Genomics and Genetics

Genomics and Genetics

Genome Sequencing

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https://doi.org/10.12688/f1000research.162894.1
Genome Note metrics AWAITING PEER REVIEW
The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
[version 1; peer review: awaiting peer review]
Abderrahmane Eleiwa, Pol Mestre, Ana Usie, Ester Vilaprinyo, Alberto Marin-Sanguino, Albert Sorribas, Cristobal Richart, Judit Salces-Ortiz, Rosa Fernández, Mar Biarnés, Noélia Antilles, Jesus Nadal, Rui Alves
Peer Reviewers Invited
  • Funders
  • Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya
  • Fundação para a Ciência e a Tecnologia
  • Fundacio Rovira i Virgili
  • European Research Council
  • Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement
PUBLISHED 02 Sep 2025
https://doi.org/10.12688/f1000research.163701.2
Genome Note metrics
Revised
Reference genome and reproduction-focused transcriptome for the threatened alpine tree frog (Litoria verreauxii alpina)
[version 2; peer review: 2 approved]
Alexander S. Wendt, Laura Brannelly
Peer Reviewers Yanbo Sun; Martin Knytl
  • Funders
  • American Australian Association
  • University of Melbourne
  • Australian Research Council
LATEST VERSION PUBLISHED 02 Sep 2025
https://doi.org/10.12688/f1000research.166849.1
Genome Note metrics AWAITING PEER REVIEW
Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii
[version 1; peer review: awaiting peer review]
Imron Imron, Fajar Anggraeni, Rahmat Hidayat, Jadmiko Darmawan, Otong Zenal Arifin, Daniel Frikli Mokodongan, Rosita Rosita, Luthfi Nurhidayat
Peer Reviewers Invited
  • Funder
  • Lembaga Pengelola Dana Pendidikan
PUBLISHED 14 Aug 2025
https://doi.org/10.12688/f1000research.160546.2
Genome Note metrics
Revised
The complete genome sequences of Bacillus velezensis B26: a promising biocontrol agent and biofertilizer
[version 2; peer review: 3 approved]
Venkatesh Kamath B, Sandeep Mallya, Subrahmanyam Volety Mallikarjuna, Kiran Kumar Kolathur
Peer Reviewers Saranya Nallusamy; Surajit Basak; Diego Sauka
LATEST VERSION PUBLISHED 08 Jul 2025
https://doi.org/10.12688/f1000research.161461.2
Genome Note metrics
Revised
The genome sequence of Tethysbaena scabra (Pretus, 1991), the first known in the peracarid crustacean order Thermosbaenacea.
[version 2; peer review: 1 approved, 1 approved with reservations]
Joan Pons, Karen D. Schöninger-Almaraz, Laura Triginer-Llabrés, Carlos Juan, Damià Jaume, José A. Jurado-Rivera
Peer Reviewers Pascal Angst; Martin Schwentner
  • Funders
  • Govern de les Illes Balears
  • Institut d'Estudis Catalans
LATEST VERSION PUBLISHED 04 Jul 2025
https://doi.org/10.12688/f1000research.159115.2
Genome Note metrics
Revised
The first mitochondrial genome of Haemagogus equinus from Jamaica
[version 2; peer review: 1 approved, 1 approved with reservations]
Simone L. Sandiford, Simmoy A. A. Noble, Samra A. Pierre, Douglas E. Norris, Renee Ali
Peer Reviewers Din Syafruddin and Puji Budi Setia Asih; Craig Wilding
  • Funders
  • NSF-Accelerator Project D-688: Computing the Biome
  • Global Infectious Diseases Research Training Program
  • Johns Hopkins Malaria Research Institute and Bloomberg Philanthropies
  • University at Buffalo Clinical and Translational Science Institute
LATEST VERSION PUBLISHED 02 Jul 2025
https://doi.org/10.12688/f1000research.123591.2
Data Note metrics
Revised
Squalomix: shark and ray genome analysis consortium and its data sharing platform
[version 2; peer review: 2 approved]
