A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae by Changwei Bi, Ning Sun, Zhuangwei Hou, Xiaogang Dai, Huaitong Wu, Fuchuan Han, Zefu Wang, Tongming Yin

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Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs by Guangquan Lv, Peiyu Yang, Ao Guo, Minghao Cao, Dong Li, Zhe Liu, Mingyu Wang, Jingchun Sun, Rongrong Ding, Taiyong Yu

“…Abstract Background Traditional genomic analysis relies on a single reference genome, which struggles to effectively characterize the genetic diversity among populations. …”
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A chromosome-level reference genome for the critically endangered Southern Corroboree frog (Pseudophryne corroboree) [version 1; peer review: 2 approved] by Lee Berger, Tiffany A. Kosch, Deon Gilbert, Andrew J. Crawford, David Hunter, Damian Goodall, Linelle Abueg, Michael McFadden, Giulio Formenti, Joanna Collins, Nivesh Jain, Tatiana Tilley, Conor Whelan, Brian O'Toole, Matthieu Muffato, Ira Cooke, Olivier Fedrigo, Bethan Yates, Erich D. Jarvis, Jennifer Balacco, Lee F. Skerratt

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Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference by Michael V. Westbury, Eline D. Lorenzen

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Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression by Jianchao Hu, Lu Gui, Zhongzi Wu, Lusheng Huang

“…Finally, we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs. …”
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Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights by Daniel Wibberg, Zofia Bakuła, Iván García-Cunchillos, Jan Gawor, Robert Gromadka, Anna Karnkowska, Jacek Bielecki, Tomasz Jagielski

“…Abstract Background Prototheca (Chlorophyta: Trebouxiophyceae) is a genus of non-photosynthetic microalgae that causes increasingly frequent infections in both humans and animals, collectively referred to as protothecosis The genetic landscape of the Prototheca algae has remained largely uncharted until recent advances in sequencing and genomics. …”
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The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs by Heng Du, Lei Zhou, Zhen Liu, Yue Zhuo, Meilin Zhang, Qianqian Huang, Shiyu Lu, Kai Xing, Li Jiang, Jian-Feng Liu

“…Based on the deep sequencing (~25.95×) of these pigs, we identify 63.62 million genomic variants, and provide a population-specific reference panel to improve the imputation performance of Chinese domestic pig populations. …”
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Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types by Jin Li, Christopher Cullis

“…Overall, this study presents the first high-quality genome assembly of marama bean, offering a valuable genomic reference for understanding its unique biology and highlighting its potential for crop improvement in challenging environments.…”
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Extending gene set variation analysis with a reference dataset to stabilize scores by Lorin Towle-Miller, William Jordan, Alexandre Lockhart, Johannes Freudenburg, Aman Virmani, Mandy Bergquist, Jeffrey Miecznikowski, Will Powley

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Progress in plant genome sequencing: research directions by M. K. Bragina, D. A. Afonnikov, E. A. Salina

“…In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.…”
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Sequence-based prioritization of i-Motif candidates in the human genome by Veronica Remori, Michela Prest, Mauro Fasano, Mauro Fasano

“…The human reference genome (hg38) was scanned using a custom regular expression targeting cytosine-rich motifs, followed by scoring each sequence with the PSSM. …”
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Lactuca super-pangenome provides insights into lettuce genome evolution and domestication by Shuai Cao, Nunchanoke Sawettalake, Lisha Shen

“…Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. …”
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The Impact of Narratives on the Legal and Regulatory Discourse of Heritable Human Genome Editing by Olga C Pandos

“…Notably, Heritable Human Genome Editing (HHGE), which refers to the editing of germline cells for the purpose of reproduction, has significant potential for therapeutic application. …”
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Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS) by Pei-Ju Chin, Jaysheel D. Bhavsar, Trent J. Bosma, Madolyn L. MacDonald, Shawn W. Polson, Arifa S. Khan

“…In this study, we have refined our original comprehensive Reference Virus Database (RVDB) for greater accuracy of virus detection with a reduced computational burden. …”
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The first chromosome-level genome of the lappet moth Trabala vishnou (Lepidoptera: Lasiocampidae) by Ya-Lin Pu, Tian-Zhu Yan, Hao-Ran Wang, Kai Gao, Hai-Peng Zhao

“…A total of 1,630 non-coding RNAs and 12,895 protein-coding genes have been identified within the genome. The first chromosome-level genome of T. vishnou serves as a valuable reference for elucidating the evolution of functional traits in Lasiocampidae family and will facilitate the development of strategies for controlling defoliating pests.…”
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Chromosome-level genome assembly of Marco Polo Blister Beetle (Hycleus marcipoli) by Wenhui Zhu, Delong Guan, Jiawei Wang, Linlin Nie, Binbin Yao, Sheng-Quan Xu

“…Despite the availability of fragmented genomes of Hycleus, a high-quality, chromosome-level genome reference is not yet available for this diverse genus. …”
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Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection by Melissa Rincon-Sandoval, Rishi De-Kayne, Stephen D. Shank, Stacy Pirro, Alfred Ko’ou, Linelle Abueg, Alan Tracey, Jackie Mountcastle, Brian O’Toole, Jennifer Balacco, Giulio Formenti, Erich D. Jarvis, Dahiana Arcila, Sergei L. Kosakovsky Pond, Aaron Davis, Devin D. Bloom, Ricardo Betancur-R

“…Here, we generate and analyze one long-read reference genome and 66 short-read whole genome assemblies, in conjunction with genomic data for 54 additional species. …”
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Universal amplification and sequencing of foot-and-mouth disease virus complete genomes using nanopore technology by Andrew E. Shaw, Kebaneilwe Lebani, Lina González Gordon, Ugonna E. Ihearahu, Jemma Wadsworth, Hayley M. Hicks, Noemi Polo, Graham Freimanis, Dennis Muhanguzi, Chandana Tennakoon, Richard J. Orton, Nick J. Knowles, Antonello Di Nardo, Ryan A. Waters, Barend MdeC Bronsvoort, Donald P. King

“…A bioinformatics pipeline was used to assemble genomes based upon blastn and reference assembly. …”
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Oar_Finn: the genome assembly and annotation of an exceptionally fertile Finnsheep (Ovis aries) Ewe by Juha Kantanen, Melak Weldenegodguad, Kisun Pokharel

“…Abstract Objectives Finnsheep, a highly prolific breed of sheep, has been globally exported for improving fertility traits of many sheep breeds. Published genomic studies of Finnsheep have been based on Texel and Rambouillet reference genomes, which may not capture its unique genetic features. …”
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The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima by Qianqian Mu, Zijian Li, Mingyang Liu, Baojun Zhao, Zhihui Yang, Zhenmin Bao, Jingjie Hu, Pingping Liu

“…However, the lack of genomic reference limits our in-depth understanding of this species in genome-based breeding, conservation, evolution and adaptation. …”
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