Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

The Plant Journal, Год журнала: 2016, Номер 89(4), С. 789 - 804

Опубликована: Ноя. 8, 2016

Summary The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of biology. A comprehensive annotation its genome paves the way understanding functions and activities all types transcripts, including mRNA , various classes non‐coding RNA small . TAIR 10 update had profound impact on but was released more than 5 years ago. Maintaining accuracy continues to be prerequisite future progress. Using an integrative pipeline, we assembled tissue‐specific ‐Seq libraries from 113 datasets constructed 48 359 transcript models protein‐coding genes eleven tissues. In addition, annotated micro long intergenic nucleolar natural antisense transcript, nuclear using published in‐house analytic results. Altogether, identified 635 novel genes, 508 transcribed regions, 5178 s, 35 846 loci that were formerly unannotated. Analysis splicing events based expression profiles revealed landscapes gene structures, untranslated intricate previously appreciated. Furthermore, present 692 uniformly expressed housekeeping 43% whose human orthologs are also genes. This updated with substantially increased resolution will not only further our biological processes this other species.

Язык: Английский

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Control of Meiotic Crossovers: From Double-Strand Break Formation to Designation

Annual Review of Genetics, Год журнала: 2016, Номер 50(1), С. 175 - 210

Опубликована: Сен. 20, 2016

Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis homologous recombination, whereby DNA double-strand breaks are introduced into genome and subsequently repaired generate either noncrossovers or crossovers. Although recombination essential for chromosome pairing during prophase I, resulting crossovers critical maintaining homolog interactions enabling accurate segregation at first meiotic division. Thus, placement, timing, frequency crossover formation must be exquisitely controlled. In this review, we discuss proteins involved in formation, their designation, rules governing crossovers, all within context important landmarks I. We draw together designation data organisms, analyze evolutionary divergence, propose universal model regulation.

Язык: Английский

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A single-cell analysis of the Arabidopsis vegetative shoot apex

Developmental Cell, Год журнала: 2021, Номер 56(7), С. 1056 - 1074.e8

Опубликована: Март 18, 2021

Язык: Английский

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African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(20), С. 5213 - 5218

Опубликована: Май 4, 2017

Over the past 20 y, many studies have examined history of plant ecological and molecular model, Arabidopsis thaliana, in Europe North America. Although these informed us about recent species, early has remained elusive. In a large-scale genomic analysis African A. we sequenced genomes 78 modern herbarium samples from Africa analyzed together with over 1,000 previously Eurasian samples. striking contrast to expectations, find that all individuals sampled are native this continent, including those sub-Saharan Africa. Moreover, show harbors greatest variation represents deepest thaliana lineage. Our results also reveal evidence selfing, major defining characteristic evolved single geographic region, best represented today within Demographic inference supports model which ancestral population began split by 120-90 kya, during last interglacial Abbassia pluvial, populations subsequently separated one another at around 40 kya. This bears similarities patterns observed for diverse humans, implying key role climatic events pluvial periods shaping histories current distributions wide range species.

Язык: Английский

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A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system

Nature Plants, Год журнала: 2020, Номер 6(9), С. 1167 - 1178

Опубликована: Авг. 31, 2020

Язык: Английский

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Fruit ripening: the role of hormones, cell wall modifications, and their relationship with pathogens

Journal of Experimental Botany, Год журнала: 2019, Номер 70(11), С. 2993 - 3006

Опубликована: Март 8, 2019

Fruits result from complex biological processes that begin soon after fertilization. Among these are cell division and expansion, accumulation of secondary metabolites, an increase in carbohydrate biosynthesis. Later fruit ripening is accomplished by chlorophyll degradation wall lysis. Fruit maturation essential step to optimize seed dispersal, controlled a network transcription factors genetic regulators strongly influenced phytohormones. Abscisic acid (ABA) ethylene the major senescence both dry fleshy fruits, as demonstrated numerous ripening-defective mutants, effects exogenous hormone application, transcriptome analyses. While best characterized player final fruit's life, ABA also has key regulatory role, promoting production acting stress-related response drought pathogen attack. In this review, we focus on role relation interconnected biotic abiotic phenomena affect senescence. We integrate discuss most recent data available regarding processes, which crucial for post-harvest conservation food safety.

Язык: Английский

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Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

The Plant Cell, Год журнала: 2022, Номер 35(1), С. 67 - 108

Опубликована: Авг. 26, 2022

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these include the need better understand how plants detect water availability, temperature, salinity, rising carbon dioxide (CO2) levels; environmental signals interface endogenous signaling development (e.g. circadian clock flowering time); this integrated controls downstream responses stomatal regulation, proline metabolism, growth versus defense balance). The plasma membrane comes up frequently a site key transport events mechanosensing lipid-derived signaling, aquaporins). Adaptation extremes CO2 affects hydraulic architecture transpiration, well root shoot morphology, ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution crop resilience face changing increasingly unpredictable environments. Exploration diversity within among species can help us know which represent fundamental limits ones be circumvented bringing new trait combinations together. Better defining what constitutes beneficial resistance different contexts making connections between genes phenotypes, laboratory field observations, are overarching challenges.

Язык: Английский

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The pan-genome and local adaptation of Arabidopsis thaliana

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 6, 2023

Abstract Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution genomic structural variations (SVs) and their associate genes to local adaptation this widely distribute remains unclear. Here, we de novo assemble chromosome-level genomes 32 A. ecotypes determine that variable expand gene pool in different thus assist adaptation. We develop graph-based pan-genome identify 61,332 SVs overlap with 18,883 genes, some which are highly involved ecological species. For instance, observe specific 332 bp insertion promoter region HPCA1 Tibet-0 ecotype enhances expression, thereby promotes alpine environments. These findings augment our understanding molecular mechanisms underlying across diverse habitats.

Язык: Английский

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Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

New Phytologist, Год журнала: 2019, Номер 222(3), С. 1638 - 1651

Опубликована: Фев. 8, 2019

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, relationships among major lineages in remain unresolved, hampering comparative research. Here, we inferred a phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well sequenced genome 16 together 50 52 currently recognized tribes. A third samples were derived from herbarium material, facilitating broad taxonomic coverage family. Six clades formed successive sister groups to rest Brassicaceae. We also recovered strong support for novel tribes, resolved position taxa previously not assigned tribe. utility these phylogenetic results is illustrated through investigation genome-wide expression signatures that distinguish simple complex leaves Our study provides an easily extendable dataset further advances systematics timely higher-level framework wide range studies multiple traits intensively investigated group plants.

Язык: Английский

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A Highly Efficient Agrobacterium-Mediated Method for Transient Gene Expression and Functional Studies in Multiple Plant Species

Plant Communications, Год журнала: 2020, Номер 1(5), С. 100028 - 100028

Опубликована: Фев. 6, 2020

Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used species such as

Язык: Английский

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