To further the potential of biomolecular analyses based on this species, this study generated the first genome of a Chrysiptera fish from a male individual collected in Okinawa, Japan. Using PacBio and HiFI long-read sequencing with 94.5x coverage, a chromosome-scale genome was assembled and 28,173 genes identified and annotated. Peer review gathered more parameters and details on the quality, and the final assembly comprised of 896 Mb pairs across 91 contigs, and a BUSCO completeness of 97.6%. This reference genome should therefore be of high value for future genetic-based approaches, from population structure to gene expression analyses.
      

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte