[HTML][HTML] Plant pan-genomics: Recent advances, new challenges, and roads ahead

W Li, J Liu, H Zhang, Z Liu, Y Wang, L Xing… - Journal of Genetics and …, 2022 - Elsevier
Pan-genomics can encompass most of the genetic diversity of a species or population and
has proved to be a powerful tool for studying genomic evolution and the origin and …

[HTML][HTML] Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes

S Naithani, CH Deng, SK Sahu, P Jaiswal - Biomolecules, 2023 - mdpi.com
The availability of multiple sequenced genomes from a single species made it possible to
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …

Plant pangenome: impacts on phenotypes and evolution

C Tranchant-Dubreuil, M Rouard, F Sabot - Annual Plant Reviews, 2019 - hal.science
With the emergence of low-cost high-throughput sequencing technologies, numerous
studies have shown that a single genome is not enough to identify all the genes present in a …

Graph-based pan-genomes: increased opportunities in plant genomics

S Wang, YQ Qian, RP Zhao, LL Chen… - Journal of …, 2023 - academic.oup.com
Due to the development of sequencing technology and the great reduction in sequencing
costs, an increasing number of plant genomes have been assembled, and numerous …

Plant pan-genomics comes of age

L Lei, E Goltsman, D Goodstein, GA Wu… - Annual Review of …, 2021 - annualreviews.org
A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species.
Numerous studies have shown that plant pan-genomes are typically much larger than the …

Plant pan-genomes are the new reference

PE Bayer, AA Golicz, A Scheben, J Batley, D Edwards - Nature plants, 2020 - nature.com
Recent years have seen a surge in plant genome sequencing projects and the comparison
of multiple related individuals. The high degree of genomic variation observed led to the …

Building pan-genome infrastructures for crop plants and their use in association genetics

M Jayakodi, M Schreiber, N Stein, M Mascher - DNA Research, 2021 - academic.oup.com
Pan-genomic studies aim at representing the entire sequence diversity within a species to
provide useful resources for evolutionary studies, functional genomics and breeding of …

Plant pan-genomics and its applications

J Shi, Z Tian, J Lai, X Huang - Molecular Plant, 2023 - cell.com
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are
not shared among individuals. The variable DNA sequences, along with the conserved core …

[HTML][HTML] How the pan-genome is changing crop genomics and improvement

R Della Coletta, Y Qiu, S Ou, MB Hufford, CN Hirsch - Genome biology, 2021 - Springer
Crop genomics has seen dramatic advances in recent years due to improvements in
sequencing technology, assembly methods, and computational resources. These advances …

ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline

M Tahir Ul Qamar, X Zhu, F Xing, LL Chen - Bioinformatics, 2019 - academic.oup.com
Since the idea of pan-genomics emerged several tools and pipelines have been introduced
for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been …