Results 61 to 70 of about 174,716 (299)

A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence

Frontiers in Plant Science
Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species.
Meiye Jiang, Meiye Jiang, Meiye Jiang, Meili Chen, Meili Chen, Jingyao Zeng, Jingyao Zeng, Zhenglin Du, Zhenglin Du, Jingfa Xiao, Jingfa Xiao, Jingfa Xiao   +11 more
doaj   +1 more source

Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability

BMC Genomics, 2019
Background Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of ...
Dekang Zhu, Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu, Yu You, Xiaoyue Chen, Anchun Cheng   +16 more
doaj   +1 more source

PRAP: Pan Resistome analysis pipeline

BMC Bioinformatics, 2020
Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species.
Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi   +7 more
doaj   +1 more source

Distributed hybrid-indexing of compressed pan-genomes for scalable and fast sequence alignment.

PLoS ONE, 2021
Computational pan-genomics utilizes information from multiple individual genomes in large-scale comparative analysis. Genetic variation between case-controls, ethnic groups, or species can be discovered thoroughly using pan-genomes of such subpopulations.
Altti Ilari Maarala, Ossi Arasalo, Daniel Valenzuela, Veli Mäkinen, Keijo Heljanko   +4 more
doaj   +1 more source

Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts

, 2014
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades.
AlKindy, Bassam, Bahi, Jacques M., Couchot, Jean-François, Guyeux, Christophe, Salomon, Michel   +4 more
core   +1 more source

A super pan-genomic landscape of rice

Cell Research, 2022
AbstractPan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.
Lianguang Shang, Xiaoxia Li, Huiying He, Qiaoling Yuan, Yanni Song, Zhaoran Wei, Hai Lin, Min Hu, Fengli Zhao, Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou, Jiayang Li, Zuofeng Zhu, Guosheng Xiong, Jue Ruan, Qian Qian   +43 more
openaire   +2 more sources

Screening and epitope characterization of Nidogen‐2‐specific nanobodies

FEBS Open Bio, EarlyView.
Camel immunization and phage display were employed to generate high‐affinity VHH nanobodies against Nidogen‐2. After library construction, biopanning, ELISA screening, sequencing, and recombinant expression, selected nanobodies were purified and characterized, leading to the preliminary exploration of a nanobody‐based sandwich ELISA for specific ...
Jianchuan Wen, Qianqian Cui, Zhongyun Lan, Yingjun Wang, Shuaiying Zhao, Wenxuan Feng, Yunfeng Liu, Qiting Huang, Dongna Zhang, Jianfeng Xu   +9 more
wiley   +1 more source

Environmental shaping of codon usage and functional adaptation across microbial communities. [PDF]

, 2013
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the ...
Achtman, Altschul, Arumugam, Boto, Botzman, Bruggemann, Burke, Caro-Quintero, Chen, Diene, Donner, Foerstner, Forsberg, Gill, Hershberg, Horvath, Hunyadkurti, Huson, Ikemura, István Nagy, Jensen, Johnson, Kanaya, Kanehisa, Karlin, Keeling, Keller, Kristian Vlahoviček, Kuo, Larimer, Malmstrom, Martin, Maša Roller, McDaniel, McDowell, Mira, Myers, Oda, Plotkin, R Development Core Team, Retchless, Rocha, Sharp, Sharp, Sowell, Staley, Supek, Supek, Tatusov, Tettelin, Tina Perica, Tringe, Tuller, Tuller, Tuller, Turnbaugh, Tyson, Vedran Lucić, Venter, Verberkmoes, Vieira-Silva, Whitman, Willenbrock, Wilmes   +63 more
core   +1 more source

Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function

FEBS Open Bio, EarlyView.
We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke, Michal Banasik, Rokas Juodeikis, Martin J. Warren, Richard W. Pickersgill   +4 more
wiley   +1 more source

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains.

PLoS ONE
Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products.
Md Shahedur Rahman, Md Ebrahim Khalil Shimul, Md Anowar Khasru Parvez   +2 more
doaj   +1 more source