Genomics and Genetics

Genomics and Genetics

Genome Sequencing

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https://doi.org/10.12688/f1000research.144155.1
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Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
[version 1; peer review: 2 approved with reservations]
Efratenta Katherina Depari, Nurheni Wijayanto, Lina Karlinasari, Mohamad Rafi, Iskandar Zulkarnaen Siregar
Peer Reviewers Hoang Dang Khoa Do; Maria Stefanie Dwiyanti
  • Funder
  • Beasiswa Pendidikan Pascasarjana Dalam Negeri (BPPDN) 2019
PUBLISHED 05 Apr 2024
https://doi.org/10.12688/f1000research.138150.3
Genome Note metrics
Revised
Plastid genome of Passiflora tripartita var. mollissima (poro-poro) from Huánuco, Peru
[version 3; peer review: 2 approved]
Flavio Aliaga, Mario Zapata-Cruz, Silvia Ana Valverde-Zavaleta
Peer Reviewers Rahul G Shelke; Abdullah Abdullah
  • Funder
  • Plant Sience Laboratory
LATEST VERSION PUBLISHED 19 Feb 2024
https://doi.org/10.12688/f1000research.129958.4
Research Article metrics
Revised
The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophilism
[version 4; peer review: 2 approved, 1 approved with reservations]
Ryoma Sato, Yuri Kondo, Sakae Agarie
Peer Reviewers Qijie Guan; Xin-Guang Zhu; Zbigniew Miszalski
  • Funder
  • JSPS KAKENHI
LATEST VERSION PUBLISHED 04 Jan 2024
https://doi.org/10.12688/f1000research.138571.2
Genome Note metrics
Revised
The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione)
[version 2; peer review: 3 approved]
Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov, Carolyn J. Hogg
Peer Reviewers Natalie Forsdick; Sandra Goutte; Matheus Azambuja
  • Funders
  • Australian Federal Government Bushfire Recovery Scheme
  • Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
  • NCRIS supported Bioplatforms Australia Threatened Species Initiative
LATEST VERSION PUBLISHED 16 Nov 2023
https://doi.org/10.12688/f1000research.122019.2
Research Article metrics
Revised
Observation of SARS-CoV-2 genome characteristics and clinical manifestations within eight family clusters from GH and GK clades in Jakarta, Indonesia
[version 2; peer review: 2 approved with reservations, 2 not approved]
Fera Ibrahim, Augustine Natasha, Andi Yasmon, Fithriyah Fithriyah, Anis Karuniawati, Rivia Gina Rahmawaty, Yulia Saharman, Pratiwi Sudarmono
Peer Reviewers So Nakagawa; Serafeim C. Chaintoutis; Pakorn Aiewsakun; Gusti N Mahardika
  • Funder
  • Direktorat Riset and Pengembangan, Universitas Indonesia
LATEST VERSION PUBLISHED 16 Oct 2023
https://doi.org/10.12688/f1000research.130251.2
Brief Report metrics
Revised
Multiomic sequencing of paired primary and metastatic small bowel carcinoids
[version 2; peer review: 2 approved]
Mackenzie D. Postel, Sourat Darabi, James R. Howe, Winnie S. Liang, David W. Craig, Michael J. Demeure
Peer Reviewers Phillip Stafford; Anela Blažević
  • Funder
  • WHH Foundation
LATEST VERSION PUBLISHED 04 Oct 2023
https://doi.org/10.12688/f1000research.127937.2
Genome Note metrics
Revised
Characterization of the Complete Chloroplast Genome of Gaultheria nummularioides D.Don 1825 (Ericaceae)
[version 2; peer review: 2 approved]
Xiao-Juan Cheng, Yan-Ling Xu, Catherine M. Bush, Yan-Jun Lin, Xin-Yu Du, Lu Lu
Peer Reviewers Xing Huang; Hoang Dang Khoa Do
  • Funders
  • Program Innovative Research Team in Science and Technology in Yunnan Province
