Results 81 to 90 of about 1,556 (147)

Tree Fruit and Nut Crops at the Dawn of the Pangenomic Era

Horticulturae
Tree fruit and nut crops are a critical component of the global economy, producing at least 400 million tonnes of produce in 2022 and nourishing a growing population of approximately 8 billion humans every year.
June Labbancz, Amit Dhingra
doaj   +1 more source

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

PLoS Computational Biology, 2020
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species.
Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P C Rocha, David Vallenet   +13 more
doaj   +1 more source

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

New Phytologist, Volume 250, Issue 5, Page 2723-2741, June 2026.
Summary Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven
Kevin A. Bird, Joanna L. Rifkin, Chloee M. McLaughlin, Avril M. Harder, Pawan Basnet, Ella Katz, Tomáš Brůna, Kerrie Barry, LoriBeth Boston, Christopher Daum, Jie Guo, Anna Lipzen, Christopher Plott, Jerry W. Jenkins, Rachel Walstead, Shanmugam Rajasekar, Jayson Talag, Katherine Frels, Kathleen Greenham, Shelby Ellison, Jane Grimwood, Jeremy Schmutz, Patrick P. Edger, J. Chris Pires, John T. Lovell, Daniel J. Kliebenstein   +25 more
wiley   +1 more source

The design and construction of reference pangenome graphs

, 2020
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists remain an open challenge.
Li, Heng, Feng, Xiaowen, Chu, Chong
openaire   +2 more sources

Personalized pangenome references [PDF]

International audiencePangenomes reduce reference bias by representing genetic diversity better than a single reference sequence. Yet when comparing a sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for
Carroll, Andrew, Eskandar, Parsa, Chang, Xian, Chang, Pi-Chuan, Paten, Benedict, Kolmogorov, Mikhail, Eizenga, Jordan, M, Novak, Adam, M, Sirén, Jouni, Monlong, Jean, Ungaro, Matteo, Tommaso, Hickey, Glenn   +11 more
core   +4 more sources

Vernalization regulatory network identifies potential novel functions for genes in the HvVRN2 locus

New Phytologist, Volume 250, Issue 6, Page 4036-4053, June 2026.
Summary Flowering is controlled by environmental and genetic factors. Vernalization requirement in barley (Hordeum vulgare L.) is determined by the allele in HvVRN1 and the presence of locus HvVRN2, which consists of two zinc‐finger and CONSTANS‐like domains (ZCCT) genes: HvVRN2a and HvVRN2b.
Francesc Montardit‐Tarda, Irene Puyó, Bruno Contreras‐Moreira, Ildikó Karsai, Philippa Borrill, Ana M. Casas, Ernesto Igartua   +6 more
wiley   +1 more source

Defining and cataloging variants in pangenome graphs

Abstract Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to ‘reference bias’. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a ‘genetic variant.’
Pouria Salehi Nowbandegani, Shenghan Zhang, Haoyang Hu, Heng Li, Luke J. O’Connor   +4 more
openaire   +2 more sources

AhBWR15, A Novel RLK Gene, Confers Resistance to Ralstonia solanacearum in Peanut

Plant Biotechnology Journal, Volume 24, Issue 6, Page 3861-3875, June 2026.
ABSTRACT Bacterial wilt (BW), a severe soil‐borne disease caused by Ralstonia solanacearum, significantly impedes global peanut production. Despite its impact, the mechanisms underlying BW resistance in peanut remain unclear. Herein, we selected the highly resistant variety Nongdahua108 (H108) and the susceptible variety Nongdahua107 (H107) to develop ...
Zenghui Cao, Kai Zhao, Hao Li, Xingli Ma, Di Cao, Yanzhe Li, Sasa Hu, Qian Ma, Yaoyao Li, Yi Fan, Mengtian Hou, Kunkun Zhao, Ding Qiu, Fangping Gong, Zhongfeng Li, Rui Ren, Dongmei Yin   +16 more
wiley   +1 more source

Pangenome structures : design, construction, and applications [PDF]

The human {pangenome represents a set of genomic sequences of diverse humans. Any two sequences from this set are likely to be identical in large subsequences. Differences (so-called variations) predominantly involve just one or a few nucleotides.
Büchler, Thomas
core   +1 more source

Haplotype Matching with GBWT for Pangenome Graphs

Traditionally, variations from a linear reference genome were used to represent large sets of haplotypes compactly. In the linear reference genome based paradigm, the positional Burrows-Wheeler transform (PBWT) has traditionally been used to perform efficient haplotype matching.
Ahsan Sanaullah, Seba Villalobos, Degui Zhi, Shaojie Zhang   +3 more
openaire   +2 more sources