Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1068-8_22
Abstract: Plant genomes can withstand small- and large-scale duplications, at a far greater success than any other kingdom in the tree of life, resulting in the existence and evolution of gene families, often with over a… read more here.
Keywords: start; start domains; plant genomes; identification ... See more keywords
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations.
Sign Up to like & getrecommendations! Published in 2020 at "Nature genetics"
DOI: 10.1038/s41588-020-00717-7
Abstract: Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our… read more here.
Keywords: whole chromosome; mapping; plant; plant genomes ... See more keywords
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-00504-2
Abstract: Abstract Over the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major… read more here.
Keywords: interactive hub; plant; plant genomes; pathway ... See more keywords
Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac511
Abstract: Abstract LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification… read more here.
Keywords: software; ltr retrotransposons; plant genomes; deep learning ... See more keywords
Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
Sign Up to like & getrecommendations! Published in 2020 at "Plant Biotechnology Journal"
DOI: 10.1111/pbi.13456
Abstract: Summary Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there have been a number of studies… read more here.
Keywords: plant; long read; allopolyploid crop; plant genomes ... See more keywords
De novo phasing resolves haplotype sequences in complex plant genomes
Sign Up to like & getrecommendations! Published in 2022 at "Plant Biotechnology Journal"
DOI: 10.1111/pbi.13815
Abstract: Summary Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype‐resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as… read more here.
Keywords: phasing resolves; plant genomes; complex plant; genome phasing ... See more keywords
Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2022.1025122
Abstract: Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal… read more here.
Keywords: plant genomes; stress resistance; abiotic stress; resistance ... See more keywords
PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2023.1178069
Abstract: Plants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). The primary mechanism of ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes have been studied… read more here.
Keywords: plant genomes; genes across; across 100; plant ... See more keywords
Specificities and Dynamics of Transposable Elements in Land Plants
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DOI: 10.3390/biology11040488
Abstract: Simple Summary Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They… read more here.
Keywords: land plants; plant genomes; transposable elements; elements land ... See more keywords
ENet-6mA: Identification of 6mA Modification Sites in Plant Genomes Using ElasticNet and Neural Networks
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms23158314
Abstract: N6-methyladenine (6mA) has been recognized as a key epigenetic alteration that affects a variety of biological activities. Precise prediction of 6mA modification sites is essential for understanding the logical consistency of biological activity. There are… read more here.
Keywords: enet 6ma; 6ma modification; plant genomes; modification sites ... See more keywords
DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code
Sign Up to like & getrecommendations! Published in 2020 at "Plants"
DOI: 10.3390/plants9020247
Abstract: N6-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due… read more here.
Keywords: plant; plant genomes; modification plant; methyladenine modification ... See more keywords