Results 81 to 90 of about 52,855 (250)

Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli

Frontiers in Microbiology, 2016
Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting
Shixiang Sun, Jingfa Xiao, Huiyong Zhang, Zhang Zhang   +3 more
doaj   +1 more source

Two Routes to Land: Genomic Underpinnings of Parallel Aerial Egg Deposition in Aquatic Old‐World Pila and New‐World Pomacea (Ampullariidae)

Advanced Science, EarlyView.
Comparative genomics of Gondwana‐diverged Pila and Pomacea reveals parallel evolution of aerial oviposition. Convergent chromosomal rearrangements reshape regulatory landscapes within topologically associating domains. Lineage‐specific gene family expansions and viral‐derived perivitelline proteins (PV1) underpin desiccation resistance.
Yufei Zhou, Huawei Mu, Xueying Nie, Yue Gao, Hui Wang, Ling Fang, Tiangang Luan, Monthon Ganmanee, Jian‐Wen Qiu, Jin Sun, Jack Chi‐Ho Ip   +10 more
wiley   +1 more source

Ribo-seq enlightens codon usage bias [PDF]

DNA Research, 2017
Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of
Paulet, Damien, David, Alexandre, Rivals, Eric   +2 more
openaire   +3 more sources

Analysis of factors shaping synonymous codon usage in pseudorabies virus

浙江大学学报. 农业与生命科学版, 2007
Synonymous codon usage and the main factors shaping codon usage in pseudorabies virus were reported in order to understand the architecture and evolution of pseudorabies virus.
YIN Hua-ping, GUO Wan-zhu, XU Zhi-wen, YANG Li   +3 more
doaj   +1 more source

The Selective Advantage of Synonymous Codon Usage Bias in Salmonella. [PDF]

PLoS Genetics, 2016
The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is
Gerrit Brandis, Diarmaid Hughes
doaj   +1 more source

Transposase‐Assisted Donor Tethering Boosts Large‐Fragment HDR in Plants

Advanced Science, EarlyView.
A transposase‐assisted donor tethering strategy is developed to enhance homology‐directed repair in plants. By recruiting donor DNA to double‐strand breaks and synergizing with repair pathway reprogramming and transcription‐coupled donor design, this system markedly improves large‐fragment targeted insertion efficiency, providing a robust platform for ...
Sha Wei, Kai Zhang, Shuke Deng, Jinjie Chen, Xiaomei Huang, Jingfei Guo, Yuqing Wu, Yingjie Guo, Zhen Liang   +8 more
wiley   +1 more source

A study on the codon usage bias of arenavirus common genes

Frontiers in Microbiology
IntroductionThe Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus, Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between the different genera has not yet been studied comparatively.MethodsWe retrieved the ...
Pablo Daniel Thomas, María Florencia Ferrer, Mauricio J. Lozano, Ricardo Martín Gómez   +3 more
doaj   +1 more source

DMS‐MaPseq and DREEM Analyses Implicate the Critical Role of RNA Structural Dynamics in Turnip Yellow Mosaic Virus Pathogenicity

Advanced Science, EarlyView.
RNA structural profiling of Turnip Yellow Mosaic Virus by DMS‐MaPseq and DREEM analyses uncover that viral genome‐wide RSS is highly complicated and heterogeneous, with alternative RSSs widely distributed across the genome. Notably, the viral 3’ tRNA‐like structure adopts alternative conformations in vivo.
Jiaying Zhu, Changhao Li, Chisimbily Onyia, Xindi Li, Xingxing Yan, Songxiao Zhong, Taerin Oh, Xiuren Zhang   +7 more
wiley   +1 more source

PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes

Advanced Science, EarlyView.
A plant genomic foundation model pre‐trained on 12 species enables both accurate gene prediction and de novo gene design. Through AI‐human knowledge screening, seven designed sequences showed transcriptional activity in plants, with two expressing stable proteins—demonstrating the first DNA‐RNA‐protein expression of LLM‐generated genes in plants and ...
Changhao Li, Qizhe Zhang, Hanchen Chen, Kepeng Lin, Chengfang Luo, Mengying Yang, Wei Xu, Fan Yao, Jianbing Yan, Qing‐Yong Yang, Xuehai Hu   +10 more
wiley   +1 more source

Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains

BMC Genomics
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species.
Wei Gao, Xiaodie Chen, Jing He, Ajia Sha, Yingyong Luo, Wenqi Xiao, Zhuang Xiong, Qiang Li   +7 more
doaj   +1 more source