Li, Ming Xu, Xiwen Liu, Shanshan Fan, Guangyi Zhou, Qian Chen, Songlin
Published in
Molecular ecology resources
Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, ...
Halladjian, Sarkis Kouril, David Miao, Haichao Groller, M Eduard Viola, Ivan Isenberg, Tobias
Published in
IEEE transactions on visualization and computer graphics
We present Multiscale Unfolding, an interactive technique for illustratively visualizing multiple hierarchical scales of DNA in a single view, showing the genome at different scales and demonstrating how one scale spatially folds into the next. The DNA's extremely long sequential structure-arranged differently on several distinct scale levels-is of...
Berry, Sophia
THE dataset contains genome sequences of Klebsiella pneumoniae strains from a global panel of clinical isolates collected in 2012.
Choufa, Caroline Tidjani, Abdoul-Razak Gauthier, Anthony Harb, Manar Lao, Julie Leblond-Bourget, Nathalie Vos, Michiel Leblond, Pierre Bontemps, Cyril
Published in
Frontiers in Microbiology
Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we...
Aphalo, Pedro J Sadras, Victor O
Published in
Journal of experimental botany
We review mechanisms for pre-emptive acclimation in plants and propose a conceptual model linking developmental and evolutionary ecology with the acquisition of information through sensing of cues and signals. The idea is that plants acquire much of the information in the environment not from individual cues and signals but instead from their joint...
Ren, Ruohan Yin, Changchuan S-T Yau, Stephen
Published in
Journal of computational biology : a journal of computational molecular cell biology
The comparison of DNA sequences is of great significance in genomics analysis. Although the traditional multiple sequence alignment (MSA) method is popularly used for evolutionary analysis, optimally aligning k sequences becomes computationally intractable when k increases due to the intrinsic computational complexity of MSA. Despite numerous k-mer...
Patil, Prakash Goudappa Jamma, Shivani N, Manjunatha Bohra, Abhishek Pokhare, Somnath Dhinesh Babu, Karuppannan Murkute, Ashutosh A. Marathe, Rajiv A.
Published in
Frontiers in Plant Science
Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron ...
Sreeharsha, Rachapudi Venkata Mudalkar, Shalini Reddy, Attipalli Ramachandra
Published in
Frontiers in Plant Science
Due to rapid industrialization, the consumption of petro-products has increased, while fossil fuel resources have been gradually depleted. There has been a resurgence of interest in plant-derived biofuels as a sustainable alternative to fossil fuels for the purpose of reducing greenhouse gas emissions. Pongamia pinnata L., which is also known as Mi...
Wu, Tao Ma, Ting Xu, Tian Pan, Li Zhang, Yanli Li, Yongjie Ning, Delu
Published in
Frontiers in Genetics
The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding of the evolution of this species. Using a h...
Casto, Amanda M Rogers, Julia H Link, Amy C Boeckh, Michael Jackson, Michael L Uyeki, Timothy M Englund, Janet A Starita, Lea M Chu, Helen Y
Published in
The Journal of infectious diseases
Residents and staff of emergency shelters for people experiencing homelessness (PEH) are at high risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The importance of shelter-related transmission of SARS-CoV-2 in this population remains unclear. It is also unknown whether there is significant spread of shelter-relat...
