A Growth-Based Framework for Leaf Shape Development and Diversity

Cell, Journal Year: 2019, Volume and Issue: 177(6), P. 1405 - 1418.e17

Published: May 1, 2019

How do genes modify cellular growth to create morphological diversity? We study this problem in two related plants with differently shaped leaves: Arabidopsis thaliana (simple leaf shape) and Cardamine hirsuta (complex shape leaflets). use live imaging, modeling, genetics deconstruct these organ-level differences into their cell-level constituents: amount, direction, differentiation. show that depends on the interplay of modes: a conserved organ-wide mode reflects differentiation; local, directional involves patterning foci along edge. Shape diversity results from distinct effects homeobox SHOOTMERISTEMLESS broadens relative edge-patterning, enabling leaflet emergence, while REDUCED COMPLEXITY inhibits locally around emerging leaflets, accentuating created by patterning. demonstrate predictivity our findings reconstructing key features C. morphology A. thaliana. VIDEO ABSTRACT.

Language: Английский

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BRAD V3.0: an upgraded Brassicaceae database

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D1432 - D1441

Published: Oct. 19, 2021

Abstract The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica V2.0), and represents an important community portal hosting genome information for multiple related plant species. Since last update in 2015, complex genomes of numerous species have been decoded, accompanied by many omics datasets. To provide up-to-date service, we report here a major upgrade portal. Model-View-ViewModel (MVVM) framework re-engineered to enable easy sustainable maintenance database. collection increased 26 species, along with optimization user interface. Features previous retained, additional new tools exploring syntenic genes, gene expression variation data. In ‘Syntenic Gene @ Subgenome’ module, added features view sequence alignment phylogenetic relationships genes. New modules include ‘MicroSynteny’ viewing synteny selected fragment pairs, ‘Polymorph’ retrieval updated provides substantial expansion genomic data comprehensive improvement service available research community.

Language: Английский

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Molecular mechanisms of shade tolerance in plants

New Phytologist, Journal Year: 2023, Volume and Issue: 239(4), P. 1190 - 1202

Published: June 6, 2023

Summary Shade tolerance is an ecological concept used in a wide range of disciplines, from plant physiology to landscaping or gardening. It refers the strategy some plants persist and even thrive environments with low light levels because shade produced by vegetation proximity (e.g. understory). influences organization, structure, functioning, dynamics communities. However, little known about its molecular genetic basis. By contrast, there good understanding on how deal other plants, divergent most crops respond proximity. While generally shade‐avoiding species strongly elongate response shade‐tolerant do not. Here we review mechanisms that control regulation hypocotyl elongation as reference framework understand tolerance. Comparative studies indicate implemented components also regulate species. These components, however, show differential properties explain how, same stimulus, while ones

Language: Английский

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Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

New Phytologist, Journal Year: 2019, Volume and Issue: 222(3), P. 1638 - 1651

Published: Feb. 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.

Language: Английский

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Regulation of glucosinolate biosynthesis

Journal of Experimental Botany, Journal Year: 2020, Volume and Issue: 72(1), P. 70 - 91

Published: Oct. 14, 2020

Abstract Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes model species Arabidopsis and many crop species. In past 13 years, regulation glucosinolate synthesis in has been intensively studied, with recent research revealing complex molecular mechanisms that connect production responses to other central pathways. this review, we discuss how biosynthesis is ecologically relevant for plants, it controlled transcription factors, transcriptional machinery interacts hormonal, environmental, epigenetic mechanisms. We present players regulation, MYB basic helix–loop–helix as well plant hormone jasmonate, together hormones environmental signals allow coordinated rapid genes. Furthermore, highlight regulatory connections between glucosinolates, auxin, sulfur metabolism emerging insights open questions on biosynthesis.

