Results 61 to 70 of about 1,556 (147)

Graph Pangenomes Track Genetic Variants for Crop Improvement

International Journal of Molecular Sciences, 2022
Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated ...
Amir Hameed, Pawel Poznanski, Anna Nadolska-Orczyk, Waclaw Orczyk   +3 more
openaire   +2 more sources

Revisiting the Molecular Roadmap for Sugar Crops: Genome Reading, Trait Writing and Variety Redesigning

Plant Biotechnology Journal, EarlyView.
ABSTRACT Sugar crops, including but not limited to sugarcane, sugar beet, sweet sorghum and stevia, are major sources of sugar production in the world. However, conventional breeding approaches, limited by long breeding cycles, low efficiency and restricted capacity to improve complex traits in sugar crops, are increasingly insufficient to address the ...
Peilin Wang, Qibin Wu, Wenzhi Wang, Prakash Lakshmanan, Yangrui Li, Khushi Muhammad, Yuguang Wang, Youxiong Que   +7 more
wiley   +1 more source

Graph construction method impacts variation representation and analyses in a bovine super-pangenome

Genome Biology, 2023
Background Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown.
Alexander S. Leonard, Danang Crysnanto, Xena M. Mapel, Meenu Bhati, Hubert Pausch   +4 more
doaj   +1 more source

Molecular insights and translational opportunities to enhance heat tolerance in rice

The Plant Genome, Volume 19, Issue 3, September 2026.
Abstract Heat stress is an increasingly serious threat to rice (Oryza sativa L.) productivity, yet the genetic and regulatory architecture underlying thermotolerance remain poorly resolved and fragmented across studies. Earlier research focused on individual pathways or specific developmental stages; however, recent advances now support an integrated ...
Prabhat Rana, Chanderkant Chaudhary, Rajat Pruthi, Mansi Sharma, Bhupinderjeet Singh, Ravi Kiran Reddy Kondi, Mallesham Bulle, Prasanta K. Subudhi   +7 more
wiley   +1 more source

Cluster efficient pangenome graph construction with nf-core/pangenome

Bioinformatics
Abstract Motivation Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues.
Simon Heumos, Michael L Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino, Peter Heringer, Philipp Ehmele, Pjotr Prins, Erik Garrison, Sven Nahnsen   +9 more
openaire   +4 more sources

PharmVar GeneFocus: CYP1A2—Clinical Impact, Genetic Variation, and Updated Nomenclature

Clinical Pharmacology &Therapeutics, Volume 120, Issue 2, Page 313-323, August 2026.
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP1A2 gene. CYP1A2 plays a crucial role in the biotransformation of several commonly used drugs, including antipsychotics, antidepressants, anxiolytics, and methylxanthines.
Katalin Monostory, Gonzalo Villapalos Garcia, Dora Koller, Solomon Adams, Chad A. Bousman, Evangelia Eirini Tsermpini, Michelle Whirl‐Carrillo, Amy J. Turner, Volker M. Lauschke, Mohamed Nagy, Erin C. Boone, Teri E. Klein, Pablo Zubiaur, Andrea Gaedigk   +13 more
wiley   +1 more source

PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome‐based RNA‐seq data analysis

Journal of Integrative Plant Biology, Volume 68, Issue 7, Page 2001-2017, July 2026.
PanGraphRNA is an easy‐to‐use platform that improves RNA‐seq analysis by using graph pangenomes instead of a single reference genome. It increases read alignment accuracy, detects important genes missed by traditional methods, and works across major crops, helping researchers obtain more reliable transcriptome results for diverse plant research and ...
Yifan Bu, Zhixu Qiu, Wen Sun, Yishui Han, Yifan Liu, Jing Yang, Minggui Song, Zenglin Li, Songyu Liu, Yuzhou Zhang, Chuang Ma   +10 more
wiley   +1 more source

Pangenome analysis reveals the genetic mechanism underlying high‐altitude adaptation in Qinghai–Xizang (Tibet) Plateau Rhododendron

Journal of Integrative Plant Biology, Volume 68, Issue 7, Page 2166-2188, July 2026.
Pan‐genome analysis reveals that high‐altitude Rhododendron species resist alpine cold stress by rapidly sensing and engaging the chilling response pathway and genes that directly and indirectly protect the plant from UV radiation. Heritable genomic features such as long terminal repeats contribute to the adaptive diversification of Rhododendron ...
Haoyang Zhou, Zhongping Xu, Fanhuang Zeng, Haiyu Sang, Zhenhua Liu, Miao Sun, Qiang Fu, Kaige Zhao, Daming Tan, Manzhu Bao, Shuangxia Jin, Xiuqun Liu   +11 more
wiley   +1 more source

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study

BMC Genomics
Background The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire ...
Harpreet Kaur, Laura M. Shannon, Deborah A. Samac   +2 more
doaj   +1 more source

Integrative host–microbiome modeling uncovers the implication of oral–gut translocation in advanced cirrhosis

iMeta, Volume 5, Issue 3, June 2026.
Liver cirrhosis is associated with profound disruption of host–microbiome metabolic interactions. Using paired oral and fecal metagenomics combined with genome‐scale metabolic modeling, we investigated how microbial translocation along the oral–gut axis influences microbial metabolism at different cirrhosis severities.
Yi Jin, Frederick Clasen, Fernando Garcia‐Guevara, Sania Arif, Robert Schierwagen, Gholamreza Bidkhori, Michael Praktiknjo, Maximilian J. Brol, Frank E. Uschner, Florence A. Castelli, Nicolas Pons, Benoit Quinquis, Nathalie Galleron, Kevin Da Silva, Christophe Junot, Debbie L. Shawcross, David L. Moyes, Rajiv Jalan, S. Dusko Ehrlich, Vishal C. Patel, Jonel Trebicka, Saeed Shoaie   +21 more
wiley   +1 more source