  • National Natural Science Foundation of China
  • Scientific Research Fund Project of Yunnan Education Department
LATEST VERSION PUBLISHED 04 Sep 2023
https://doi.org/10.12688/f1000research.135174.1
Genome Note metrics
Complete mitochondrial genome and the phylogenetic position of a new Annelida species belonging to the genus Syllis
[version 1; peer review: 1 approved with reservations, 1 not approved]
Jun Young Chae, JinHo Kim, Tae-Wook Kang, Jae il Lee, Hyung-Ho Lee, Moo-Sang Kim
Peer Reviewers Yingdong Li; Zhi Wang
  • Funder
  • National Research Foundation
PUBLISHED 31 Aug 2023
https://doi.org/10.12688/f1000research.131326.2
Research Article metrics
Revised
Genetic diversity and population structure of Capitulum mitella (Linnaeus, 1767) in Fujian (China) revealed by mtDNA COI sequences
[version 2; peer review: 2 approved]
Rouxin Sun, Zhilan Zhang, Qiong Wu, Peng Xiang, Yanguo Wang, Bingpeng Xing
Peer Reviewers Jun Sun; Alex Nahnson Nehemia
  • Funders
  • The Marine Biological Sample Museum
  • Department of Science and Technology of Fujian Province, China
  • Natural Science Foundation of Xiamen, China
LATEST VERSION PUBLISHED 13 Jul 2023
https://doi.org/10.12688/f1000research.131283.2
Genome Note metrics
Revised
The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758
[version 2; peer review: 2 approved]
Glenn Chang, Samantha Jones, Sreeja Leelakumari, Jahanshah Ashkani, Luka Culibrk, Kieran O'Neill, Kane Tse, Dean Cheng, Eric Chuah, Helen McDonald, Heather Kirk, Pawan Pandoh, Sauro Pari, Valeria Angelini, Christopher Kyle, Giorgio Bertorelle, Yongjun Zhao, Andrew Mungall, Richard Moore, Sibelle Vilaça, Steven Jones
Peer Reviewers Richard Challis; Cinta Pegueroles
  • Funders
  • Canadian BioGenome Project
  • CanSeq150 program
  • European Union's Horizon 2020 Research and Innovation Programme (Marie Skłodowska-Curie grant agreement)
LATEST VERSION PUBLISHED 27 Jun 2023
https://doi.org/10.12688/f1000research.127990.2
Genome Note metrics
Revised
Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya
[version 2; peer review: 2 approved]
Rachael Gachogo, Irene Karegi, Brian Ogoti, Victor Musyoki, Dino Martins, Frank Onyambu, Joseph Kamau
Peer Reviewers Meenakshi S. Iyer; Janet Midega
LATEST VERSION PUBLISHED 16 May 2023
https://doi.org/10.12688/f1000research.121402.2
Genome Note metrics
Revised
Whole genome sequencing data of Candida krusei, the pathogen causing Candidaemia, from Department of Parasitology Culture Collection, Faculty of Medicine Universitas Indonesia
[version 2; peer review: 2 approved]
Fadilah Fadilah, Robiatul Adawiyah, Retno Wahyuningsih, Anna Rozaliyani, Ayu Eka Fatril, Rafika Indah Paramita, Linda Erlina, Khaerunissa Anbar Istiadi
Peer Reviewers Xuepeng Sun; Atanu Banerjee
  • Funder
  • Universitas Indonesia
LATEST VERSION PUBLISHED 29 Mar 2023
https://doi.org/10.12688/f1000research.130734.1
Genome Note metrics
The first genome sequence of Anopheles squamous from Macha, Zambia
[version 1; peer review: 2 approved]
Valerie T. Nguyen, Travis C. Collier, Sangwoo Seok, Xiaodi Wang, Monicah M. Mburu, Limonty Simubali, Mary E. Gebhardt, Douglas E. Norris, Yoosook Lee
Peer Reviewers Megan A. Riddin; Tara Roth
  • Funders
  • Department of Entomology and Nematology, University of Florida
  • University of Florida
  • Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health
