A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa by Kazumichi Fujiwara, Atsushi Toyoda, Bhim B. Biswa, Takushi Kishida, Momi Tsuruta, Yasukazu Nakamura, Noriko Kimura, Shoko Kawamoto, Yutaka Sato, Toshio Katsuki, Sakura 100 Genome Consortium, Tsuyoshi Koide

“…Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. …”
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Genomic data suggest parallel dental vestigialization within the xenarthran radiation by Emerling, Christopher A, Gibb, Gillian C, Tilak, Marie-Ka, Hughes, Jonathan J, Kuch, Melanie, Duggan, Ana T, Poinar, Hendrik N, Nachman, Michael W, Delsuc, Frédéric

“…The recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. …”
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Chromosome-level genome assembly of Malus niedzwetzkyana, the mother of Rosybloom crabapple by Ruizhen Wang, Jian Quan, Boyang Liu, Yu Wei, Hengxing Liu, Ran He, Ling Guo, Leiming Dong

“…We present a high-quality chromosome-scale genome for MN with a size of 672.64 Mb, anchored to 17 chromosomes and with a high BUSCO completeness score of 98.6%, reaching the ‘gold standard’ level. …”
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Enhancing diagnostic outcomes in kidney genetic disorders: the KidGen national kidney genomics study protocol by Amali Mallawaarachchi, Hugh McCarthy, Thomas A. Forbes, Kushani Jayasinghe, Chirag Patel, Stephen I. Alexander, Tiffany Boughtwood, Jeffrey Braithwaite, Aron Chakera, Sam Crafter, Ira W. Deveson, Randall Faull, Trudie Harris, Lilian Johnstone, Matthew Jose, Anna Leaver, Melissa H. Little, Daniel MacArthur, Tessa Mattiske, Christine Mincham, Kathy Nicholls, Catherine Quinlan, Michael C. J. Quinn, Gopala Rangan, Jessica Ryan, Cas Simons, Ian Smyth, Madhivanan Sundaram, Peter Trnka, Laura Wedd, Erik Biros, Zornitza Stark, Andrew Mallett

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The promising role of nanopore sequencing in cancer diagnostics and treatment by Xinming Su, Qingyuan Lin, Bin Liu, Chuntao Zhou, Liuyi Lu, Zihao Lin, Jiahua Si, Yuemin Ding, Shiwei Duan

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A video intervention to improve patient understanding of tumor genomic testing in patients with cancer by Deloris J. Veney, Lai Y. Wei, Amanda E. Toland, Carolyn J. Presley, Heather L. Hampel, Tasleem J. Padamsee, Clara N. Lee, William J. Irvin Jr, Michael J. Bishop, James J. Kim, Shelly R. Hovick, Leigha A. Senter, Daniel G. Stover

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Solving an enigma in the tree of life, at the origins of teleost fishes by Parey, Elise, Berthelot, Camille, Roest Crollius, Hugues, Guiguen, Yann

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Characterization of genomic profiling of Mexican women with breast cancer using EndoPredict by Diana Carolina Correa Sandoval, Jose Luis Guzman Murguia, Diego Alberto Guajardo Nieto

Subjects: “…Genomics…”
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Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species by Wallner, Adrian, Klonowska, Agnieszka, Guigard, Ludivine, King, Eoghan, Rimbault, Isabelle, Ngonkeu, Eddy, Nguyen, Phuong, Béna, Gilles, Moulin, Lionel

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Responsible governance of genomics data and biospecimens in the context of broad consent: experiences of a pioneering access committee in Africa by Kobus Herbst, R Kerr, Daima Bukini, Ahmed Rebai, Akin Abayomi, P Andanda, J Mabuka, R Wamuyu, C Dandara

“…International collaboration in genomic research is gaining momentum in African countries and is often supported by external funding. …”
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UV-induced reorganization of 3D genome mediates DNA damage response by Veysel Oğulcan Kaya, Ogün Adebali

“…Abstract While it is well-established that UV radiation threatens genomic integrity, the precise mechanisms by which cells orchestrate DNA damage response and repair within the context of 3D genome architecture remain unclear. …”
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Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species by Tian-Rui Wang, Xin Ning, Si-Si Zheng, Yu Li, Zi-Jia Lu, Hong-Hu Meng, Bin-Jie Ge, Gregor Kozlowski, Meng-Xiao Yan, Yi-Gang Song

“…Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. …”
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slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes by Petr, Martin, Haller, Benjamin C., Ralph, Peter L., Racimo, Fernando

“…To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. …”
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Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing by Naiyi Xu, Linyun Zhang, Feifan Chen, Zhengfu Feng, Jiangtao Zheng, DongHua Li, Yongju Zhao, Xiangtao Kang

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Heritable human genome editing in South Africa – time for a reality check by M Ramsay, M Pepper, J de Vries, S Mahomed, E Flack-Davison

Subjects: “…Heritable human genome editing, reproductive cloning, National Health Research Ethics Council Guidelines, National Health Act, South Africa…”
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Comparative gametogenesis and genomic signatures associated with pollen sterility in the seedless mutant of grapevine by Siddhi Chavan, Satish Phalake, Sujata Tetali, Vitthal T. Barvkar, Ravindra Patil

“…This study represents a comprehensive attempt to identify putative candidate genes associated with parthenocarpic pollen sterility in grapes using genomic approaches.…”
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Protocol to Retrieve Unknown Flanking DNA Using Fork PCR for Genome Walking by Hongjing Wu, Hao Pan, Haixing Li

“…PCR-based genome walking is one of the prevalent techniques implemented to acquire unknown flanking genomic DNAs. …”
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Cancer phylogenetic tree inference at scale from 1000s of single cell genomes by Salehi, Sohrab, Dorri, Fatemeh, Chern, Kevin, Kabeer, Farhia, Rusk, Nicole, Funnell, Tyler, Williams, Marc J., Lai, Daniel, Andronescu, Mirela, Campbell, Kieran R., McPherson, Andrew, Aparicio, Samuel, Roth, Andrew, Shah, Sohrab P., Bouchard-Côté, Alexandre

“…A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations. …”
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Genome Characteristic of NDM-5-Producing Klebsiella Quasipneumoniae and Klebsiella Pneumoniae in China by Chen L, Liu R, Ye H, Qian J, Lou D

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Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC by William Boulton, Asaf Salamov, Igor V. Grigoriev, Sara Calhoun, Kurt LaButti, Robert Riley, Kerrie Barry, Allison A. Fong, Clara J. M. Hoppe, Katja Metfies, Kersten Oetjen, Sarah Lena Eggers, Oliver Müller, Jessie Gardner, Mats A. Granskog, Anders Torstensson, Marc Oggier, Aud Larsen, Gunnar Bratbak, Andrew Toseland, Richard M. Leggett, Vincent Moulton, Thomas Mock

“…The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. …”
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