Language: Английский

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Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

BMC Biology, Journal Year: 2017, Volume and Issue: 15(1)

Published: Aug. 29, 2017

Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to high nutritional value seeds, with potential help alleviate malnutrition security concerns, particularly in arid semiarid regions developing world. Here, we present reference-quality assembly amaranth genome which will assist agronomic development species. Utilizing single-molecule, real-time sequencing (Pacific Biosciences) chromatin interaction mapping (Hi-C) close gaps scaffold contigs, respectively, improved our previously reported Illumina-based produce chromosome-scale N50 24.4 Mb. The 16 largest scaffolds contain 98% likely represent haploid chromosomes (n = 16). To demonstrate accuracy utility this approach, produced physical genetic maps identified candidate genes for betalain pigmentation pathway. facilitated genome-wide syntenic comparison other Amaranthaceae species, revealing chromosome loss fusion events explain reduction from ancestral number 18) tetraploid member Amaranthaceae. method here minimizes cost by relying primarily on short-read technology is one first uses vivo Hi-C plant genome. Our analyses implicate as major evolutionary 2n 32 amaranths clearly establish homoeologous relationship most subgenome chromosomes, facilitate future investigations intragenomic changes occurred post polyploidization.

Language: Английский

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Enhancer evolution and the origins of morphological novelty

Current Opinion in Genetics & Development, Journal Year: 2017, Volume and Issue: 45, P. 115 - 123

Published: May 18, 2017

Language: Английский

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The influence of elevation on genetic structure and variability in a wetland crucifer of the Rocky Mountains

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

Abstract Premise In mountain ecosystems, environmental conditions (e.g., temperature, ultraviolet radiation) covary with elevation, potentially limiting gene flow over steep gradients. We hypothesized that, (1) due to stark elevational differences in factors, populations from dissimilar elevations montane versus alpine) are more strongly differentiated than similar elevations; (2) patterns of migration reflect downslope dispersal upslope dispersal; and (3) alpine at the cold edge show evidence expansion, while warm have declined. Methods DNA polymorphisms whole‐genome sequences were studied 6–10 genotypes each Cardamine cordifolia found three sites (ranging 2200 2800 m a.s.l.) 3000 3500 a.s.l.). Statistical analyses assessed population structure, genetic diversity, migration, historical demography since Pleistocene. Results Populations maintained very high levels nucleotide diversity (π range: 0.062–0.071) weakly (pairwise F ST = 0.027) on average. Migration among was also inferred, no directionality across elevation bands. Demographic inference suggests that both declined size Conclusions Environmental represent diffuse barriers flow. Recent polyploidy clonal reproduction likely explain excess heterozygosity within populations. The similarity highly connected refugia during Pleistocene; such results may indicate will respond similarly changing associated climate change.

Language: Английский

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Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BMC Biology, Journal Year: 2019, Volume and Issue: 17(1)

Published: Nov. 22, 2019

Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation decreased over past century, nutritional benefits have garnered increased interest human consumption. We report development of fully annotated, chromosome-scale assemblies extant progenitor species As- and Cp-subgenomes, atlantica eriantha respectively. The diploid serve as important genetic resources improving common oat's adaptive food quality characteristics.The A. genome span 3.69 3.78 Gb with an N50 513 535 Mb, Annotation genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance analogs across both species. Analysis these classified much repetitive sequence (~ 83%), including species-specific, centromeric-specific, telomeric-specific repeats. LTR retrotransposons make up most elements. Genome-wide syntenic comparisons other members Pooideae revealed orthologous relationships, while maps from clarified subgenome origins 21 linkage groups. utility genomes was demonstrated by identifying putative candidate genes flowering time (HD3A) crown rust (Pc91). also investigate phylogenetic relationships among A- C-genome species.The we here are first tribe Poeae, subtribe Aveninae. Our analyses provide insight into evolution complexity oat, origin, homoeologous major intra- intergenomic rearrangements. They annotation framework needed to accelerate discovery plant breeding.

Language: Английский

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Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota

Science China Life Sciences, Journal Year: 2019, Volume and Issue: 62(7), P. 947 - 958

Published: May 10, 2019

Language: Английский

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