Genomics and Genetics

Genomics and Genetics

Genome Sequencing

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https://doi.org/10.12688/f1000research.173356.1
Genome Note metrics AWAITING PEER REVIEW
The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat
[version 1; peer review: awaiting peer review]
Rahadian Pratama, Linda Sukmarini, Akhirta Atikana, Shanti Ratnakomala, Fahrurrozi Fahrurrozi, Puspita Lisdiyanti
Peer Reviewers Invited
  • Funders
  • Rumah Program Biodiversitas, ORHL-BRIN
  • Rumah Program Artificial, Intelligence, Big Data & Teknologi Komputasi, OREI-BRIN
  • Riset dan Inovasi untuk Indonesia Maju—Indonesia Endowment Funds for Education (LPDP)
PUBLISHED 24 Nov 2025
https://doi.org/10.12688/f1000research.140134.3
Genome Note metrics
Revised
The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae)
[version 3; peer review: 3 approved with reservations]
Hoang Danh Nguyen, Thi Diem Quynh Nguyen, Minh Thiet Vu, Hoang Dang Khoa Do
Peer Reviewers Jessica D. Rey; Qiang Li; Shiou Yih Lee
  • Funder
  • Nguyen Tat Thanh University
LATEST VERSION PUBLISHED 21 Nov 2025
https://doi.org/10.12688/f1000research.166849.2
Genome Note metrics
Revised
Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii
[version 2; peer review: 2 approved with reservations, 1 not approved]
Imron Imron, Fajar Anggraeni, Rahmat Hidayat, Jadmiko Darmawan, Otong Zenal Arifin, Daniel Frikli Mokodongan, Rosita Rosita, Luthfi Nurhidayat
Peer Reviewers Gulab D. Khedkar; Geoffrey C. Waldbieser; Haiyang Liu
  • Funder
  • Lembaga Pengelola Dana Pendidikan
LATEST VERSION PUBLISHED 10 Nov 2025
https://doi.org/10.12688/f1000research.153918.1
Genome Note metrics
Chromosome-level genome assembly of the hamour (orange-spotted grouper), Epinephelus coioides
[version 1; peer review: 2 approved]
Razan Khalifa, Tim Bean, Dana Albatesh, Ronny van Aerle, Zenaba Kahtir, Zainab Hizam, Marta Gut, Francisco Câmara, Fernando Cruz, Jèssica Gómez-Garrido, Tyler Alioto, Eduarda Santos, Alexandra Leitão, Diana Minardi
Peer Reviewers Jayan Duminda M Senevirathna; Merly Escalona
  • Funders
  • Spanish Government, Ministry of Science, Innovation and Universities and Generalitat de Catalunya through the Departament de Recerca i Universitats and Departament de Salut
  • Qatar National Research Fund
  • Roslin Institute Strategic Programme Award
PUBLISHED 29 Oct 2025
https://doi.org/10.12688/f1000research.170584.1
Research Article metrics
Characterization of the Complete Mitochondrial Genome and Evaluation of COI Barcoding in Philonis inermis (Coleoptera: Curculionidae: Cryptorhynchinae) Using Genome Skimming
[version 1; peer review: 2 approved with reservations]
Alejandra Clavijo-Giraldo, Sandra Uribe Soto, Andrés Gómez-Palacio
Peer Reviewers Renee Ali; Michael J Raupach
  • Funder
  • This research was funded by the Gorgon Barrow Island Net Conservation Benefits Fund, administered by the Government of Western Australia, the Commonwealth Scientific and Industrial Research Organi-sation (CSIRO), and the Department of Biodiversity, Conservation and Attractions. Additional support was provided by Project Hermes 57653 (Universidad Nacional de Colombia, Sede Medellín).
PUBLISHED 28 Oct 2025
https://doi.org/10.12688/f1000research.171863.1
Genome Note metrics
Draft genome sequence of a predatory bacterium from northern peatland soil
[version 1; peer review: 1 approved with reservations]
Tatiana Demina, Riina Ihonen, Minna K. Männistö, Jenni Hultman
Peer Reviewers Kai Blin and Judit Szenei
  • Funders
  • Research Council of Finland
  • Kone Foundation
PUBLISHED 21 Oct 2025
https://doi.org/10.12688/f1000research.131600.2
Genome Note metrics
Revised
The complete mitochondrial genome Hainan Gymnure, Neohylomys hainanensis
[version 2; peer review: 2 approved, 1 approved with reservations]
Feiyun Tu, Xiaodan Hou, Qiujie Lu, Xiaofei Zhai
Peer Reviewers Michael Allen; Perinçek Seçkinozan Şeker; Kai He
  • Funder
  • Natural Science Foundation of Hainan Province
LATEST VERSION PUBLISHED 20 Oct 2025
https://doi.org/10.12688/f1000research.161461.3
Genome Note metrics
Revised
The genome sequence of Tethysbaena scabra (Pretus, 1991), the first known in the peracarid crustacean order Thermosbaenacea.
[version 3; peer review: 2 approved]
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 19 Sep 2025
https://doi.org/10.12688/f1000research.162894.1
Genome Note metrics
The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758
[version 1; peer review: 2 approved]
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 Marc Palmada-Flores; Greta Bellinzona
  • 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.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.159115.2
Genome Note metrics
Revised
The first mitochondrial genome of Haemagogus equinus from Jamaica
[version 2; peer review: 2 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; Alexey Makunin
  • 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
Isolation and complete genome sequence of Citrobacter bacteriophage Ursula
[version 1; peer review: 1 approved]
A.K. Golomidova, E.E. Kulikov, A.D. Efimov, I.S. Belalov, A.S. Kuznetsov, A.V. Letarov, L.I. Popova
Peer Reviewers Donus Gencer
  • 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
1-20 of 70 ARTICLES
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