Results 1 to 10 of about 174,716 (299)

IPGA: A handy integrated prokaryotes genome and pan‐genome analysis web service

iMeta, 2022
Pan‐genomics is one of the most powerful means to study genomic variation and obtain a sketch of genes within a defined clade of species. Though there are a lot of computational tools to achieve this, an integrated framework to evaluate their performance 
Dingzhong Sun, Jinfeng Wang, Wenyu Shi
exaly   +2 more sources

PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks. [PDF]

Nat Commun
Pan-genome analysis is a crucial method for studying genomic dynamics. By creating pan-genome maps for prokaryotic organisms, we can gain valuable insights into their genetic diversity and ecological adaptability.
Bu C, Zhang H, Zhang F, Liang W, Gao H, Zhao J, Lv F, Xue R, Liu Q, Zhang Z, Jin Z, Xiao J.   +11 more
europepmc   +2 more sources

From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding. [PDF]

Front Plant Sci
With the rapid advancement of sequencing technologies and bioinformatics, coupled with significant progress in sequencing efficiency and reduced costs, substantial breakthroughs have been achieved in plant functional genomics, evolutionary genetics, and ...
Liu C, Xu H, Li Z, Wang Y, Zhang J, Qiao S, Zhang H.   +6 more
europepmc   +2 more sources

Integrating pan-genome with metagenome for microbial community profiling

Computational and Structural Biotechnology Journal, 2021
Advances in sequencing technology have led to the increased availability of genomes and metagenomes, which has greatly facilitated microbial pan-genome and metagenome analysis in the community.
Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning   +3 more
doaj   +1 more source

Oryza pan-genomics: A new foundation for future rice research and improvement

Crop Journal, 2021
The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized genomic research in plants. However, rice pan-genomic studies so far have been limited mostly
Chao Huang, Zhuo Chen, Chengzhi Liang
doaj   +1 more source

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

Frontiers in Plant Science, 2021
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world.
Pradeep Ruperao, Nepolean Thirunavukkarasu, Prasad Gandham, Sivasubramani Selvanayagam, Mahalingam Govindaraj, Baloua Nebie, Eric Manyasa, Rajeev Gupta, Roma Rani Das, Damaris A. Odeny, Harish Gandhi, David Edwards, Santosh P. Deshpande, Abhishek Rathore   +13 more
doaj   +1 more source

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Genome Biology, 2021
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have ...
Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal   +10 more
doaj   +1 more source

Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity

Microbiology Spectrum, 2022
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used ...
Na Liu, Danping Liu, Kexin Li, Songnian Hu, Zilong He   +4 more
doaj   +1 more source

The phased pan-genome of tetraploid European potato [PDF]

Nature
Sergio Tusso, Manish Goel, Raúl Y Wijfjes   +2 more
exaly   +2 more sources

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Nature Communications, 2023
Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O.
Yong Zhou, Zhichao Yu, Dmytro Chebotarov, Kapeel Chougule, Zhenyuan Lu, Luis F. Rivera, Nagarajan Kathiresan, Noor Al-Bader, Nahed Mohammed, Aseel Alsantely, Saule Mussurova, João Santos, Manjula Thimma, Maxim Troukhan, Alice Fornasiero, Carl D. Green, Dario Copetti, David Kudrna, Victor Llaca, Mathias Lorieux, Andrea Zuccolo, Doreen Ware, Kenneth McNally, Jianwei Zhang, Rod A. Wing   +24 more
doaj   +1 more source