Osamu Nishimura, John Rozewicki, Kazuaki Yamaguchi, Kaori Tatsumi, Yuta Ohishi, Tazro Ohta, Masaru Yagura, Taiki Niwa, Chiharu Tanegashima, Akinori Teramura, Shotaro Hirase, Akane Kawaguchi, Milton Tan, Salvatore D'Aniello, Filipe Castro, André Machado, Mitsumasa Koyanagi, Akihisa Terakita, Ryo Misawa, Masayuki Horie, Junna Kawasaki, Takashi Asahida, Atsuko Yamaguchi, Kiyomi Murakumo, Rui Matsumoto, Iker Irisarri, Norio Miyamoto, Atsushi Toyoda, Sho Tanaka, Tatsuya Sakamoto, Yasuko Semba, Shinya Yamauchi, Kazuyuki Yamada, Kiyonori Nishida, Itsuki Kiyatake, Keiichi Sato, Susumu Hyodo, Mitsutaka Kadota, Yoshinobu Uno, Shigehiro Kuraku
Peer Reviewers Mélanie Debiais-Thibaud; Dan Larhammar and David Lagman
  • Funders
  • RIKEN Center for Biosystems Dynamics Research
  • National Institute of Genetics
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 08 May 2025
https://doi.org/10.12688/f1000research.157311.3
Genome Note metrics
Revised
The complete mitogenome of an unidentified Oikopleura species
[version 3; peer review: 3 approved, 1 approved with reservations]
Johannes Nicolaus Wibisana, Charles Plessy, Nicolas Dierckxsens, Aki Masunaga, Jiashun Miao, Nicholas M. Luscombe
Peer Reviewers Carmela Gissi; Ayelet Voskoboynik; Daniel M Chourrout; Thomas Stach
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 06 May 2025
https://doi.org/10.12688/f1000research.163516.1
Method Article metrics
NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling
[version 1; peer review: 1 approved, 1 approved with reservations]
Hyunjin Shim
Peer Reviewers Ruslan Kalendar; Runsheng Li
PUBLISHED 10 Apr 2025
https://doi.org/10.12688/f1000research.157851.2
Genome Note metrics
Revised
A reference genome for the eastern bettong (Bettongia gaimardi)
[version 2; peer review: 3 approved]
Luke W Silver, Richard J Edwards, Linda Neaves, Adrian D. Manning, Carolyn J Hogg, Sam Banks
Peer Reviewers Naoki Osada; Jonathan J Hughes; Németh Attila
  • Funder
  • Australian Research Council
LATEST VERSION PUBLISHED 27 Jan 2025
https://doi.org/10.12688/f1000research.159170.1
Genome Note metrics AWAITING PEER REVIEW
Isolation and complete genome sequence of Citrobacter bacteriophage Ursula
[version 1; peer review: awaiting peer review]
A.K. Golomidova, E.E. Kulikov, A.D. Efimov, I.S. Belalov, A.S. Kuznetsov, A.V. Letarov, L.I. Popova
Peer Reviewers Invited
  • Funder
  • Ministry of Science and Higher Education of the Russian Federation
PUBLISHED 15 Jan 2025
https://doi.org/10.12688/f1000research.156485.1
Genome Note metrics
The genome sequence of the Violet Copper, Lycaena helle (Denis & Schiffermüller, 1775)
[version 1; peer review: 2 approved]
Clara Pladevall, Roger Caritg, Francisco Cámara, Silvia Carbonell, Jèssica Gómez-Garrido, Fernando Cruz, Marta Gut, Vanesa Arroyo, Benjamin Komac, Roger Vila, Roderic Guigó, Tyler S. Alioto, Manel Niell
Peer Reviewers Panagiotis Ioannidis; Sivasankaran Kuppusamy
PUBLISHED 10 Jan 2025
https://doi.org/10.12688/f1000research.157774.1
Genome Note metrics
A compilation of histidine kinase genes in Enterobacter hormaechei strain HCF3 isolated from the North West Province of South Africa
[version 1; peer review: 2 approved with reservations]
Ebere Loveyn Udeh, Sarah Oluwatobi Otun, Lerato Lisbeth Njaki Makhetha, Khayalethu Ntushelo
Peer Reviewers Reetika Debroy; Angeliki Mavroidi
  • Funder
  • National Research Foundation (NRF)
PUBLISHED 06 Dec 2024
https://doi.org/10.12688/f1000research.140344.2
Research Article metrics
Revised