  • National Institutes of Health
  • College of Agricultural and Life Sciences, University of Florida
  • Bloomberg Philanthropies
PUBLISHED 24 Mar 2023
https://doi.org/10.12688/f1000research.131637.1
Genome Note metrics
The complete genome sequences of Penicillium concavorugulosum
[version 1; peer review: 1 not approved]
Khosi Ramachela, Galaletsang Segone
Peer Reviewers Anthony A. Adegoke
PUBLISHED 23 Mar 2023
https://doi.org/10.12688/f1000research.131600.1
Genome Note metrics
The complete mitochondrial genome Hainan Gymnure Neohylomys hainanensis
[version 1; peer review: 2 approved with reservations]
Feiyun Tu, Xiaodan Hou, Qiujie Lu, Xiaofei Zhai
Peer Reviewers Michael Allen; Perinçek Seçkinozan Şeker
  • Funder
  • Natural Science Foundation of Hainan Province
PUBLISHED 16 Mar 2023
https://doi.org/10.12688/f1000research.129413.1
Genome Note metrics
The complete mitochondrial genome of the hybrid snow crab Chionoecetes opilio (♀) × C. japonicus (♂) (Crustacea: Decapoda: Majoidea) and its phylogenetic analysis
[version 1; peer review: 1 approved, 1 approved with reservations]
Bong Han Yun, Yong Hwi Kim, Ho-Seop Han, Hye Jin Kim, Jong Yeon Park, In-Chul Bang
Peer Reviewers Jongwoo Jung; Christopher M Austin
  • Funders
  • Soonchunhyang University
  • Ministry of Oceans and Fisheries
PUBLISHED 20 Feb 2023
https://doi.org/10.12688/f1000research.127935.1
Genome Note metrics
Draft genome of a clinical Pseudomonas qingdaonensis isolate from a hospitalized patient at Kenyatta National Hospital, Kenya
[version 1; peer review: 2 approved]
Brian Ogoti, Racheal Gachogo, Frank Onyambu
Peer Reviewers Gerald Mboowa; Aquillah Kanzi
  • Funder
  • Center of Molecular Biosciences
PUBLISHED 21 Dec 2022
https://doi.org/10.12688/f1000research.129212.1
Genome Note metrics
An updated version of the Madagascar periwinkle genome
[version 1; peer review: 2 approved]
Clément Cuello, Emily Amor Stander, Hans J. Jansen, Thomas Dugé De Bernonville, Audrey Oudin, Caroline Birer Williams, Arnaud Lanoue, Nathalie Giglioli Guivarc'h, Nicolas Papon, Ron P. Dirks, Michael Krogh Jensen, Sarah Ellen O'Connor, Sébastien Besseau, Vincent Courdavault
Peer Reviewers Evangelos Tatsis; Amit Rai
  • Funders
  • ARD CVL Biopharmaceutical program of the Région Centre-Val de Loire
  • Agence Nationale de la Recherche
  • Horizon 2020
PUBLISHED 21 Dec 2022
https://doi.org/10.12688/f1000research.124719.1
Genome Note metrics
Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri
[version 1; peer review: 2 approved with reservations]
Osamu Nishimura, Kazuaki Yamaguchi, Yuichiro Hara, Kaori Tatsumi, Jeramiah J Smith, Mitsutaka Kadota, Shigehiro Kuraku
Peer Reviewers Vincent Laudet; Daniel Ocampo Daza
  • Funders
  • RIKEN Center for Biosystems Dynamics Research
  • Japan Society for the Promotion of Science
  • National Science Foundation
PUBLISHED 08 Nov 2022
https://doi.org/10.12688/f1000research.121947.1
Genome Note metrics
Identification of the exuviae of larva from Teinopalpus aureus Mell, 1923 using the complete mitochondrial genome
[version 1; peer review: 2 approved with reservations]
Lei-Lei Liu, Li-Hua Zhang, Guo-Hang Weng, Wei-Qin Wang, Xi-Cheng Gong, Shan-Biao Wang, Shu-Sheng Zhang
Peer Reviewers Chang-Bae Kim; Xue-yan Li
  • Funder
  • Zhejiang Normal University
PUBLISHED 31 Oct 2022
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