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
[version 2; peer review: 2 approved]
Friederike Hanssen, Gisela Gabernet, Famke Bäuerle, Bianca Stöcker, Felix Wiegand, Nicholas H. Smith, Christian Mertes, Avirup Guha Neogi, Leon Brandhoff, Anna Ossowski, Janine Altmueller, Kerstin Becker, Andreas Petzold, Marc Sturm, Tyll Stöcker, Sugirthan Sivalingam, Fabian Brand, Axel Schmidt, Andreas Buness, Alexander J. Probst, Susanne Motameny, Johannes Köster
Peer Reviewers Justin M. Zook; Kez Cleal
  • Funders
  • German Federal Ministry for Education and Research
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 12 Sep 2024
https://doi.org/10.12688/f1000research.144352.2
Genome Note metrics
Revised
A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor)
[version 2; peer review: 2 approved, 1 approved with reservations]
Luke W. Silver, Dejan Stojanovic, Katherine A. Farquharson, Lauren Alexander, Emma Peel, Katherine Belov, Carolyn J. Hogg
Peer Reviewers Charles Feigin; Phred Benham; Joan Ferrer Obiol
  • Funders
  • NCRIS funded BioPlatforms Threatened Species Initiative
  • Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
LATEST VERSION PUBLISHED 27 Aug 2024
https://doi.org/10.12688/f1000research.150836.2
Genome Note metrics
Revised
The genomes of the aquarium sponges Tethya wilhelma and Tethya minuta (Porifera: Demospongiae)
[version 2; peer review: 2 approved]
Gert Wörheide, Warren R. Francis, Fabian Deister, Stefan Krebs, Dirk Erpenbeck, Sergio Vargas
Peer Reviewers Bernie Degnan; Eric Bautista-Guerrero
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Villum Fonden
  • H2020 Marie Skłodowska-Curie Actions
  • LMUexcellent
LATEST VERSION PUBLISHED 01 Aug 2024
https://doi.org/10.12688/f1000research.139906.2
Data Note metrics
Revised
A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa
[version 2; peer review: 1 approved]
Sarah Oluwatobi Otun, Khayalethu Ntushelo
Peer Reviewers Iris Yedidia
LATEST VERSION PUBLISHED 17 Jun 2024
https://doi.org/10.12688/f1000research.145790.2
Genome Note metrics
Revised
Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies
[version 2; peer review: 2 approved with reservations]
Richard Andreas Salindeho, Fifi Gus Dwiyanti, Rahadian Pratama, Deden Derajat Matra, Muhammad Majiidu, Iskandar Z. Siregar
Peer Reviewers Hoang Dang Khoa Do; Jakub Sawicki
  • Funder
  • National Competitive Basic Research 2022-2023
LATEST VERSION PUBLISHED 21 May 2024
https://doi.org/10.12688/f1000research.144007.1
Genome Note metrics
Isolation and complete genome sequence of Aeromonas bacteriophage Gekk3-15
[version 1; peer review: 2 approved, 1 approved with reservations]
A.K. Golomidova, E.E. Kulikov, A.S. Kuznetsov, P. Yu. Pechenov, I.S. Belalov, A.V. Letarov, E.E. Galyov
Peer Reviewers Ruben Avendaño-Herrera; Ben Temperton and Liam Boot-Handford; Reham M El Tarabili
  • Funders
  • Ministry of Science and Higher Education of the Russian Federation
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 24 Apr 2024
https://doi.org/10.12688/f1000research.148511.1
Genome Note metrics
Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata
[version 1; peer review: 1 approved, 1 approved with reservations]
Meghan K. Yap-Chiongco, Stacy Pirro, Rebecca M. Varney, Hiroshi Saito, Kenneth M. Halanych, Kevin M. Kocot
Peer Reviewers Gloria Arriagada; Alice Dennis
  • Funders
  • Iridian Genomes
  • National Science Foundation
PUBLISHED 23 Apr 2024
1-20 of 65 ARTICLES
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